From a09c72e25c0ddfa7b34c26c2f926becf0d11ddd0 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 13:01:18 -0400
Subject: [PATCH 01/49] V2a "received all doses"

---
 facebook/delphiFacebook/R/contingency_indicators.R |  4 +++-
 facebook/delphiFacebook/R/contingency_variables.R  | 13 +++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index ffaa54f76..856f0cf44 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -172,7 +172,9 @@ get_aggs <- function() {
     "pct_vaccinated_booster_probyes", "v_vaccinated_booster_probyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_booster_probno", "v_vaccinated_booster_probno", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_booster_defno", "v_vaccinated_booster_defno", compute_binary, jeffreys_multinomial_factory(4),
-    
+
+    "pct_vaccine_all_doses", "v_received_all_doses", compute_binary, jeffreys_binary,
+
     "pct_flu_vaccinated_2021", "v_flu_vaccinated_2021", compute_binary, jeffreys_binary,
     
     
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 93ce4a18e..705a28e04 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -212,6 +212,19 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$v_accept_covid_vaccine[input_data$start_dt < wave6_mod_date] <- NA
   }
 
+  if ("V2a" %in% names(input_data)) {
+    # coded as 1 = Yes, received all recommended doses, 2 = Plan to receive all recommended doses,
+    # 3 = Don't plan to receive all recommended doses.
+    input_data$v_received_all_doses <- case_when(
+      input_data$V2a == 1 ~ 1,
+      input_data$V2a == 2 ~ 0,
+      input_data$V2a == 3 ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$v_received_all_doses <- NA_real_
+  }
+
   # hesitant_vaccine
   # Percentage who would definitely or probably NOT choose to get vaccinated
   input_data$v_hesitant_vaccine <- NA

From 3da694647631e107752b6c27dbf24943712539d2 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 13:13:36 -0400
Subject: [PATCH 02/49] Q36 "yes financial threat"

---
 facebook/delphiFacebook/R/contingency_indicators.R |  2 ++
 facebook/delphiFacebook/R/variables.R              | 11 +++++++++++
 2 files changed, 13 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 856f0cf44..0e9739dd8 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -375,6 +375,8 @@ get_aggs <- function() {
     "pct_test_reason_travel", "t_tested_reason_travel", compute_binary, jeffreys_binary,
 
     # mental health
+    "pct_financial_threat", "mh_financial_threat", compute_binary, jeffreys_binary,
+
     "pct_worried_become_ill", "mh_worried_ill", compute_binary, jeffreys_binary,
     "pct_finance", "mh_worried_finances", compute_binary, jeffreys_binary,
     # pre-wave 10
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index 137d62d76..bc930211f 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -224,6 +224,17 @@ code_mental_health <- function(input_data, wave) {
   } else {
     input_data$mh_worried_catch_covid <- NA
   }
+
+  if ("Q36" %in% names(input_data)) {
+    # Included in waves 1, 2, 3. Coded as 1 = substantial threat,
+    # 2 = moderate threat, 3 = not much of a threat, 4 = not a threat at all
+    input_data$mh_financial_threat <- case_when(
+      is.na(input_data$Q36) ~ NA,
+      input_data$Q36 == 1 ~ TRUE,
+      TRUE ~ FALSE)
+  } else {
+    input_data$mh_financial_threat <- NA
+  }
   
   return(input_data)
 }

From f41aff04b3a7df5f657125b910e37a8eb9c00292 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 15:04:59 -0400
Subject: [PATCH 03/49] C14a "wear mask + some of the time"

---
 facebook/delphiFacebook/R/contingency_indicators.R |  1 +
 facebook/delphiFacebook/R/variables.R              | 10 +++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 0e9739dd8..a3fc03254 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -73,6 +73,7 @@ get_aggs <- function() {
     ## Mask wearing and distancing
     "pct_wearing_mask_5d", "c_mask_often", compute_binary, jeffreys_binary,
     "pct_wearing_mask_7d", "c_mask_often_7d", compute_binary, jeffreys_binary,
+    "pct_wearing_mask_7d_alt", "c_mask_some_often_7d", compute_binary, jeffreys_binary,
     "pct_others_masked", "c_others_masked", compute_binary, jeffreys_binary,
     "pct_others_masked_public", "c_others_masked_public", compute_binary, jeffreys_binary,
     "pct_others_distanced_public", "c_others_distanced_public", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index bc930211f..dcbcd7f17 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -253,7 +253,7 @@ code_mask_contact <- function(input_data, wave) {
     case_when(
       is.na(item) ~ NA,
       item == 6 ~ NA,
-      item == 1 | item ==  2 ~ TRUE,
+      item == 1 | item == 2 ~ TRUE,
       TRUE ~ FALSE)
   }
   
@@ -281,8 +281,16 @@ code_mask_contact <- function(input_data, wave) {
     # added in wave 8. wearing mask most or all of the time (last 7 days);
     # exclude respondents who have not been in public
     input_data$c_mask_often_7d <- most_always(input_data$C14a)
+    # Same indicator but include "sometimes" wear mask in public
+    input_data$c_mask_some_often_7d <- case_when(
+      is.na(input_data$C14a) ~ NA,
+      input_data$C14a == 6 ~ NA,
+      input_data$C14a == 1 | input_data$C14a == 2 | input_data$C14a == 3 ~ TRUE,
+      TRUE ~ FALSE)
+
   } else {
     input_data$c_mask_often_7d <- NA
+    input_data$c_mask_some_often_7d <- NA
   }
 
   if ("C16" %in% names(input_data)) {

From 71a985c3bcca8ac78ab0ae9fc0dced4092ecbaae Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 15:19:23 -0400
Subject: [PATCH 04/49] H1 people distancing + "some of the time"

---
 facebook/delphiFacebook/R/contingency_indicators.R | 1 +
 facebook/delphiFacebook/R/variables.R              | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index a3fc03254..6bb789ab9 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -77,6 +77,7 @@ get_aggs <- function() {
     "pct_others_masked", "c_others_masked", compute_binary, jeffreys_binary,
     "pct_others_masked_public", "c_others_masked_public", compute_binary, jeffreys_binary,
     "pct_others_distanced_public", "c_others_distanced_public", compute_binary, jeffreys_binary,
+    "pct_others_distanced_public_alt", "c_others_distanced_some_public", compute_binary, jeffreys_binary,
     
     "pct_cli", "hh_p_cli", compute_household_binary, jeffreys_count,
     "pct_ili", "hh_p_ili", compute_household_binary, jeffreys_count,
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index dcbcd7f17..7dcb437fd 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -316,13 +316,22 @@ code_mask_contact <- function(input_data, wave) {
   if ("H1" %in% names(input_data)) {
     # added in wave 11. most/all *others* in public in the last 7 days; exclude
     # respondents who have not been in public.
+    # Coded as 1 = no people in public are distancing, 2 = a few people are,
+    # 3 = some people are, 4 = most people are, 5 = all people are, 6 = I have not been in public
     input_data$c_others_distanced_public <- case_when(
       is.na(input_data$H1) ~ NA,
       input_data$H1 == 6 ~ NA,
       input_data$H1 == 4 | input_data$H1 == 5 ~ TRUE,
       TRUE ~ FALSE)
+    # include others in public are distanced "sometimes"
+    input_data$c_others_distanced_some_public <- case_when(
+      is.na(input_data$H1) ~ NA,
+      input_data$H1 == 6 ~ NA,
+      input_data$H1 == 4 | input_data$H1 == 5 | input_data$H1 == 3 ~ TRUE,
+      TRUE ~ FALSE)
   } else {
     input_data$c_others_distanced_public <- NA
+    input_data$c_others_distanced_some_public <- NA
   }
 
   if ("C3" %in% names(input_data)) {

From 320420c06402d3f480d94503a8116e927d228e8e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 15:42:18 -0400
Subject: [PATCH 05/49] C16/H2 people masked + "some of the time"

---
 .../delphiFacebook/R/contingency_indicators.R   |  5 +++++
 facebook/delphiFacebook/R/variables.R           | 17 +++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 6bb789ab9..e75408605 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -74,8 +74,13 @@ get_aggs <- function() {
     "pct_wearing_mask_5d", "c_mask_often", compute_binary, jeffreys_binary,
     "pct_wearing_mask_7d", "c_mask_often_7d", compute_binary, jeffreys_binary,
     "pct_wearing_mask_7d_alt", "c_mask_some_often_7d", compute_binary, jeffreys_binary,
+
     "pct_others_masked", "c_others_masked", compute_binary, jeffreys_binary,
+    "pct_others_masked_alt", "c_others_some_masked", compute_binary, jeffreys_binary,
+
     "pct_others_masked_public", "c_others_masked_public", compute_binary, jeffreys_binary,
+    "pct_others_masked_public_alt", "c_others_masked_some_public", compute_binary, jeffreys_binary,
+
     "pct_others_distanced_public", "c_others_distanced_public", compute_binary, jeffreys_binary,
     "pct_others_distanced_public_alt", "c_others_distanced_some_public", compute_binary, jeffreys_binary,
     
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index 7dcb437fd..c7597268a 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -296,21 +296,38 @@ code_mask_contact <- function(input_data, wave) {
   if ("C16" %in% names(input_data)) {
     # added in wave 5. most/all *others* seen in public wearing masks; exclude
     # respondents who have not been in public.
+    # Coded as 5 = no people in public are wearing masks, 4 = a few people are,
+    # 3 = some people are, 2 = most people are, 1 = all people are, 6 = I have not been in public
     input_data$c_others_masked <- most_always(input_data$C16)
+    # include others in public are masked "sometimes"
+    input_data$c_others_some_masked <- case_when(
+      is.na(input_data$C16) ~ NA,
+      input_data$C16 == 6 ~ NA,
+      input_data$C16 == 1 | input_data$C16 == 2 | input_data$C16 == 3 ~ TRUE,
+      TRUE ~ FALSE)
   } else {
     input_data$c_others_masked <- NA
+    input_data$c_others_some_masked <- NA
   }
   
   if ("H2" %in% names(input_data)) {
     # added in wave 11, replaces C16. most/all *others* seen in public wearing
     # masks; exclude respondents who have not been in public. Coding is reversed.
+    # Coded as 1 = no people in public are wearing masks, 2 = a few people are,
+    # 3 = some people are, 4 = most people are, 5 = all people are, 6 = I have not been in public
     input_data$c_others_masked_public <- case_when(
       is.na(input_data$H2) ~ NA,
       input_data$H2 == 6 ~ NA,
       input_data$H2 == 4 | input_data$H2 == 5 ~ TRUE,
       TRUE ~ FALSE)
+    input_data$c_others_masked_some_public <- case_when(
+      is.na(input_data$H2) ~ NA,
+      input_data$H2 == 6 ~ NA,
+      input_data$H2 == 4 | input_data$H2 == 5 | input_data$H2 == 3 ~ TRUE,
+      TRUE ~ FALSE)
   } else {
     input_data$c_others_masked_public <- NA
+    input_data$c_others_masked_some_public <- NA
   }
   
   if ("H1" %in% names(input_data)) {

From 081b8c186779e80cb9d3669a1e45145b1869e337 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 16:41:51 -0400
Subject: [PATCH 06/49] H3 friends vaccinated + "some"

---
 facebook/delphiFacebook/R/contingency_indicators.R | 2 ++
 facebook/delphiFacebook/R/variables.R              | 6 ++++++
 2 files changed, 8 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index e75408605..111ed5150 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -143,7 +143,9 @@ get_aggs <- function() {
     "pct_hesitant_vaccine", "v_hesitant_vaccine", compute_binary, jeffreys_binary,
     "pct_vaccinated_or_accept", "v_covid_vaccinated_or_accept", compute_binary, jeffreys_binary,
     "pct_vaccinated_appointment_or_accept", "v_covid_vaccinated_appointment_or_accept", compute_binary, jeffreys_binary,
+
     "pct_covid_vaccinated_friends", "v_covid_vaccinated_friends", compute_binary, jeffreys_binary,
+    "pct_covid_vaccinated_friends_alt", "v_covid_vaccinated_some_friends", compute_binary, jeffreys_binary,
     
     "pct_vaccinate_children", "v_vaccinate_children", compute_binary, jeffreys_binary,
     "pct_vaccinate_child_oldest", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index c7597268a..7e77f2b62 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -912,8 +912,14 @@ code_vaccines <- function(input_data, wave) {
       is.na(input_data$H3) ~ NA,
       input_data$H3 == 4 | input_data$H3 == 6 ~ TRUE,
       TRUE ~ FALSE)
+    # Add "some" people
+    input_data$v_covid_vaccinated_some_friends <- case_when(
+      is.na(input_data$H3) ~ NA,
+      input_data$H3 == 4 | input_data$H3 == 6 | input_data$H3 == 3 ~ TRUE,
+      TRUE ~ FALSE)
   } else {
     input_data$v_covid_vaccinated_friends <- NA
+    input_data$v_covid_vaccinated_some_friends <- NA
   }
   
   if ("V2d" %in% names(input_data)) {

From a150e3aed6f0a21671fda4d62607bdad5927cfcd Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 16:54:51 -0400
Subject: [PATCH 07/49] C17* historical flu vaccines

---
 .../delphiFacebook/R/contingency_indicators.R     |  2 ++
 facebook/delphiFacebook/R/variables.R             | 15 +++++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 111ed5150..b755a6b08 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -184,6 +184,8 @@ get_aggs <- function() {
 
     "pct_vaccine_all_doses", "v_received_all_doses", compute_binary, jeffreys_binary,
 
+    "pct_flu_vaccine_june_2020", "v_flu_vaccinated_june_2020", compute_binary, jeffreys_binary,
+    "pct_flu_vaccine_july_2020", "v_flu_vaccinated_july_2020", compute_binary, jeffreys_binary,
     "pct_flu_vaccinated_2021", "v_flu_vaccinated_2021", compute_binary, jeffreys_binary,
     
     
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index 7e77f2b62..f051f0e1b 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -960,7 +960,22 @@ code_vaccines <- function(input_data, wave) {
     input_data$v_vaccinated_booster_defno   <- NA
   }
   
+  if ("C17" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 4 = "No", 2 = "I don't know"
+    input_data$v_flu_vaccinated_june_2020 <- input_data$C17 == 1
+  } else {
+    input_data$v_flu_vaccinated_june_2020 <- NA
+  }
+
+  if ("C17a" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 2 = "No", 3 = "I don't know"
+    input_data$v_flu_vaccinated_july_2020 <- input_data$C17a == 1
+  } else {
+    input_data$v_flu_vaccinated_july_2020 <- NA
+  }
+
   if ("C17b" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 2 = "No", 3 = "I don't know"
     input_data$v_flu_vaccinated_2021 <- input_data$C17b == 1
   } else {
     input_data$v_flu_vaccinated_2021 <- NA

From facc7651eb636d4a73c68b5230d080a70c3ba1f2 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 16:59:25 -0400
Subject: [PATCH 08/49] C2 flu vaccine last 12m

---
 facebook/delphiFacebook/R/contingency_indicators.R | 1 +
 facebook/delphiFacebook/R/variables.R              | 7 +++++++
 2 files changed, 8 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index b755a6b08..4a47fd507 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -184,6 +184,7 @@ get_aggs <- function() {
 
     "pct_vaccine_all_doses", "v_received_all_doses", compute_binary, jeffreys_binary,
 
+    "pct_flu_shot_1y", "v_flu_vaccinated_1y", compute_binary, jeffreys_binary,
     "pct_flu_vaccine_june_2020", "v_flu_vaccinated_june_2020", compute_binary, jeffreys_binary,
     "pct_flu_vaccine_july_2020", "v_flu_vaccinated_july_2020", compute_binary, jeffreys_binary,
     "pct_flu_vaccinated_2021", "v_flu_vaccinated_2021", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index f051f0e1b..f2f4c1159 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -960,6 +960,13 @@ code_vaccines <- function(input_data, wave) {
     input_data$v_vaccinated_booster_defno   <- NA
   }
   
+  if ("C2" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 2 = "No"
+    input_data$v_flu_vaccinated_1y <- input_data$C2 == 1
+  } else {
+    input_data$v_flu_vaccinated_1y <- NA
+  }
+
   if ("C17" %in% names(input_data)) {
     # Coded as 1 = "Yes", 4 = "No", 2 = "I don't know"
     input_data$v_flu_vaccinated_june_2020 <- input_data$C17 == 1

From f3bd9393ddec91573dd63b06a19758c74b5ce08e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 10 Jun 2022 17:32:36 -0400
Subject: [PATCH 09/49] mental health + sometimes

---
 .../delphiFacebook/R/contingency_indicators.R | 20 +++++++++++++------
 facebook/delphiFacebook/R/variables.R         | 17 ++++++++++++++++
 2 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 4a47fd507..cae4663e0 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -390,17 +390,25 @@ get_aggs <- function() {
     "pct_financial_threat", "mh_financial_threat", compute_binary, jeffreys_binary,
 
     "pct_worried_become_ill", "mh_worried_ill", compute_binary, jeffreys_binary,
+    "pct_worried_catch_covid", "mh_worried_catch_covid", compute_binary, jeffreys_binary,
+
     "pct_finance", "mh_worried_finances", compute_binary, jeffreys_binary,
-    # pre-wave 10
+    "pct_finance_alt", "mh_very_worried_finances", compute_binary, jeffreys_binary,
+
     "pct_anxious_5d", "mh_anxious", compute_binary, jeffreys_binary,
-    "pct_depressed_5d", "mh_depressed", compute_binary, jeffreys_binary,
-    "pct_felt_isolated_5d", "mh_isolated", compute_binary, jeffreys_binary,
-    # wave 10+
+    "pct_anxious_5d_alt", "mh_some_anxious", compute_binary, jeffreys_binary,
     "pct_anxious_7d", "mh_anxious_7d", compute_binary, jeffreys_binary,
+    "pct_anxious_7d_alt", "mh_some_anxious_7d", compute_binary, jeffreys_binary,
+
+    "pct_depressed_5d", "mh_depressed", compute_binary, jeffreys_binary,
+    "pct_depressed_5d_alt", "mh_some_depressed", compute_binary, jeffreys_binary,
     "pct_depressed_7d", "mh_depressed_7d", compute_binary, jeffreys_binary,
+    "pct_depressed_7d_alt", "mh_some_depressed_7d", compute_binary, jeffreys_binary,
+
+    "pct_felt_isolated_5d", "mh_isolated", compute_binary, jeffreys_binary,
+    "pct_isolated_5d_alt", "mh_some_isolated", compute_binary, jeffreys_binary,
     "pct_felt_isolated_7d", "mh_isolated_7d", compute_binary, jeffreys_binary,
-    # wave 11
-    "pct_worried_catch_covid", "mh_worried_catch_covid", compute_binary, jeffreys_binary,
+    "pct_isolated_7d_alt", "mh_some_isolated_7d", compute_binary, jeffreys_binary,
     
     # travel outside state
     # pre-wave 10
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index f2f4c1159..dde43b881 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -197,20 +197,37 @@ code_mental_health <- function(input_data, wave) {
   
   if (wave >= 4 && wave < 10) {
     input_data$mh_worried_ill <- input_data$C9 == 1 | input_data$C9 == 2
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious <- input_data$C8_1 == 3 | input_data$C8_1 == 4
+    input_data$mh_some_anxious <- input_data$C8_1 == 3 | input_data$C8_1 == 4 | input_data$C8_1 == 2
     input_data$mh_depressed <- input_data$C8_2 == 3 | input_data$C8_2 == 4
+    input_data$mh_some_depressed <- input_data$C8_2 == 3 | input_data$C8_2 == 4 | input_data$C8_2 == 2
     input_data$mh_isolated <- input_data$C8_3 == 3 | input_data$C8_3 == 4
+    input_data$mh_some_isolated <- input_data$C8_3 == 3 | input_data$C8_3 == 4 | input_data$C8_3 == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
   } else if (wave == 10) {
     input_data$mh_worried_ill <- input_data$C9 == 1 | input_data$C9 == 2
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious_7d <- input_data$C8a_1 == 3 | input_data$C8a_1 == 4
+    input_data$mh_some_anxious_7d <- input_data$C8a_1 == 3 | input_data$C8a_1 == 4 | input_data$C8a_1 == 2
     input_data$mh_depressed_7d <- input_data$C8a_2 == 3 | input_data$C8a_2 == 4
+    input_data$mh_some_depressed_7d <- input_data$C8a_2 == 3 | input_data$C8a_2 == 4 | input_data$C8a_2 == 2
     input_data$mh_isolated_7d <- input_data$C8a_3 == 3 | input_data$C8a_3 == 4
+    input_data$mh_some_isolated_7d <- input_data$C8a_3 == 3 | input_data$C8a_3 == 4 | input_data$C8a_3 == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
   } else if (wave >= 11) {
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious_7d <- input_data$C18a == 3 | input_data$C18a == 4
+    input_data$mh_some_anxious_7d <- input_data$C18a == 3 | input_data$C18a == 4 | input_data$C18a == 2
     input_data$mh_depressed_7d <- input_data$C18b == 3 | input_data$C18b == 4
+    input_data$mh_some_depressed_7d <- input_data$C18b == 3 | input_data$C18b == 4 | input_data$C18b == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
   }
 
   if ("G1" %in% names(input_data)) {

From 29a8baa66ea863bd346d462c6a7deec921ab1728 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 13 Jun 2022 10:21:12 -0400
Subject: [PATCH 10/49] C11/C12 historical in contact with COVID-+ person

---
 .../delphiFacebook/R/contingency_indicators.R |  4 ++++
 .../delphiFacebook/R/contingency_variables.R  | 24 +++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index cae4663e0..abca97b99 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -88,7 +88,11 @@ get_aggs <- function() {
     "pct_ili", "hh_p_ili", compute_household_binary, jeffreys_count,
     "pct_hh_cmnty_cli", "hh_community_yes", compute_binary, jeffreys_binary,
     "pct_nohh_cmnty_cli", "community_yes", compute_binary, jeffreys_binary,
+
     "pct_direct_contact", "c_direct_contact", compute_binary, jeffreys_binary,
+    "pct_direct_contact_covid", "c_direct_contact_covid", compute_binary, jeffreys_binary,
+    "pct_direct_contact_covid_hh", "c_direct_contact_covid_hh", compute_binary, jeffreys_binary,
+
     "pct_avoid_contact", "c_avoid_contact", compute_binary, jeffreys_binary,
     "pct_avoid_contact_7d", "c_avoid_contact_7d", compute_binary, jeffreys_binary,
     
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 705a28e04..9699c6e04 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1054,6 +1054,30 @@ code_behaviors <- function(input_data, wave) {
     input_data$c_direct_contact <- NA
   }
 
+  if ("C11" %in% names(input_data)) {
+    # Had "direct contact" with someone COVID-positive in the last 24 hours
+    # Coded as 1 = Yes, 2 = No
+    input_data$c_direct_contact_covid <- case_when(
+      input_data$C11 == 1 ~ 1,
+      input_data$C11 == 2 ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$c_direct_contact_covid <- NA_real_
+  }
+
+  if (all(c("C11", "C12") %in% names(input_data))) {
+    # C12: was the person in C11 a member of your household
+    # Coded as 1 = Yes, 2 = No
+    input_data$c_direct_contact_covid_hh <- case_when(
+      input_data$C11 == 1 & input_data$C12 == 1 ~ 1,
+      input_data$C11 == 2 | input_data$C12 == 2 ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$c_direct_contact_covid_hh <- NA_real_
+  }
+
   # avoid_contact
   # Percentage of respondents that have reported having intentionally avoided
   # contact with other people all or most of the time

From fe26aa4a0f44beff2ff64f4bc0aee21caed8a669 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 13 Jun 2022 11:55:34 -0400
Subject: [PATCH 11/49] all work_outside_home varieties

---
 facebook/delphiFacebook/R/binary.R               |  4 ++--
 .../delphiFacebook/R/contingency_indicators.R    |  7 +++++--
 .../delphiFacebook/R/contingency_variables.R     | 16 ++++++++++++++++
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/facebook/delphiFacebook/R/binary.R b/facebook/delphiFacebook/R/binary.R
index 0a2470098..b6c277bad 100644
--- a/facebook/delphiFacebook/R/binary.R
+++ b/facebook/delphiFacebook/R/binary.R
@@ -59,8 +59,8 @@ get_binary_indicators <- function() {
     
     # work outside home
     # pre-wave 4
-    "wip_smoothed_work_outside_home_5d", "weight_unif", "c_work_outside_5d", 6, compute_binary_response, jeffreys_binary,
-    "wip_smoothed_wwork_outside_home_5d", "weight", "c_work_outside_5d", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_work_outside_home_5d", "weight_unif", "c_work_outside_5d", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wwork_outside_home_5d", "weight", "c_work_outside_5d", 6, compute_binary_response, jeffreys_binary,
     # wave 4+, pre-wave 10
     "smoothed_work_outside_home_1d", "weight_unif", "a_work_outside_home_1d", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wwork_outside_home_1d", "weight", "a_work_outside_home_1d", 6, compute_binary_response, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index abca97b99..86d89c8b1 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -421,14 +421,17 @@ get_aggs <- function() {
     "pct_travel_outside_state_7d", "c_travel_state_7d", compute_binary, jeffreys_binary,
     
     # activities outside the home
+    "pct_work_outside_home_5d", "c_work_outside_5d", compute_binary, jeffreys_binary,
     "pct_work_outside_home_1d", "a_work_outside_home_1d", compute_binary, jeffreys_binary,
+    "pct_work_outside_home_4w", "c_work_outside_home_4w", compute_binary, jeffreys_binary,
+    "pct_work_outside_home_indoors_1d", "a_work_outside_home_indoors_1d", compute_binary, jeffreys_binary,
+
     "pct_shop_1d", "a_shop_1d", compute_binary, jeffreys_binary,
     "pct_restaurant_1d", "a_restaurant_1d", compute_binary, jeffreys_binary,
     "pct_spent_time_1d", "a_spent_time_1d", compute_binary, jeffreys_binary,
     "pct_large_event_1d", "a_large_event_1d", compute_binary, jeffreys_binary,
     "pct_public_transit_1d", "a_public_transit_1d", compute_binary, jeffreys_binary,
-    
-    "pct_work_outside_home_indoors_1d", "a_work_outside_home_indoors_1d", compute_binary, jeffreys_binary,
+
     "pct_shop_indoors_1d", "a_shop_indoors_1d", compute_binary, jeffreys_binary,
     "pct_restaurant_indoors_1d", "a_restaurant_indoors_1d", compute_binary, jeffreys_binary,
     "pct_spent_time_indoors_1d", "a_spent_time_indoors_1d", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 9699c6e04..4b1957bdd 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1078,6 +1078,22 @@ code_behaviors <- function(input_data, wave) {
     input_data$c_direct_contact_covid_hh <- NA_real_
   }
 
+  # Work outside the home
+  if (all(c("D9", "D10") %in% names(input_data))) {
+    # D9: in the past 4 weeks, did you work
+    # Coded as 1 = Yes, 2 = No
+    # D10: if answered yes to D9, was your work in the last 4w outisde your home
+    # Coded as 1 = Yes, 2 = No
+    input_data$c_direct_contact_covid_hh <- case_when(
+      input_data$D9 == 1 & input_data$D10 == 1 ~ 1,
+      input_data$D9 == 2 | input_data$D10 == 2 ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$c_direct_contact_covid_hh <- NA_real_
+  }
+
+
   # avoid_contact
   # Percentage of respondents that have reported having intentionally avoided
   # contact with other people all or most of the time

From 918fd8e78ddd9ee6f624505810da4f7e02ba90ee Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 13 Jun 2022 16:16:41 -0400
Subject: [PATCH 12/49] work with high-risk populations

---
 .../delphiFacebook/R/contingency_indicators.R |  5 +-
 .../delphiFacebook/R/contingency_variables.R  | 47 ++++++++++++-------
 2 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 86d89c8b1..ed0f8f12b 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -423,7 +423,7 @@ get_aggs <- function() {
     # activities outside the home
     "pct_work_outside_home_5d", "c_work_outside_5d", compute_binary, jeffreys_binary,
     "pct_work_outside_home_1d", "a_work_outside_home_1d", compute_binary, jeffreys_binary,
-    "pct_work_outside_home_4w", "c_work_outside_home_4w", compute_binary, jeffreys_binary,
+    "pct_work_outside_home_4w", "a_work_outside_home_4w", compute_binary, jeffreys_binary,
     "pct_work_outside_home_indoors_1d", "a_work_outside_home_indoors_1d", compute_binary, jeffreys_binary,
 
     "pct_shop_1d", "a_shop_1d", compute_binary, jeffreys_binary,
@@ -436,6 +436,9 @@ get_aggs <- function() {
     "pct_restaurant_indoors_1d", "a_restaurant_indoors_1d", compute_binary, jeffreys_binary,
     "pct_spent_time_indoors_1d", "a_spent_time_indoors_1d", compute_binary, jeffreys_binary,
     "pct_large_event_indoors_1d", "a_large_event_indoors_1d", compute_binary, jeffreys_binary,
+
+    "pct_work_healthcare_5d", "a_work_healthcare_5d", compute_binary, jeffreys_binary,
+    "pct_work_nursing_home_5d", "a_work_nursing_home_5d", compute_binary, jeffreys_binary,
     
     # masked activities outside the home
     "pct_mask_work_outside_home_1d", "a_mask_work_outside_home_1d", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 4b1957bdd..7fb2e7aa2 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1078,22 +1078,6 @@ code_behaviors <- function(input_data, wave) {
     input_data$c_direct_contact_covid_hh <- NA_real_
   }
 
-  # Work outside the home
-  if (all(c("D9", "D10") %in% names(input_data))) {
-    # D9: in the past 4 weeks, did you work
-    # Coded as 1 = Yes, 2 = No
-    # D10: if answered yes to D9, was your work in the last 4w outisde your home
-    # Coded as 1 = Yes, 2 = No
-    input_data$c_direct_contact_covid_hh <- case_when(
-      input_data$D9 == 1 & input_data$D10 == 1 ~ 1,
-      input_data$D9 == 2 | input_data$D10 == 2 ~ 0,
-      TRUE ~ NA_real_
-    )
-  } else {
-    input_data$c_direct_contact_covid_hh <- NA_real_
-  }
-
-
   # avoid_contact
   # Percentage of respondents that have reported having intentionally avoided
   # contact with other people all or most of the time
@@ -1134,6 +1118,21 @@ code_behaviors <- function(input_data, wave) {
 #' 
 #' @return augmented data frame
 code_addl_activities <- function(input_data, wave) {
+  # Work outside the home
+  if (all(c("D9", "D10") %in% names(input_data))) {
+    # D9: in the past 4 weeks, did you work
+    # Coded as 1 = Yes, 2 = No
+    # D10: if answered yes to D9, was your work in the last 4w outisde your home
+    # Coded as 1 = Yes, 2 = No
+    input_data$a_work_outside_home_4w <- case_when(
+      input_data$D9 == 1 & input_data$D10 == 1 ~ 1,
+      input_data$D9 == 2 | input_data$D10 == 2 ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$a_work_outside_home_4w <- NA_real_
+  }
+
   calc_masking_given_activity <- function(activity, masked_during_activity) {
     case_when(
       activity & masked_during_activity ~ TRUE,
@@ -1204,6 +1203,22 @@ code_addl_activities <- function(input_data, wave) {
     input_data$a_mask_public_transit_1d <- NA
   }
   
+  if ("C4" %in% names(input_data)) {
+    # Worked/volunteered in healthcare (hospital, medical office, etc) in last 5 days
+    # Coded as 1 = Yes, 2 = No
+    input_data$a_work_healthcare_5d <- input_data$C4 == 1
+  } else {
+    input_data$a_work_healthcare_5d <- NA
+  }
+
+  if ("C5" %in% names(input_data)) {
+    # Worked/visited nursing home, etc, in last 5 days
+    # Coded as 1 = Yes, 2 = No
+    input_data$a_work_nursing_home_5d <- input_data$C5 == 1
+  } else {
+    input_data$a_work_nursing_home_5d <- NA
+  }
+
   return(input_data)
 }
 

From 9a65ac64a73ec114761324e017a66ba62e21e12e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 13 Jun 2022 16:51:05 -0400
Subject: [PATCH 13/49] reasons why people are not planning to complete the
 vaccine series

---
 .../delphiFacebook/R/contingency_indicators.R | 17 ++++++++
 facebook/delphiFacebook/R/variables.R         | 39 ++++++++++++++++++-
 2 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index ed0f8f12b..c098f702c 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -279,6 +279,23 @@ get_aggs <- function() {
     "pct_barrier_other", "v_hesitancy_reason_other", compute_binary, jeffreys_binary,
     "pct_barrier_dislike_vaccines_generally", "v_hesitancy_reason_dislike_vaccines_generally", compute_binary, jeffreys_binary,
     
+    # vaccine incomplete reasons
+    "pct_vaccine_incomplete_sideeffect", "v_vaccine_incomplete_sideeffect", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_allergic", "v_vaccine_incomplete_allergic", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_wontwork", "v_vaccine_incomplete_wontwork", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_dontbelieve", "v_vaccine_incomplete_dontbelieve", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_dontlike", "v_vaccine_incomplete_dontlike", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_not_recommended", "v_vaccine_incomplete_not_recommended", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_wait", "v_vaccine_incomplete_wait", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_otherpeople", "v_vaccine_incomplete_otherpeople", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_cost", "v_vaccine_incomplete_cost", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_distrust_vaccine", "v_vaccine_incomplete_distrust_vaccine", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_distrust_gov", "v_vaccine_incomplete_distrust_gov", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_health", "v_vaccine_incomplete_health", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_other", "v_vaccine_incomplete_other", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_pregnant", "v_vaccine_incomplete_pregnant", compute_binary, jeffreys_binary,
+    "pct_vaccine_incomplete_religion", "v_vaccine_incomplete_religion", compute_binary, jeffreys_binary,
+
     # vaccine "don't need" reasons
     "pct_dontneed_reason_had_covid", "v_dontneed_reason_had_covid_5abc_6", compute_binary, jeffreys_binary,
     "pct_dontneed_reason_dont_spend_time", "v_dontneed_reason_dont_spend_time_5abc_6", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index dde43b881..f52624e26 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -674,7 +674,44 @@ code_vaccines <- function(input_data, wave) {
     input_data$v_hesitancy_reason_religious <- NA_real_
     input_data$v_hesitancy_reason_dislike_vaccines_generally <- NA_real_
   }
-  
+
+  if ("V5d" %in% names(input_data)) {
+    # introduced in Wave 8, removed in Wave 11
+    vaccine_incomplete_reasons <- split_options(input_data$V5d)
+
+    input_data$v_vaccine_incomplete_sideeffect <- is_selected(vaccine_incomplete_reasons, "1")
+    input_data$v_vaccine_incomplete_allergic <- is_selected(vaccine_incomplete_reasons, "2")
+    input_data$v_vaccine_incomplete_wontwork <- is_selected(vaccine_incomplete_reasons, "3")
+    input_data$v_vaccine_incomplete_dontbelieve <- is_selected(vaccine_incomplete_reasons, "4")
+    input_data$v_vaccine_incomplete_dontlike <- is_selected(vaccine_incomplete_reasons, "5")
+    input_data$v_vaccine_incomplete_not_recommended <- is_selected(vaccine_incomplete_reasons, "6")
+    input_data$v_vaccine_incomplete_wait <- is_selected(vaccine_incomplete_reasons, "7")
+    input_data$v_vaccine_incomplete_otherpeople <- is_selected(vaccine_incomplete_reasons, "8")
+    input_data$v_vaccine_incomplete_cost <- is_selected(vaccine_incomplete_reasons, "9")
+    input_data$v_vaccine_incomplete_distrust_vaccine <- is_selected(vaccine_incomplete_reasons, "10")
+    input_data$v_vaccine_incomplete_distrust_gov <- is_selected(vaccine_incomplete_reasons, "11")
+    input_data$v_vaccine_incomplete_health <- is_selected(vaccine_incomplete_reasons, "12")
+    input_data$v_vaccine_incomplete_other <- is_selected(vaccine_incomplete_reasons, "13")
+    input_data$v_vaccine_incomplete_pregnant <- is_selected(vaccine_incomplete_reasons, "14")
+    input_data$v_vaccine_incomplete_religion <- is_selected(vaccine_incomplete_reasons, "15")
+  } else {
+    input_data$v_vaccine_incomplete_sideeffect <- NA_real_
+    input_data$v_vaccine_incomplete_allergic <- NA_real_
+    input_data$v_vaccine_incomplete_wontwork <- NA_real_
+    input_data$v_vaccine_incomplete_dontbelieve <- NA_real_
+    input_data$v_vaccine_incomplete_dontlike <- NA_real_
+    input_data$v_vaccine_incomplete_not_recommended <- NA_real_
+    input_data$v_vaccine_incomplete_wait <- NA_real_
+    input_data$v_vaccine_incomplete_otherpeople <- NA_real_
+    input_data$v_vaccine_incomplete_cost <- NA_real_
+    input_data$v_vaccine_incomplete_distrust_vaccine <- NA_real_
+    input_data$v_vaccine_incomplete_distrust_gov <- NA_real_
+    input_data$v_vaccine_incomplete_health <- NA_real_
+    input_data$v_vaccine_incomplete_other <- NA_real_
+    input_data$v_vaccine_incomplete_pregnant <- NA_real_
+    input_data$v_vaccine_incomplete_religion <- NA_real_
+  }
+
   if ( "V6" %in% names(input_data) ) {
     # introduced in Wave 8
     dontneed_reasons <- split_options(input_data$V6)

From 0420df6021a69438008982c400b0c6cbe37080f7 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 13 Jun 2022 18:03:44 -0400
Subject: [PATCH 14/49] reasons why not tested for covid

---
 .../delphiFacebook/R/contingency_indicators.R |  9 ++++++++
 .../delphiFacebook/R/contingency_variables.R  | 22 +++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index c098f702c..eddd7ba8d 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -395,6 +395,15 @@ get_aggs <- function() {
     "pct_tested_positive_14d", "t_tested_positive_14d", compute_binary, jeffreys_binary,
     "pct_wanted_test_14d", "t_wanted_test_14d", compute_binary, jeffreys_binary,
     "pct_ever_tested", "t_ever_tested", compute_binary, jeffreys_binary,
+
+    "pct_reason_not_tested_tried", "t_reason_not_tested_tried", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_appointment", "t_reason_not_tested_appointment", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_location", "t_reason_not_tested_location", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_cost", "t_reason_not_tested_cost", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_time", "t_reason_not_tested_time", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_travel", "t_reason_not_tested_travel", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_stigma", "t_reason_not_tested_stigma", compute_binary, jeffreys_binary,
+    "pct_reason_not_tested_none", "t_reason_not_tested_none", compute_binary, jeffreys_binary,
     
     ## testing reasons
     "pct_test_reason_sick", "t_tested_reason_sick", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 7fb2e7aa2..a5d8cf3c9 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -290,6 +290,28 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$t_ever_tested <- NA
   }
   
+  if ( "B12a" %in% names(input_data) ) {
+    not_tested_reasons <- split_options(input_data$B12a)
+
+    input_data$t_reason_not_tested_tried <- is_selected(not_tested_reasons, "1")
+    input_data$t_reason_not_tested_appointment <- is_selected(not_tested_reasons, "2")
+    input_data$t_reason_not_tested_location <- is_selected(not_tested_reasons, "3")
+    input_data$t_reason_not_tested_cost <- is_selected(not_tested_reasons, "4")
+    input_data$t_reason_not_tested_time <- is_selected(not_tested_reasons, "5")
+    input_data$t_reason_not_tested_travel <- is_selected(not_tested_reasons, "6")
+    input_data$t_reason_not_tested_stigma <- is_selected(not_tested_reasons, "7")
+    input_data$t_reason_not_tested_none <- is_selected(not_tested_reasons, "8")
+  } else {
+    input_data$t_reason_not_tested_tried <- NA
+    input_data$t_reason_not_tested_appointment <- NA
+    input_data$t_reason_not_tested_location <- NA
+    input_data$t_reason_not_tested_cost <- NA
+    input_data$t_reason_not_tested_time <- NA
+    input_data$t_reason_not_tested_travel <- NA
+    input_data$t_reason_not_tested_stigma <- NA
+    input_data$t_reason_not_tested_none <- NA
+  }
+
   return(input_data)
 }
 

From f09d2dcdaca44dbe8c654fccc86c8cba21f800bd Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 14 Jun 2022 11:11:03 -0400
Subject: [PATCH 15/49] B* all followups to unusual symptoms question

---
 .../delphiFacebook/R/contingency_indicators.R |  8 ++++
 .../delphiFacebook/R/contingency_variables.R  | 45 +++++++++++++++++++
 2 files changed, 53 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index eddd7ba8d..2b5b59c93 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -97,6 +97,10 @@ get_aggs <- function() {
     "pct_avoid_contact_7d", "c_avoid_contact_7d", compute_binary, jeffreys_binary,
     
     # symptoms
+    "pct_taken_temp", "t_taken_temp", compute_binary, jeffreys_binary,
+
+    "pct_cough_mucus", "symp_cough_mucus", compute_binary, jeffreys_binary,
+
     "pct_symp_fever", "symp_fever", compute_binary, jeffreys_binary,
     "pct_symp_cough", "symp_cough", compute_binary, jeffreys_binary,
     "pct_symp_shortness_breath", "symp_shortness_breath", compute_binary, jeffreys_binary,
@@ -396,6 +400,10 @@ get_aggs <- function() {
     "pct_wanted_test_14d", "t_wanted_test_14d", compute_binary, jeffreys_binary,
     "pct_ever_tested", "t_ever_tested", compute_binary, jeffreys_binary,
 
+    "pct_unusual_symptom_tested", "t_unusual_symptom_tested", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_hospital", "t_unusual_symptom_hospital", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care", "t_unusual_symptom_medical_care", compute_binary, jeffreys_binary,
+
     "pct_reason_not_tested_tried", "t_reason_not_tested_tried", compute_binary, jeffreys_binary,
     "pct_reason_not_tested_appointment", "t_reason_not_tested_appointment", compute_binary, jeffreys_binary,
     "pct_reason_not_tested_location", "t_reason_not_tested_location", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index a5d8cf3c9..c0fe11149 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -284,12 +284,50 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$v_vaccine_timing_dontknow <- NA
   }
   
+  if ("B3" %in% names(input_data)) {
+    input_data$t_taken_temp <- input_data$B3 == 1
+  } else {
+    input_data$t_taken_temp <- NA
+  }
+
   if ("B8" %in% names(input_data)) {
     input_data$t_ever_tested <- input_data$B8 == 1
   } else {
     input_data$t_ever_tested <- NA
   }
   
+  if ("B5" %in% names(input_data)) {
+    input_data$t_unusual_symptom_tested <- case_when(
+      input_data$B5 %in% c(1, 2, 3) ~ 1,
+      input_data$B5 %in% c(4, 5) ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$t_unusual_symptom_tested <- NA
+  }
+
+  if ("B6" %in% names(input_data)) {
+    input_data$t_unusual_symptom_hospital <- case_when(
+      input_data$B6 %in% c(1, 3) ~ 1,
+      input_data$B6 %in% c(2) ~ 0,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$t_unusual_symptom_hospital <- NA
+  }
+
+  if ("B7" %in% names(input_data)) {
+    # Coded as 8 = no medical care sought, 1-6 = various types of medical care sought,
+    # 7 = care sought but not received
+    input_data$t_unusual_symptom_medical_care <- case_when(
+      input_data$B7 == "8" ~ 0,
+      !is.na(input_data$B7) ~ 1,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$t_unusual_symptom_medical_care <- NA
+  }
+
   if ( "B12a" %in% names(input_data) ) {
     not_tested_reasons <- split_options(input_data$B12a)
 
@@ -1047,6 +1085,13 @@ code_addl_symptoms <- function(input_data, wave) {
     input_data$symp_sleep_changes_unusual <- NA
     input_data$symp_stuffy_nose_unusual <- NA
   }
+
+  if ("B4" %in% names(input_data)) {
+    # Cough with mucus given have cough in last 1 day
+    input_data$symp_cough_mucus <- input_data$B4 == 1
+  } else {
+    input_data$symp_cough_mucus <- NA
+  }
   
   return(input_data)
 }

From 0df4d159782d0093808d378d24713055e75d1b7f Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 14 Jun 2022 12:04:30 -0400
Subject: [PATCH 16/49] D10 work for pay outside home among those working

---
 facebook/delphiFacebook/R/contingency_indicators.R | 2 ++
 facebook/delphiFacebook/R/contingency_variables.R  | 8 ++++++++
 2 files changed, 10 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 2b5b59c93..c58b8f9a9 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -460,6 +460,8 @@ get_aggs <- function() {
     "pct_work_outside_home_4w", "a_work_outside_home_4w", compute_binary, jeffreys_binary,
     "pct_work_outside_home_indoors_1d", "a_work_outside_home_indoors_1d", compute_binary, jeffreys_binary,
 
+    "pct_work_for_pay_outside_home_4w", "a_work_for_pay_outside_home_4w", compute_binary, jeffreys_binary,
+
     "pct_shop_1d", "a_shop_1d", compute_binary, jeffreys_binary,
     "pct_restaurant_1d", "a_restaurant_1d", compute_binary, jeffreys_binary,
     "pct_spent_time_1d", "a_spent_time_1d", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index c0fe11149..05421c2a1 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1200,6 +1200,14 @@ code_addl_activities <- function(input_data, wave) {
     input_data$a_work_outside_home_4w <- NA_real_
   }
 
+  if ("D10" %in% names(input_data)) {
+    # D10: if answered yes to D9, was your work in the last 4w outisde your home
+    # Coded as 1 = Yes, 2 = No
+    input_data$a_work_for_pay_outside_home_4w <- input_data$D10 == 1
+  } else {
+    input_data$a_work_for_pay_outside_home_4w <- NA_real_
+  }
+
   calc_masking_given_activity <- function(activity, masked_during_activity) {
     case_when(
       activity & masked_during_activity ~ TRUE,

From 23758e68f0d3e25b8f127b9cad4663c0d4666cda Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 14 Jun 2022 15:29:51 -0400
Subject: [PATCH 17/49] define variables we want to find the mean for

---
 .../delphiFacebook/R/contingency_indicators.R |  7 ++++-
 .../delphiFacebook/R/contingency_variables.R  | 26 +++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index c58b8f9a9..b9d8bccfa 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -542,7 +542,12 @@ get_aggs <- function() {
     "pct_school_safety_measures_vaccine_staff", "s_school_safety_measures_vaccine_staff", compute_binary, jeffreys_binary,
     "pct_school_safety_measures_vaccine_students", "s_school_safety_measures_vaccine_students", compute_binary, jeffreys_binary,
     "pct_school_safety_measures_cafeteria", "s_school_safety_measures_cafeteria", compute_binary, jeffreys_binary,
-    "pct_school_safety_measures_dont_know", "s_school_safety_measures_dont_know", compute_binary, jeffreys_binary
+    "pct_school_safety_measures_dont_know", "s_school_safety_measures_dont_know", compute_binary, jeffreys_binary,
+
+    # Means
+    "mean_days_symptoms", "symp_n_days", compute_mean, I,
+    "mean_ppl_symptoms_household", "hh_number_sick", compute_mean, I,
+    "mean_ppl_symptoms_community", "community_number_sick", compute_mean, I
   )
 
   aggs <- create_aggs_product(regions, groups, indicators)
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 05421c2a1..1af2da773 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -951,6 +951,32 @@ code_attempt_vaccine <- function(input_data, wave) {
 #' 
 #' @return data frame augmented with demographic grouping variables
 code_addl_symptoms <- function(input_data, wave) {
+  if ("B2b" %in% names(input_data)) {
+    # How many days have you had one or more new or unusual symptom?
+    # Free response
+    input_data$symp_n_days <- case_when(
+      input_data$B2b < 0 ~ NA_real_,
+      input_data$B2b > 1000 ~ NA_real_,
+      is.na(input_data$B2b) ~ NA_real_,
+      TRUE ~ as.integer(input_data$B2b)
+      )
+  } else {
+    input_data$symp_n_days <- NA_real_
+  }
+
+  if ("A4" %in% names(input_data)) {
+    # How many additional people in your community do you know who are sick with fever + another symptom?
+    # Free response
+    input_data$community_number_sick <- case_when(
+      input_data$A4 < 0 ~ NA_real_,
+      input_data$A4 > 100 ~ NA_real_,
+      is.na(input_data$A4) ~ NA_real_,
+      TRUE ~ as.integer(input_data$A4)
+      )
+  } else {
+    input_data$community_number_sick <- NA_real_
+  }
+
   # anosmia
   # Percentage of respondents experiencing anosmia
   # loss of taste or smell / # any B2 response

From bca27e83104de8938dbd26b57153fec4bdfbb34e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 14 Jun 2022 16:35:01 -0400
Subject: [PATCH 18/49] define mean + percentiles calc function

---
 facebook/delphiFacebook/NAMESPACE             |  4 +++
 .../delphiFacebook/R/contingency_aggregate.R  | 18 ++++++----
 .../delphiFacebook/R/contingency_calculate.R  | 34 +++++++++++++++++++
 .../delphiFacebook/R/contingency_indicators.R |  8 ++---
 .../delphiFacebook/R/contingency_variables.R  | 26 +++++++-------
 .../man/compute_numeric_mean.Rd               | 28 +++++++++++++++
 6 files changed, 96 insertions(+), 22 deletions(-)
 create mode 100644 facebook/delphiFacebook/man/compute_numeric_mean.Rd

diff --git a/facebook/delphiFacebook/NAMESPACE b/facebook/delphiFacebook/NAMESPACE
index 47752e3b4..7846002a4 100644
--- a/facebook/delphiFacebook/NAMESPACE
+++ b/facebook/delphiFacebook/NAMESPACE
@@ -121,6 +121,10 @@ importFrom(stringi,stri_split)
 importFrom(stringi,stri_sub)
 importFrom(stringi,stri_trans_tolower)
 importFrom(stringi,stri_trim)
+importFrom(survey,oldsvyquantile)
+importFrom(survey,svydesign)
+importFrom(survey,svymean)
+importFrom(survey,svyvar)
 importFrom(tibble,add_column)
 importFrom(tibble,tribble)
 importFrom(utils,tail)
diff --git a/facebook/delphiFacebook/R/contingency_aggregate.R b/facebook/delphiFacebook/R/contingency_aggregate.R
index 5380ecbe5..fb2b8fe98 100644
--- a/facebook/delphiFacebook/R/contingency_aggregate.R
+++ b/facebook/delphiFacebook/R/contingency_aggregate.R
@@ -78,19 +78,18 @@ produce_aggregates <- function(df, aggregations, cw_list, params) {
     ## "effective_sample_size", "represented"), add here.
     # If these names change (e.g. `sample_size` to `n`), update
     # `contingency-combine.R`.
-    keep_vars <- c("val", "se", "sample_size", "represented")
-
+    keep_vars <- c("val", "se", "sd", "p25", "p50", "p75", "sample_size", "represented")
     for (agg_id in names(dfs_out)) {
       if (nrow(dfs_out[[agg_id]]) == 0) {
         dfs_out[[agg_id]] <- NULL
         next
       }
       agg_metric <- aggregations$name[aggregations$id == agg_id]
-      map_old_new_names <- keep_vars
-      names(map_old_new_names) <- paste(keep_vars, agg_metric, sep="_")
-
+      
+      tmp_keep_vars <- intersect(keep_vars, names(dfs_out[[agg_id]]))
+      names(tmp_keep_vars) <- paste(tmp_keep_vars, agg_metric, sep="_")
       dfs_out[[agg_id]] <- rename(
-        dfs_out[[agg_id]][, c(agg_group, keep_vars)], all_of(map_old_new_names))
+        dfs_out[[agg_id]][, c(agg_group, tmp_keep_vars)], all_of(tmp_keep_vars))
     }
 
     if ( length(dfs_out) != 0 ) {
@@ -366,6 +365,13 @@ summarize_aggregations_group <- function(group_df, aggregations, target_group, g
       dfs_out[[aggregation]]$sample_size <- sample_size
       dfs_out[[aggregation]]$effective_sample_size <- new_row$effective_sample_size
       dfs_out[[aggregation]]$represented <- new_row$represented
+
+      if (all(c("sd", "p25", "p50", "p75") %in% names(new_row))) {
+        dfs_out[[aggregation]]$sd <- new_row$sd
+        dfs_out[[aggregation]]$p25 <- new_row$p25
+        dfs_out[[aggregation]]$p50 <- new_row$p50
+        dfs_out[[aggregation]]$p75 <- new_row$p75
+      }
     }
   }
 
diff --git a/facebook/delphiFacebook/R/contingency_calculate.R b/facebook/delphiFacebook/R/contingency_calculate.R
index 12727e794..229611ce5 100644
--- a/facebook/delphiFacebook/R/contingency_calculate.R
+++ b/facebook/delphiFacebook/R/contingency_calculate.R
@@ -104,3 +104,37 @@ post_convert_count_to_pct <- function(df) {
   return(mutate(df,
                 val = 100 * .data$val / sum(.data$val, na.rm=TRUE)))
 }
+
+#' Return numeric response estimates. Val is the mean of a numeric vector.
+#'
+#' This function takes vectors as input and computes the response values
+#' (a point estimate named "val" and 25, 50, and 75th percentiles).
+#'
+#' @param response a vector of multiple choice responses
+#' @param weight a vector of sample weights for inverse probability weighting;
+#'   invariant up to a scaling factor
+#' @param sample_size The sample size to use, which may be a non-integer (as
+#'   responses from ZIPs that span geographical boundaries are weighted
+#'   proportionately, and survey weights may also be applied)
+#' @param total_represented Number of people represented in sample, which may
+#'   be a non-integer
+#'
+#' @return a list of named mean and other descriptive statistics
+#'
+#' @importFrom survey svydesign svymean svyvar oldsvyquantile
+compute_numeric_mean <- function(response, weight, sample_size, total_represented)
+{
+  assert(length(response) == length(weight))
+  
+  design <- svydesign(id = ~1, weight = ~weight, data = data.frame(response, weight))
+  return(list(val = as.data.frame(svymean(~response, na.rm = TRUE, design = design))[,"mean"],
+              se = NA_real_,
+              sd = as.data.frame(sqrt(svyvar(~response, na.rm = TRUE, design = design)))[,"variance"],
+              p25 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.25))[,"0.25"],
+              p50 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.5))[,"0.5"],
+              p75 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.75))[,"0.75"],
+              sample_size = sample_size,
+              effective_sample_size = sample_size,
+              represented = total_represented
+  ))
+}
diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index b9d8bccfa..86af04c61 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -544,10 +544,10 @@ get_aggs <- function() {
     "pct_school_safety_measures_cafeteria", "s_school_safety_measures_cafeteria", compute_binary, jeffreys_binary,
     "pct_school_safety_measures_dont_know", "s_school_safety_measures_dont_know", compute_binary, jeffreys_binary,
 
-    # Means
-    "mean_days_symptoms", "symp_n_days", compute_mean, I,
-    "mean_ppl_symptoms_household", "hh_number_sick", compute_mean, I,
-    "mean_ppl_symptoms_community", "community_number_sick", compute_mean, I
+    # Means. No post-processing required.
+    "mean_days_symptoms", "symp_n_days", compute_numeric_mean, I,
+    "mean_ppl_symptoms_household", "hh_number_sick", compute_numeric_mean, I,
+    "mean_ppl_symptoms_community", "community_number_sick", compute_numeric_mean, I
   )
 
   aggs <- create_aggs_product(regions, groups, indicators)
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 1af2da773..458ef0364 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -954,27 +954,29 @@ code_addl_symptoms <- function(input_data, wave) {
   if ("B2b" %in% names(input_data)) {
     # How many days have you had one or more new or unusual symptom?
     # Free response
+    suppressWarnings({ B2b_int <- as.integer(input_data$B2b) })
     input_data$symp_n_days <- case_when(
-      input_data$B2b < 0 ~ NA_real_,
-      input_data$B2b > 1000 ~ NA_real_,
-      is.na(input_data$B2b) ~ NA_real_,
-      TRUE ~ as.integer(input_data$B2b)
-      )
+      B2b_int < 0 ~ NA_integer_,
+      B2b_int > 1000 ~ NA_integer_,
+      is.na(B2b_int) ~ NA_integer_,
+      TRUE ~ B2b_int
+    )
   } else {
-    input_data$symp_n_days <- NA_real_
+    input_data$symp_n_days <- NA_integer_
   }
 
   if ("A4" %in% names(input_data)) {
     # How many additional people in your community do you know who are sick with fever + another symptom?
     # Free response
+    suppressWarnings({ A4_int <- as.integer(input_data$A4) })
     input_data$community_number_sick <- case_when(
-      input_data$A4 < 0 ~ NA_real_,
-      input_data$A4 > 100 ~ NA_real_,
-      is.na(input_data$A4) ~ NA_real_,
-      TRUE ~ as.integer(input_data$A4)
-      )
+      A4_int < 0 ~ NA_integer_,
+      A4_int > 100 ~ NA_integer_,
+      is.na(A4_int) ~ NA_integer_,
+      TRUE ~ A4_int
+    )
   } else {
-    input_data$community_number_sick <- NA_real_
+    input_data$community_number_sick <- NA_integer_
   }
 
   # anosmia
diff --git a/facebook/delphiFacebook/man/compute_numeric_mean.Rd b/facebook/delphiFacebook/man/compute_numeric_mean.Rd
new file mode 100644
index 000000000..a714804d0
--- /dev/null
+++ b/facebook/delphiFacebook/man/compute_numeric_mean.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contingency_calculate.R
+\name{compute_numeric_mean}
+\alias{compute_numeric_mean}
+\title{Return numeric response estimates. Val is the mean of a numeric vector.}
+\usage{
+compute_numeric_mean(response, weight, sample_size, total_represented)
+}
+\arguments{
+\item{response}{a vector of multiple choice responses}
+
+\item{weight}{a vector of sample weights for inverse probability weighting;
+invariant up to a scaling factor}
+
+\item{sample_size}{The sample size to use, which may be a non-integer (as
+responses from ZIPs that span geographical boundaries are weighted
+proportionately, and survey weights may also be applied)}
+
+\item{total_represented}{Number of people represented in sample, which may
+be a non-integer}
+}
+\value{
+a list of named mean and other descriptive statistics
+}
+\description{
+This function takes vectors as input and computes the response values
+(a point estimate named "val" and 25, 50, and 75th percentiles).
+}

From cf2ef612ca8b9fee3359bc717b68e7b8947adbe4 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 15 Jun 2022 13:37:42 -0400
Subject: [PATCH 19/49] test mean calculation

---
 facebook/delphiFacebook/DESCRIPTION           |  3 ++-
 .../delphiFacebook/R/contingency_calculate.R  |  3 +--
 .../testthat/test-contingency-calculate.R     | 21 +++++++++++++++++++
 3 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index ebc5011e8..51ad1e74b 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -21,7 +21,8 @@ Imports:
     data.table,
     tibble,
     purrr,
-    Rcpp
+    Rcpp,
+    survey
 Suggests:
     knitr (>= 1.15),
     rmarkdown (>= 1.4),
diff --git a/facebook/delphiFacebook/R/contingency_calculate.R b/facebook/delphiFacebook/R/contingency_calculate.R
index 229611ce5..a5ff70676 100644
--- a/facebook/delphiFacebook/R/contingency_calculate.R
+++ b/facebook/delphiFacebook/R/contingency_calculate.R
@@ -122,8 +122,7 @@ post_convert_count_to_pct <- function(df) {
 #' @return a list of named mean and other descriptive statistics
 #'
 #' @importFrom survey svydesign svymean svyvar oldsvyquantile
-compute_numeric_mean <- function(response, weight, sample_size, total_represented)
-{
+compute_numeric_mean <- function(response, weight, sample_size, total_represented) {
   assert(length(response) == length(weight))
   
   design <- svydesign(id = ~1, weight = ~weight, data = data.frame(response, weight))
diff --git a/facebook/delphiFacebook/unit-tests/testthat/test-contingency-calculate.R b/facebook/delphiFacebook/unit-tests/testthat/test-contingency-calculate.R
index 0d79c0f62..834554b9a 100644
--- a/facebook/delphiFacebook/unit-tests/testthat/test-contingency-calculate.R
+++ b/facebook/delphiFacebook/unit-tests/testthat/test-contingency-calculate.R
@@ -14,3 +14,24 @@ test_that("compute_multiple_choice returns people represented in group", {
   out <- compute_multiple_choice(response, weight, sample_size, 70.3)
   expect_identical(out, expected_output)
 })
+
+test_that("compute_numeric_mean returns correct mean and percentiles in unweighted case", {
+  response <- c(1, 2, 5, 1, 5)
+  weight <- rep(1, 5)
+  sample_size <- 5
+  total_represented <- 5000
+  
+  # Use linear interpolation.
+  quantiles <- quantile(response, probs = c(0.25, 0.5, 0.75), type=4)
+  expected_output <- list(val = mean(response),
+                          se = NA_real_,
+                          sd = sd(response),
+                          p25 = quantiles[["25%"]],
+                          p50 = quantiles[["50%"]],
+                          p75 = quantiles[["75%"]],
+                          sample_size = sample_size,
+                          effective_sample_size = sample_size,
+                          represented = total_represented)
+  out <- compute_numeric_mean(response, weight, sample_size, total_represented)
+  expect_identical(out, expected_output)
+})

From 7148e84baf5002f77d826fdaf8647f933dae944b Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 15 Jun 2022 14:55:46 -0400
Subject: [PATCH 20/49] move new mental health inds to contingency-only func

---
 .../delphiFacebook/R/contingency_variables.R  | 51 +++++++++++++++++++
 facebook/delphiFacebook/R/responses.R         |  1 +
 facebook/delphiFacebook/R/variables.R         | 22 --------
 3 files changed, 52 insertions(+), 22 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 458ef0364..72d7860cf 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1206,6 +1206,57 @@ code_behaviors <- function(input_data, wave) {
   return(input_data)
 }
 
+#' Additional mental health indicators
+#'
+#' @param input_data input data frame of raw survey data
+#' @param wave integer indicating survey version
+#'
+#' @return augmented data frame
+code_addl_mental_health <- function(input_data, wave) {
+  input_data$mh_some_anxious <- NA
+  input_data$mh_some_anxious_7d <- NA
+  input_data$mh_some_depressed <- NA
+  input_data$mh_some_depressed_7d <- NA
+  input_data$mh_some_isolated <- NA
+  input_data$mh_some_isolated_7d <- NA
+  input_data$mh_very_worried_finances <- NA
+
+  if (wave >= 4 && wave < 10) {
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
+    input_data$mh_some_anxious <- input_data$C8_1 == 3 | input_data$C8_1 == 4 | input_data$C8_1 == 2
+    input_data$mh_some_depressed <- input_data$C8_2 == 3 | input_data$C8_2 == 4 | input_data$C8_2 == 2
+    input_data$mh_some_isolated <- input_data$C8_3 == 3 | input_data$C8_3 == 4 | input_data$C8_3 == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
+  } else if (wave == 10) {
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
+    input_data$mh_some_anxious_7d <- input_data$C8a_1 == 3 | input_data$C8a_1 == 4 | input_data$C8a_1 == 2
+    input_data$mh_some_depressed_7d <- input_data$C8a_2 == 3 | input_data$C8a_2 == 4 | input_data$C8a_2 == 2
+    input_data$mh_some_isolated_7d <- input_data$C8a_3 == 3 | input_data$C8a_3 == 4 | input_data$C8a_3 == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
+  } else if (wave >= 11) {
+    # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
+    input_data$mh_some_anxious_7d <- input_data$C18a == 3 | input_data$C18a == 4 | input_data$C18a == 2
+    input_data$mh_some_depressed_7d <- input_data$C18b == 3 | input_data$C18b == 4 | input_data$C18b == 2
+    # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
+    input_data$mh_very_worried_finances <- input_data$C15 == 1
+  }
+
+  if ("Q36" %in% names(input_data)) {
+    # Included in waves 1, 2, 3. Coded as 1 = substantial threat,
+    # 2 = moderate threat, 3 = not much of a threat, 4 = not a threat at all
+    input_data$mh_financial_threat <- case_when(
+      is.na(input_data$Q36) ~ NA,
+      input_data$Q36 == 1 ~ TRUE,
+      TRUE ~ FALSE)
+  } else {
+    input_data$mh_financial_threat <- NA
+  }
+
+  return(input_data)
+}
+
 #' Activities
 #'
 #' @param input_data input data frame of raw survey data
diff --git a/facebook/delphiFacebook/R/responses.R b/facebook/delphiFacebook/R/responses.R
index c2aae5981..c5f4a8032 100644
--- a/facebook/delphiFacebook/R/responses.R
+++ b/facebook/delphiFacebook/R/responses.R
@@ -245,6 +245,7 @@ load_response_one <- function(input_filename, params, contingency_run) {
     input_data <- code_vaccine_barriers(input_data, wave)
     input_data <- code_behaviors(input_data, wave)
     input_data <- code_addl_activities(input_data, wave)
+    input_data <- code_addl_mental_health(input_data, wave)
   }
 
   return(input_data)
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index f52624e26..15a68a8a9 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -199,35 +199,24 @@ code_mental_health <- function(input_data, wave) {
     input_data$mh_worried_ill <- input_data$C9 == 1 | input_data$C9 == 2
     # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious <- input_data$C8_1 == 3 | input_data$C8_1 == 4
-    input_data$mh_some_anxious <- input_data$C8_1 == 3 | input_data$C8_1 == 4 | input_data$C8_1 == 2
     input_data$mh_depressed <- input_data$C8_2 == 3 | input_data$C8_2 == 4
-    input_data$mh_some_depressed <- input_data$C8_2 == 3 | input_data$C8_2 == 4 | input_data$C8_2 == 2
     input_data$mh_isolated <- input_data$C8_3 == 3 | input_data$C8_3 == 4
-    input_data$mh_some_isolated <- input_data$C8_3 == 3 | input_data$C8_3 == 4 | input_data$C8_3 == 2
     # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
-    input_data$mh_very_worried_finances <- input_data$C15 == 1
   } else if (wave == 10) {
     input_data$mh_worried_ill <- input_data$C9 == 1 | input_data$C9 == 2
     # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious_7d <- input_data$C8a_1 == 3 | input_data$C8a_1 == 4
-    input_data$mh_some_anxious_7d <- input_data$C8a_1 == 3 | input_data$C8a_1 == 4 | input_data$C8a_1 == 2
     input_data$mh_depressed_7d <- input_data$C8a_2 == 3 | input_data$C8a_2 == 4
-    input_data$mh_some_depressed_7d <- input_data$C8a_2 == 3 | input_data$C8a_2 == 4 | input_data$C8a_2 == 2
     input_data$mh_isolated_7d <- input_data$C8a_3 == 3 | input_data$C8a_3 == 4
-    input_data$mh_some_isolated_7d <- input_data$C8a_3 == 3 | input_data$C8a_3 == 4 | input_data$C8a_3 == 2
     # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
-    input_data$mh_very_worried_finances <- input_data$C15 == 1
   } else if (wave >= 11) {
     # All coded as 1 = none of the time, 2 = some of the time, 3 = most of the time, 4 = all of the time
     input_data$mh_anxious_7d <- input_data$C18a == 3 | input_data$C18a == 4
-    input_data$mh_some_anxious_7d <- input_data$C18a == 3 | input_data$C18a == 4 | input_data$C18a == 2
     input_data$mh_depressed_7d <- input_data$C18b == 3 | input_data$C18b == 4
-    input_data$mh_some_depressed_7d <- input_data$C18b == 3 | input_data$C18b == 4 | input_data$C18b == 2
     # Coded as 1 = very worried, 2 = somewhat worried, 3 = not too worried, 4 = not worried at all
     input_data$mh_worried_finances <- input_data$C15 == 1 | input_data$C15 == 2
-    input_data$mh_very_worried_finances <- input_data$C15 == 1
   }
 
   if ("G1" %in% names(input_data)) {
@@ -241,17 +230,6 @@ code_mental_health <- function(input_data, wave) {
   } else {
     input_data$mh_worried_catch_covid <- NA
   }
-
-  if ("Q36" %in% names(input_data)) {
-    # Included in waves 1, 2, 3. Coded as 1 = substantial threat,
-    # 2 = moderate threat, 3 = not much of a threat, 4 = not a threat at all
-    input_data$mh_financial_threat <- case_when(
-      is.na(input_data$Q36) ~ NA,
-      input_data$Q36 == 1 ~ TRUE,
-      TRUE ~ FALSE)
-  } else {
-    input_data$mh_financial_threat <- NA
-  }
   
   return(input_data)
 }

From a6ede6b01ff5543b602a1ecb20a55b26fb1a25a3 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 15 Jun 2022 14:58:11 -0400
Subject: [PATCH 21/49] move new flu shot inds to contingency-only func

---
 .../delphiFacebook/R/contingency_variables.R  | 21 +++++++++++++++++++
 facebook/delphiFacebook/R/variables.R         | 21 -------------------
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 72d7860cf..75f035b9f 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -350,6 +350,27 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$t_reason_not_tested_none <- NA
   }
 
+if ("C2" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 2 = "No"
+    input_data$v_flu_vaccinated_1y <- input_data$C2 == 1
+  } else {
+    input_data$v_flu_vaccinated_1y <- NA
+  }
+
+  if ("C17" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 4 = "No", 2 = "I don't know"
+    input_data$v_flu_vaccinated_june_2020 <- input_data$C17 == 1
+  } else {
+    input_data$v_flu_vaccinated_june_2020 <- NA
+  }
+
+  if ("C17a" %in% names(input_data)) {
+    # Coded as 1 = "Yes", 2 = "No", 3 = "I don't know"
+    input_data$v_flu_vaccinated_july_2020 <- input_data$C17a == 1
+  } else {
+    input_data$v_flu_vaccinated_july_2020 <- NA
+  }
+
   return(input_data)
 }
 
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index 15a68a8a9..5695c6a45 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -992,27 +992,6 @@ code_vaccines <- function(input_data, wave) {
     input_data$v_vaccinated_booster_defno   <- NA
   }
   
-  if ("C2" %in% names(input_data)) {
-    # Coded as 1 = "Yes", 2 = "No"
-    input_data$v_flu_vaccinated_1y <- input_data$C2 == 1
-  } else {
-    input_data$v_flu_vaccinated_1y <- NA
-  }
-
-  if ("C17" %in% names(input_data)) {
-    # Coded as 1 = "Yes", 4 = "No", 2 = "I don't know"
-    input_data$v_flu_vaccinated_june_2020 <- input_data$C17 == 1
-  } else {
-    input_data$v_flu_vaccinated_june_2020 <- NA
-  }
-
-  if ("C17a" %in% names(input_data)) {
-    # Coded as 1 = "Yes", 2 = "No", 3 = "I don't know"
-    input_data$v_flu_vaccinated_july_2020 <- input_data$C17a == 1
-  } else {
-    input_data$v_flu_vaccinated_july_2020 <- NA
-  }
-
   if ("C17b" %in% names(input_data)) {
     # Coded as 1 = "Yes", 2 = "No", 3 = "I don't know"
     input_data$v_flu_vaccinated_2021 <- input_data$C17b == 1

From fbb681b1d69b66fce4829f6997c534ea7d65a0c3 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 15 Jun 2022 15:01:37 -0400
Subject: [PATCH 22/49] move vaccine incomplete reasons to contingency-only

---
 .../delphiFacebook/R/contingency_variables.R  | 37 +++++++++++++++++++
 facebook/delphiFacebook/R/variables.R         | 37 -------------------
 2 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 75f035b9f..a71f57bc4 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -350,6 +350,43 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$t_reason_not_tested_none <- NA
   }
 
+if ("V5d" %in% names(input_data)) {
+    # introduced in Wave 8, removed in Wave 11
+    vaccine_incomplete_reasons <- split_options(input_data$V5d)
+
+    input_data$v_vaccine_incomplete_sideeffect <- is_selected(vaccine_incomplete_reasons, "1")
+    input_data$v_vaccine_incomplete_allergic <- is_selected(vaccine_incomplete_reasons, "2")
+    input_data$v_vaccine_incomplete_wontwork <- is_selected(vaccine_incomplete_reasons, "3")
+    input_data$v_vaccine_incomplete_dontbelieve <- is_selected(vaccine_incomplete_reasons, "4")
+    input_data$v_vaccine_incomplete_dontlike <- is_selected(vaccine_incomplete_reasons, "5")
+    input_data$v_vaccine_incomplete_not_recommended <- is_selected(vaccine_incomplete_reasons, "6")
+    input_data$v_vaccine_incomplete_wait <- is_selected(vaccine_incomplete_reasons, "7")
+    input_data$v_vaccine_incomplete_otherpeople <- is_selected(vaccine_incomplete_reasons, "8")
+    input_data$v_vaccine_incomplete_cost <- is_selected(vaccine_incomplete_reasons, "9")
+    input_data$v_vaccine_incomplete_distrust_vaccine <- is_selected(vaccine_incomplete_reasons, "10")
+    input_data$v_vaccine_incomplete_distrust_gov <- is_selected(vaccine_incomplete_reasons, "11")
+    input_data$v_vaccine_incomplete_health <- is_selected(vaccine_incomplete_reasons, "12")
+    input_data$v_vaccine_incomplete_other <- is_selected(vaccine_incomplete_reasons, "13")
+    input_data$v_vaccine_incomplete_pregnant <- is_selected(vaccine_incomplete_reasons, "14")
+    input_data$v_vaccine_incomplete_religion <- is_selected(vaccine_incomplete_reasons, "15")
+  } else {
+    input_data$v_vaccine_incomplete_sideeffect <- NA_real_
+    input_data$v_vaccine_incomplete_allergic <- NA_real_
+    input_data$v_vaccine_incomplete_wontwork <- NA_real_
+    input_data$v_vaccine_incomplete_dontbelieve <- NA_real_
+    input_data$v_vaccine_incomplete_dontlike <- NA_real_
+    input_data$v_vaccine_incomplete_not_recommended <- NA_real_
+    input_data$v_vaccine_incomplete_wait <- NA_real_
+    input_data$v_vaccine_incomplete_otherpeople <- NA_real_
+    input_data$v_vaccine_incomplete_cost <- NA_real_
+    input_data$v_vaccine_incomplete_distrust_vaccine <- NA_real_
+    input_data$v_vaccine_incomplete_distrust_gov <- NA_real_
+    input_data$v_vaccine_incomplete_health <- NA_real_
+    input_data$v_vaccine_incomplete_other <- NA_real_
+    input_data$v_vaccine_incomplete_pregnant <- NA_real_
+    input_data$v_vaccine_incomplete_religion <- NA_real_
+  }
+
 if ("C2" %in% names(input_data)) {
     # Coded as 1 = "Yes", 2 = "No"
     input_data$v_flu_vaccinated_1y <- input_data$C2 == 1
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index 5695c6a45..ae4407b1d 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -653,43 +653,6 @@ code_vaccines <- function(input_data, wave) {
     input_data$v_hesitancy_reason_dislike_vaccines_generally <- NA_real_
   }
 
-  if ("V5d" %in% names(input_data)) {
-    # introduced in Wave 8, removed in Wave 11
-    vaccine_incomplete_reasons <- split_options(input_data$V5d)
-
-    input_data$v_vaccine_incomplete_sideeffect <- is_selected(vaccine_incomplete_reasons, "1")
-    input_data$v_vaccine_incomplete_allergic <- is_selected(vaccine_incomplete_reasons, "2")
-    input_data$v_vaccine_incomplete_wontwork <- is_selected(vaccine_incomplete_reasons, "3")
-    input_data$v_vaccine_incomplete_dontbelieve <- is_selected(vaccine_incomplete_reasons, "4")
-    input_data$v_vaccine_incomplete_dontlike <- is_selected(vaccine_incomplete_reasons, "5")
-    input_data$v_vaccine_incomplete_not_recommended <- is_selected(vaccine_incomplete_reasons, "6")
-    input_data$v_vaccine_incomplete_wait <- is_selected(vaccine_incomplete_reasons, "7")
-    input_data$v_vaccine_incomplete_otherpeople <- is_selected(vaccine_incomplete_reasons, "8")
-    input_data$v_vaccine_incomplete_cost <- is_selected(vaccine_incomplete_reasons, "9")
-    input_data$v_vaccine_incomplete_distrust_vaccine <- is_selected(vaccine_incomplete_reasons, "10")
-    input_data$v_vaccine_incomplete_distrust_gov <- is_selected(vaccine_incomplete_reasons, "11")
-    input_data$v_vaccine_incomplete_health <- is_selected(vaccine_incomplete_reasons, "12")
-    input_data$v_vaccine_incomplete_other <- is_selected(vaccine_incomplete_reasons, "13")
-    input_data$v_vaccine_incomplete_pregnant <- is_selected(vaccine_incomplete_reasons, "14")
-    input_data$v_vaccine_incomplete_religion <- is_selected(vaccine_incomplete_reasons, "15")
-  } else {
-    input_data$v_vaccine_incomplete_sideeffect <- NA_real_
-    input_data$v_vaccine_incomplete_allergic <- NA_real_
-    input_data$v_vaccine_incomplete_wontwork <- NA_real_
-    input_data$v_vaccine_incomplete_dontbelieve <- NA_real_
-    input_data$v_vaccine_incomplete_dontlike <- NA_real_
-    input_data$v_vaccine_incomplete_not_recommended <- NA_real_
-    input_data$v_vaccine_incomplete_wait <- NA_real_
-    input_data$v_vaccine_incomplete_otherpeople <- NA_real_
-    input_data$v_vaccine_incomplete_cost <- NA_real_
-    input_data$v_vaccine_incomplete_distrust_vaccine <- NA_real_
-    input_data$v_vaccine_incomplete_distrust_gov <- NA_real_
-    input_data$v_vaccine_incomplete_health <- NA_real_
-    input_data$v_vaccine_incomplete_other <- NA_real_
-    input_data$v_vaccine_incomplete_pregnant <- NA_real_
-    input_data$v_vaccine_incomplete_religion <- NA_real_
-  }
-
   if ( "V6" %in% names(input_data) ) {
     # introduced in Wave 8
     dontneed_reasons <- split_options(input_data$V6)

From 4b6687e0fd236b3527dc3b1b990efc53ecaae321 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 15 Jun 2022 15:29:21 -0400
Subject: [PATCH 23/49] test some alt masking inds

---
 .../delphiFacebook/R/contingency_indicators.R |  1 +
 facebook/delphiFacebook/R/variables.R         | 11 +++++++---
 .../delphiFacebook/man/code_mask_contact.Rd   |  3 +--
 .../unit-tests/testthat/test-variables.R      | 20 +++++++++++++++++++
 4 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 86af04c61..485cf28af 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -72,6 +72,7 @@ get_aggs <- function() {
     # behavior
     ## Mask wearing and distancing
     "pct_wearing_mask_5d", "c_mask_often", compute_binary, jeffreys_binary,
+    "pct_wearing_mask_5d_alt", "c_mask_some_often", compute_binary, jeffreys_binary,
     "pct_wearing_mask_7d", "c_mask_often_7d", compute_binary, jeffreys_binary,
     "pct_wearing_mask_7d_alt", "c_mask_some_often_7d", compute_binary, jeffreys_binary,
 
diff --git a/facebook/delphiFacebook/R/variables.R b/facebook/delphiFacebook/R/variables.R
index ae4407b1d..fb37e0d13 100644
--- a/facebook/delphiFacebook/R/variables.R
+++ b/facebook/delphiFacebook/R/variables.R
@@ -239,8 +239,7 @@ code_mental_health <- function(input_data, wave) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with `c_travel_state`, `c_work_outside_5d`,
-#'   `c_mask_often`, `c_others_masked`
+#' @return augmented data frame
 code_mask_contact <- function(input_data, wave) {
   # private helper for both mask items, which are identically coded: 6 means the
   # respondent was not in public, 1 & 2 mean always/most, 3-5 mean some to none
@@ -268,8 +267,15 @@ code_mask_contact <- function(input_data, wave) {
     # added in wave 4. wearing mask most or all of the time; exclude respondents
     # who have not been in public
     input_data$c_mask_often <- most_always(input_data$C14)
+    # Same indicator but include "sometimes" wear mask in public
+    input_data$c_mask_some_often <- case_when(
+      is.na(input_data$C14) ~ NA,
+      input_data$C14 == 6 ~ NA,
+      input_data$C14 == 1 | input_data$C14 == 2 | input_data$C14 == 3 ~ TRUE,
+      TRUE ~ FALSE)
   } else {
     input_data$c_mask_often <- NA
+    input_data$c_mask_some_often <- NA
   }
 
   if ("C14a" %in% names(input_data)) {
@@ -282,7 +288,6 @@ code_mask_contact <- function(input_data, wave) {
       input_data$C14a == 6 ~ NA,
       input_data$C14a == 1 | input_data$C14a == 2 | input_data$C14a == 3 ~ TRUE,
       TRUE ~ FALSE)
-
   } else {
     input_data$c_mask_often_7d <- NA
     input_data$c_mask_some_often_7d <- NA
diff --git a/facebook/delphiFacebook/man/code_mask_contact.Rd b/facebook/delphiFacebook/man/code_mask_contact.Rd
index ecb0b4a96..e376e328a 100644
--- a/facebook/delphiFacebook/man/code_mask_contact.Rd
+++ b/facebook/delphiFacebook/man/code_mask_contact.Rd
@@ -12,8 +12,7 @@ code_mask_contact(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with `c_travel_state`, `c_work_outside_5d`,
-  `c_mask_often`, `c_others_masked`
+augmented data frame
 }
 \description{
 Mask and contact variables
diff --git a/facebook/delphiFacebook/unit-tests/testthat/test-variables.R b/facebook/delphiFacebook/unit-tests/testthat/test-variables.R
index 741a109a6..43d6dc1d9 100644
--- a/facebook/delphiFacebook/unit-tests/testthat/test-variables.R
+++ b/facebook/delphiFacebook/unit-tests/testthat/test-variables.R
@@ -111,10 +111,15 @@ test_that("mask items correctly coded", {
   input_data$c_travel_state <- TRUE
   input_data$c_travel_state_7d <- NA
   input_data$c_mask_often <- c(NA, TRUE, FALSE, NA, TRUE, FALSE)
+  input_data$c_mask_some_often <- c(NA, TRUE, TRUE, NA, TRUE, FALSE)
   input_data$c_mask_often_7d <- NA
+  input_data$c_mask_some_often_7d <- NA
   input_data$c_others_masked <- c(TRUE, NA, NA, FALSE, TRUE, FALSE)
+  input_data$c_others_some_masked <- c(TRUE, NA, NA, TRUE, TRUE, FALSE)
   input_data$c_others_masked_public <- NA
+  input_data$c_others_masked_some_public <- NA
   input_data$c_others_distanced_public <- NA
+  input_data$c_others_distanced_some_public <- NA
   input_data$c_work_outside_5d <- NA
 
   expect_equal(out, input_data)
@@ -131,10 +136,15 @@ test_that("mask items correctly coded", {
   input_data$c_travel_state <- TRUE
   input_data$c_travel_state_7d <- NA
   input_data$c_mask_often <- NA
+  input_data$c_mask_some_often <- NA
   input_data$c_mask_often_7d <- c(NA, TRUE, FALSE, NA, TRUE, FALSE)
+  input_data$c_mask_some_often_7d <- c(NA, TRUE, TRUE, NA, TRUE, FALSE)
   input_data$c_others_masked <- c(TRUE, NA, NA, FALSE, TRUE, FALSE)
+  input_data$c_others_some_masked <- c(TRUE, NA, NA, TRUE, TRUE, FALSE)
   input_data$c_others_masked_public <- NA
+  input_data$c_others_masked_some_public <- NA
   input_data$c_others_distanced_public <- NA
+  input_data$c_others_distanced_some_public <- NA
   input_data$c_work_outside_5d <- NA
 
   expect_equal(out, input_data)
@@ -152,10 +162,15 @@ test_that("mask items correctly coded", {
   input_data$c_travel_state <- NA
   input_data$c_travel_state_7d <- TRUE
   input_data$c_mask_often <- c(NA, TRUE, FALSE, NA, TRUE, FALSE)
+  input_data$c_mask_some_often <- c(NA, TRUE, TRUE, NA, TRUE, FALSE)
   input_data$c_mask_often_7d <- NA
+  input_data$c_mask_some_often_7d <- NA
   input_data$c_others_masked <- c(TRUE, NA, NA, FALSE, TRUE, FALSE)
+  input_data$c_others_some_masked <- c(TRUE, NA, NA, TRUE, TRUE, FALSE)
   input_data$c_others_masked_public <- NA
+  input_data$c_others_masked_some_public <- NA
   input_data$c_others_distanced_public <- NA
+  input_data$c_others_distanced_some_public <- NA
   input_data$c_work_outside_5d <- NA
 
   expect_equal(out, input_data)
@@ -174,10 +189,15 @@ test_that("mask items correctly coded", {
   input_data$c_travel_state <- NA
   input_data$c_travel_state_7d <- TRUE
   input_data$c_mask_often <- c(NA, TRUE, FALSE, NA, TRUE, FALSE)
+  input_data$c_mask_some_often <- c(NA, TRUE, TRUE, NA, TRUE, FALSE)
   input_data$c_mask_often_7d <- NA
+  input_data$c_mask_some_often_7d <- NA
   input_data$c_others_masked <- NA
+  input_data$c_others_some_masked <- NA
   input_data$c_others_masked_public <- c(FALSE, NA, NA, FALSE, FALSE, TRUE)
+  input_data$c_others_masked_some_public <- c(FALSE, NA, NA, TRUE, FALSE, TRUE)
   input_data$c_others_distanced_public <- c(FALSE, NA, NA, FALSE, FALSE, TRUE)
+  input_data$c_others_distanced_some_public <- c(FALSE, NA, NA, TRUE, FALSE, TRUE)
   input_data$c_work_outside_5d <- NA
   
   expect_equal(out, input_data)

From ad23a3d27a9a346046c6e20eb2a76eb702878a7b Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 16 Jun 2022 11:53:44 -0400
Subject: [PATCH 24/49] overall vaccine hesitancy

---
 facebook/delphiFacebook/R/contingency_indicators.R | 1 +
 facebook/delphiFacebook/R/contingency_variables.R  | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 485cf28af..022b22cab 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -150,6 +150,7 @@ get_aggs <- function() {
     "pct_accept_vaccine_no_appointment", "v_accept_covid_vaccine_no_appointment", compute_binary, jeffreys_binary,
     "pct_appointment_or_accept_vaccine", "v_appointment_or_accept_covid_vaccine", compute_binary, jeffreys_binary,
     "pct_hesitant_vaccine", "v_hesitant_vaccine", compute_binary, jeffreys_binary,
+    "pct_overall_vaccine_hesitancy", "overall_vaccine_hesitancy", compute_binary, jeffreys_binary,
     "pct_vaccinated_or_accept", "v_covid_vaccinated_or_accept", compute_binary, jeffreys_binary,
     "pct_vaccinated_appointment_or_accept", "v_covid_vaccinated_appointment_or_accept", compute_binary, jeffreys_binary,
 
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index a71f57bc4..1eff641ab 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -238,6 +238,11 @@ code_addl_vaccines <- function(input_data, wave) {
     )
   }
 
+  input_data$overall_vaccine_hesitancy <- coalesce(
+    !input_data$v_covid_vaccinated_or_accept,
+    !input_data$v_covid_vaccinated_appointment_or_accept
+  )
+
   # accept_vaccine_defyes
   # accept_vaccine_probyes
   # accept_vaccine_probno

From 1b529a56ecc7829377ea4b63b30791853ccb59d2 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 17 Jun 2022 13:02:36 -0400
Subject: [PATCH 25/49] unusual symptom followup change meaning

---
 .../delphiFacebook/R/contingency_indicators.R | 10 +++++-
 .../delphiFacebook/R/contingency_variables.R  | 35 +++++++++++++------
 2 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 022b22cab..8f60b06b9 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -403,8 +403,16 @@ get_aggs <- function() {
     "pct_ever_tested", "t_ever_tested", compute_binary, jeffreys_binary,
 
     "pct_unusual_symptom_tested", "t_unusual_symptom_tested", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_tested_positive", "t_unusual_symptom_tested_positive", compute_binary, jeffreys_binary,
     "pct_unusual_symptom_hospital", "t_unusual_symptom_hospital", compute_binary, jeffreys_binary,
-    "pct_unusual_symptom_medical_care", "t_unusual_symptom_medical_care", compute_binary, jeffreys_binary,
+
+    "pct_unusual_symptom_medical_care_called_doctor", "unusual_symptom_medical_care_called_doctor", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_telemedicine", "unusual_symptom_medical_care_telemedicine", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_visited_doctor", "unusual_symptom_medical_care_visited_doctor", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_urgent_care", "unusual_symptom_medical_care_urgent_care", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_er", "unusual_symptom_medical_care_er", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_hospital", "unusual_symptom_medical_care_hospital", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_medical_care_tried", "unusual_symptom_medical_care_tried", compute_binary, jeffreys_binary,
 
     "pct_reason_not_tested_tried", "t_reason_not_tested_tried", compute_binary, jeffreys_binary,
     "pct_reason_not_tested_appointment", "t_reason_not_tested_appointment", compute_binary, jeffreys_binary,
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 1eff641ab..c3bd1d1eb 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -302,21 +302,24 @@ code_addl_vaccines <- function(input_data, wave) {
   }
   
   if ("B5" %in% names(input_data)) {
+    # Coded as 1 = "tested and COVID+", 2 = "tested and COVID-",
+    # 3 = "tested, but no result yet", 4 = "tried to get tested but couldn't",
+    # 5 = "didn't try to get tested"
+    # Regardless of test result
     input_data$t_unusual_symptom_tested <- case_when(
       input_data$B5 %in% c(1, 2, 3) ~ 1,
       input_data$B5 %in% c(4, 5) ~ 0,
       TRUE ~ NA_real_
     )
+    # Tested with positive result
+    input_data$t_unusual_symptom_tested_positive <- input_data$B5 == 1
   } else {
     input_data$t_unusual_symptom_tested <- NA
+    input_data$t_unusual_symptom_tested_positive <- NA
   }
 
   if ("B6" %in% names(input_data)) {
-    input_data$t_unusual_symptom_hospital <- case_when(
-      input_data$B6 %in% c(1, 3) ~ 1,
-      input_data$B6 %in% c(2) ~ 0,
-      TRUE ~ NA_real_
-    )
+    input_data$t_unusual_symptom_hospital <- input_data$B6 == 1
   } else {
     input_data$t_unusual_symptom_hospital <- NA
   }
@@ -324,13 +327,23 @@ code_addl_vaccines <- function(input_data, wave) {
   if ("B7" %in% names(input_data)) {
     # Coded as 8 = no medical care sought, 1-6 = various types of medical care sought,
     # 7 = care sought but not received
-    input_data$t_unusual_symptom_medical_care <- case_when(
-      input_data$B7 == "8" ~ 0,
-      !is.na(input_data$B7) ~ 1,
-      TRUE ~ NA_real_
-    )
+    unusual_symptoms_care <- split_options(input_data$B7)
+
+    input_data$unusual_symptom_medical_care_called_doctor <- is_selected(unusual_symptoms_care, "1")
+    input_data$unusual_symptom_medical_care_telemedicine <- is_selected(unusual_symptoms_care, "2")
+    input_data$unusual_symptom_medical_care_visited_doctor <- is_selected(unusual_symptoms_care, "3")
+    input_data$unusual_symptom_medical_care_urgent_care <- is_selected(unusual_symptoms_care, "4")
+    input_data$unusual_symptom_medical_care_er <- is_selected(unusual_symptoms_care, "5")
+    input_data$unusual_symptom_medical_care_hospital <- is_selected(unusual_symptoms_care, "6")
+    input_data$unusual_symptom_medical_care_tried <- is_selected(unusual_symptoms_care, "7")
   } else {
-    input_data$t_unusual_symptom_medical_care <- NA
+    input_data$unusual_symptom_medical_care_called_doctor <- NA
+    input_data$unusual_symptom_medical_care_telemedicine <- NA
+    input_data$unusual_symptom_medical_care_visited_doctor <- NA
+    input_data$unusual_symptom_medical_care_urgent_care <- NA
+    input_data$unusual_symptom_medical_care_er <- NA
+    input_data$unusual_symptom_medical_care_hospital <- NA
+    input_data$unusual_symptom_medical_care_tried <- NA
   }
 
   if ( "B12a" %in% names(input_data) ) {

From 5ef3105a3f6ec9b3e21f6b9cbc15b69ff521e46e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 16 Jun 2022 11:13:09 -0400
Subject: [PATCH 26/49] calc more demographics

make postprocessing multinomial
---
 .../delphiFacebook/R/contingency_indicators.R | 118 +++++++++-
 .../delphiFacebook/R/contingency_variables.R  | 219 +++++++++++++++++-
 facebook/delphiFacebook/R/responses.R         |   1 +
 .../man/code_addl_demographic.Rd              |  19 ++
 .../man/code_addl_mental_health.Rd            |  19 ++
 .../delphiFacebook/man/code_addl_symptoms.Rd  |   2 +-
 .../delphiFacebook/man/code_addl_vaccines.Rd  |   2 +-
 .../man/code_attempt_vaccine.Rd               |   2 +-
 facebook/delphiFacebook/man/code_trust.Rd     |   2 +-
 .../man/code_vaccine_barriers.Rd              |   2 +-
 10 files changed, 373 insertions(+), 13 deletions(-)
 create mode 100644 facebook/delphiFacebook/man/code_addl_demographic.Rd
 create mode 100644 facebook/delphiFacebook/man/code_addl_mental_health.Rd

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 8f60b06b9..5c7b936eb 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -626,9 +626,121 @@ get_aggs <- function() {
   
   ### Combine full set and additional original tables.
   aggs <- rbind(aggs, cut1_aggs, cut2_aggs, cut3_aggs, cut456_aggs, cut456_marginal_aggs)
-  
-  weekly_aggs <- aggs
-  monthly_aggs <- rbind(aggs, monthly_aggs)
+
+
+  ### Demographic variables. Include in "overall" cuts only.
+  demo_groups <- list(c())
+  demo_indicators <- tribble(
+    ~name, ~metric, ~compute_fn, ~post_fn,
+    "pct_gender_male", "gender_male", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_gender_female", "gender_female", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_gender_nonbinary_other", "gender_nonbinary_other", compute_binary, jeffreys_multinomial_factory(3),
+
+    "pct_age_18_24", "age_18_24", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_25_34", "age_25_34", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_35_44", "age_35_44", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_45_54", "age_45_54", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_55_64", "age_55_64", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_65_74", "age_65_74", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_age_75_older", "age_75_older", compute_binary, jeffreys_multinomial_factory(7),
+
+    "pct_hispanic_latino", "hispanic", compute_binary, jeffreys_binary,
+
+    "pct_race_american_indian_alaska_native", "race_american_indian_alaska_native", compute_binary, jeffreys_multinomial_factory(6),
+    "pct_race_asian", "race_asian", compute_binary, jeffreys_multinomial_factory(6),
+    "pct_race_black_african_american", "race_black_african_american", compute_binary, jeffreys_multinomial_factory(6),
+    "pct_race_native_hawaiian_pacific_islander", "race_native_hawaiian_pacific_islander", compute_binary, jeffreys_multinomial_factory(6),
+    "pct_race_white", "race_white", compute_binary, jeffreys_multinomial_factory(6),
+    "pct_race_multiple_other", "race_multiple_other", compute_binary, jeffreys_multinomial_factory(6),
+
+    "pct_education_less_than_highschool", "education_less_than_highschool", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_highschool_or_equivalent", "education_highschool_or_equivalent", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_some_college", "education_some_college", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_2yr_degree", "education_2yr_degree", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_4yr_degree", "education_4yr_degree", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_masters", "education_masters", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_professional_degree", "education_professional_degree", compute_binary, jeffreys_multinomial_factory(9),
+    "pct_education_doctorate", "education_doctorate", compute_binary, jeffreys_multinomial_factory(9),
+
+    "pct_language_home_english", "language_home_english", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_spanish", "language_home_spanish", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_chinese", "language_home_chinese", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_vietnamese", "language_home_vietnamese", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_french", "language_home_french", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_portuguese", "language_home_portuguese", compute_binary, jeffreys_multinomial_factory(7),
+    "pct_language_home_other", "language_home_other", compute_binary, jeffreys_multinomial_factory(7),
+
+    "pct_work_for_pay_4w", "a_work_for_pay_4w", compute_binary, jeffreys_binary,
+
+    "pct_condition_asthma", "comorbid_asthma", compute_binary, jeffreys_binary,
+    "pct_condition_lung", "comorbidlungdisease", compute_binary, jeffreys_binary,
+    "pct_condition_cancer", "comorbidcancer", compute_binary, jeffreys_binary,
+    "pct_condition_diabetes", "comorbiddiabetes", compute_binary, jeffreys_binary,
+    "pct_condition_hbp", "comorbid_high_blood_pressure", compute_binary, jeffreys_binary,
+    "pct_condition_kidney", "comorbidkidneydisease", compute_binary, jeffreys_binary,
+    "pct_condition_immune", "comorbid_autoimmune", compute_binary, jeffreys_binary,
+    "pct_condition_cvd", "comorbidheartdisease", compute_binary, jeffreys_binary,
+    "pct_condition_obesity", "comorbidobese", compute_binary, jeffreys_binary,
+    "pct_condition_none", "comorbid_none", compute_binary, jeffreys_binary,
+
+    "pct_pregnant", "pregnant", compute_binary, jeffreys_binary,
+
+    "pct_smoke", "smoker", compute_binary, jeffreys_binary,
+
+    "pct_children_prek", "children_prek", compute_binary, jeffreys_binary,
+    "pct_children_gr1_5", "children_gr1_5", compute_binary, jeffreys_binary,
+    "pct_children_gr6_8", "children_gr6_8", compute_binary, jeffreys_binary,
+    "pct_children_gr9_12", "children_gr9_12", compute_binary, jeffreys_binary,
+
+    # Already in main grouping, including "overall". Just need to make sure to include in demo/parenting tables.
+    # "pct_inperson_school_fulltime", "s_inperson_school_fulltime", compute_binary, jeffreys_binary,
+    # "pct_inperson_school_parttime", "s_inperson_school_parttime", compute_binary, jeffreys_binary,
+    # "pct_inperson_school_fulltime_oldest", "s_inperson_school_fulltime_oldest", compute_binary, jeffreys_binary,
+    # "pct_remote_school_fulltime_oldest", "s_remote_school_fulltime_oldest", compute_binary, jeffreys_binary,
+    # "pct_inperson_school_parttime_oldest", "s_inperson_school_parttime_oldest", compute_binary, jeffreys_binary,
+
+    "pct_children_school_measure_mask_students", "children_school_measure_mask_students", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_mask_teachers", "children_school_measure_mask_teachers", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_same_teacher", "children_school_measure_same_teacher", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_same_students", "children_school_measure_same_students", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_outdoor", "children_school_measure_outdoor", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_entry", "children_school_measure_entry", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_class_size", "children_school_measure_class_size", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_cafeteria", "children_school_measure_cafeteria", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_playground", "children_school_measure_playground", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_desk_shield", "children_school_measure_desk_shield", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_desk_space", "children_school_measure_desk_space", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_extracurricular", "children_school_measure_extracurricular", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_supplies", "children_school_measure_supplies", compute_binary, jeffreys_binary,
+    "pct_children_school_measure_screening", "children_school_measure_screening", compute_binary, jeffreys_binary,
+
+    "pct_occ_4w_social", "occ_4w_social", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_education", "occ_4w_education", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_arts", "occ_4w_arts", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_health_prac", "occ_4w_health_prac", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_health_support", "occ_4w_health_support", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_protective", "occ_4w_protective", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_food", "occ_4w_food", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_building", "occ_4w_building", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_personal", "occ_4w_personal", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_sales", "occ_4w_sales", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_admin", "occ_4w_admin", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_construction", "occ_4w_construction", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_maintenance", "occ_4w_maintenance", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_production", "occ_4w_production", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_transportation", "occ_4w_transportation", compute_binary, jeffreys_multinomial_factory(16),
+    "pct_occ_4w_other", "occ_4w_other", compute_binary, jeffreys_multinomial_factory(16),
+
+    "pct_", "", compute_binary, jeffreys_binary,
+  )
+  demo_aggs <- create_aggs_product(
+    regsions,
+    demo_groups,
+    demo_indicators
+  )
+
+  weekly_aggs <- rbind(aggs, demo_aggs)
+  monthly_aggs <- rbind(aggs, monthly_aggs, demo_aggs)
   
   return(list("week"=weekly_aggs, "month"=monthly_aggs))
 }
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index c3bd1d1eb..34af08468 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -39,8 +39,42 @@ code_occupation <- function(input_data, wave) {
       input_data$Q64 == 16 ~ "Other",
       TRUE ~ NA_character_
     )
+
+    input_data$occ_4w_social <- input_data$Q64 == 1
+    input_data$occ_4w_education <- input_data$Q64 == 2
+    input_data$occ_4w_arts <- input_data$Q64 == 3
+    input_data$occ_4w_health_prac <- input_data$Q64 == 4
+    input_data$occ_4w_health_support <- input_data$Q64 == 5
+    input_data$occ_4w_protective <- input_data$Q64 == 6
+    input_data$occ_4w_food <- input_data$Q64 == 7
+    input_data$occ_4w_building <- input_data$Q64 == 8
+    input_data$occ_4w_personal <- input_data$Q64 == 9
+    input_data$occ_4w_sales <- input_data$Q64 == 10
+    input_data$occ_4w_admin <- input_data$Q64 == 11
+    input_data$occ_4w_construction <- input_data$Q64 == 12
+    input_data$occ_4w_maintenance <- input_data$Q64 == 13
+    input_data$occ_4w_production <- input_data$Q64 == 14
+    input_data$occ_4w_transportation <- input_data$Q64 == 15
+    input_data$occ_4w_other <- input_data$Q64 == 16
   } else {
     input_data$occupation <- NA_character_
+
+    input_data$occ_4w_social <- NA
+    input_data$occ_4w_education <- NA
+    input_data$occ_4w_arts <- NA
+    input_data$occ_4w_health_prac <- NA
+    input_data$occ_4w_health_support <- NA
+    input_data$occ_4w_protective <- NA
+    input_data$occ_4w_food <- NA
+    input_data$occ_4w_building <- NA
+    input_data$occ_4w_personal <- NA
+    input_data$occ_4w_sales <- NA
+    input_data$occ_4w_admin <- NA
+    input_data$occ_4w_construction <- NA
+    input_data$occ_4w_maintenance <- NA
+    input_data$occ_4w_production <- NA
+    input_data$occ_4w_transportation <- NA
+    input_data$occ_4w_other <- NA
   }
   
   return(input_data)
@@ -117,6 +151,8 @@ code_health <- function(input_data, wave) {
     comorbidities <- split_options(input_data$C1)
     
     input_data$comorbidheartdisease <- is_selected(comorbidities, "3")
+    input_data$comorbid_high_blood_pressure <- is_selected(comorbidities, "5")
+    input_data$comorbid_asthma <- is_selected(comorbidities, "5")
     input_data$comorbidcancer <- is_selected(comorbidities, "2")
     input_data$comorbidkidneydisease <- is_selected(comorbidities, "7")
     input_data$comorbidlungdisease <- is_selected(comorbidities, "6")
@@ -125,7 +161,9 @@ code_health <- function(input_data, wave) {
       is_selected(comorbidities, "12") |
       is_selected(comorbidities, "10")
     input_data$comorbidimmuno <- is_selected(comorbidities, "11")
+    input_data$comorbid_autoimmune <- is_selected(comorbidities, "8")
     input_data$comorbidobese <- is_selected(comorbidities, "13")
+    input_data$comorbid_none <- is_selected(comorbidities, "9")
 
     # Combo vaccine-eligibility
     input_data$eligible <- 
@@ -145,6 +183,10 @@ code_health <- function(input_data, wave) {
     input_data$comorbidimmuno <- NA
     input_data$comorbidobese <- NA
     input_data$eligible <- NA
+    input_data$comorbid_high_blood_pressure <- NA
+    input_data$comorbid_asthma <- NA
+    input_data$comorbid_none <- NA
+    input_data$comorbid_autoimmune <- NA
   }
   
   # Combo vaccine-eligibility updated to include smoking, pregnant, and obesity
@@ -202,7 +244,7 @@ code_vaccinated_breakdown <- function(input_data, wave) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with demographic grouping variables
+#' @return augmented data frame
 code_addl_vaccines <- function(input_data, wave) {
   ## Items V3 and V4 display logic was changed mid-wave 6 to be shown only to
   ## respondents indicated that they had not been vaccinated. For the purposes
@@ -434,7 +476,7 @@ if ("C2" %in% names(input_data)) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with demographic grouping variables
+#' @return augmented data frame
 code_trust <- function(input_data, wave) {
   # Drop values in vaccine_likely_<source> prior to item change date in Wave 6
   # Percentage more likely to get vaccinated if recommended by <source>
@@ -606,7 +648,7 @@ code_trust <- function(input_data, wave) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with demographic grouping variables
+#' @return augmented data frame
 code_vaccine_barriers <- function(input_data, wave) {
   # hesitant_worried_vaccine_sideeffects
   # Percentage very or moderately concerned about side effects among those who
@@ -970,7 +1012,7 @@ code_vaccine_barriers <- function(input_data, wave) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with demographic grouping variables
+#' @return augmented data frame
 code_attempt_vaccine <- function(input_data, wave) {
   # informed_access
   # Percentage of respondents who are very or moderately informed about how to
@@ -1025,7 +1067,7 @@ code_attempt_vaccine <- function(input_data, wave) {
 #' @param input_data input data frame of raw survey data
 #' @param wave integer indicating survey version
 #' 
-#' @return data frame augmented with demographic grouping variables
+#' @return augmented data frame
 code_addl_symptoms <- function(input_data, wave) {
   if ("B2b" %in% names(input_data)) {
     # How many days have you had one or more new or unusual symptom?
@@ -1363,6 +1405,15 @@ code_addl_activities <- function(input_data, wave) {
     input_data$a_work_for_pay_outside_home_4w <- NA_real_
   }
 
+  if ("D9" %in% names(input_data)) {
+    # D9: in the past 4 weeks, did you work
+    # Coded as 1 = Yes, 2 = No
+    input_data$a_work_for_pay_4w <- input_data$D9 == 1
+  } else {
+    input_data$a_work_for_pay_4w <- NA_real_
+  }
+
+
   calc_masking_given_activity <- function(activity, masked_during_activity) {
     case_when(
       activity & masked_during_activity ~ TRUE,
@@ -1452,3 +1503,161 @@ code_addl_activities <- function(input_data, wave) {
   return(input_data)
 }
 
+#' Demographics
+#'
+#' @param input_data input data frame of raw survey data
+#' @param wave integer indicating survey version
+#'
+#' @return augmented data frame
+code_addl_demographic <- function(input_data, wave) {
+  if ("D1" %in% names(input_data)) {
+    # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = no answer
+    input_data$gender_male <- case_when(
+      input_data$D1 == 1 ~ 1,
+      input_data$D1 %in% c(2, 3, 4) ~ 0,
+      input_data$D1 == 5 ~ NA_real_,
+      TRUE ~ NA_real_
+    )
+    input_data$gender_female <- case_when(
+      input_data$D1 == 2 ~ 1,
+      input_data$D1 %in% c(1, 3, 4) ~ 0,
+      input_data$D1 == 5 ~ NA_real_,
+      TRUE ~ NA_real_
+    )
+    input_data$gender_nonbinary_other <- case_when(
+      input_data$D1 %in% c(3, 4) ~ 1,
+      input_data$D1 %in% c(1, 2) ~ 0,
+      input_data$D1 == 5 ~ NA_real_,
+      TRUE ~ NA_real_
+    )
+  } else {
+    input_data$gender_male <- NA_real_
+    input_data$gender_female <- NA_real_
+    input_data$gender_nonbinary_other <- NA_real_
+  }
+
+  if ("D2" %in% names(input_data)) {
+    # Coded as 1 = 18-24, 2 = 25-34, 3 = 35-44, 4 = 45-54,
+    # 5 = 55-64, 6 = 65-74, 7 = 75+
+    input_data$age_18_24 <- input_data$D2 == 1
+    input_data$age_25_34 <- input_data$D2 == 2
+    input_data$age_35_44 <- input_data$D2 == 3
+    input_data$age_45_54 <- input_data$D2 == 4
+    input_data$age_55_64 <- input_data$D2 == 5
+    input_data$age_65_74 <- input_data$D2 == 6
+    input_data$age_75_older <- input_data$D2 == 7
+  } else {
+    input_data$age_18_24 <- NA
+    input_data$age_25_34 <- NA
+    input_data$age_35_44 <- NA
+    input_data$age_45_54 <- NA
+    input_data$age_55_64 <- NA
+    input_data$age_65_74 <- NA
+    input_data$age_75_older <- NA
+  }
+
+  # race
+  if ("D7" %in% names(input_data)) {
+    input_data$race_american_indian_alaska_native <- input_data$D7 == 1
+    input_data$race_asian <- input_data$D7 == 2
+    input_data$race_black_african_american <- input_data$D7 == 3
+    input_data$race_native_hawaiian_pacific_islander <- input_data$D7 == 4
+    input_data$race_white <- input_data$D7 == 5
+    input_data$race_multiple_other <- (input_data$D7 == 6 | grepl(",", input_data$D7))
+  } else {
+    input_data$race_american_indian_alaska_native <- NA
+    input_data$race_asian <- NA
+    input_data$race_black_african_american <- NA
+    input_data$race_native_hawaiian_pacific_islander <- NA
+    input_data$race_white <- NA
+    input_data$race_multiple_other <- NA
+  }
+
+  if ("D8" %in% names(input_data)) {
+    input_data$education_less_than_highschool <- input_data$D8 == 1
+    input_data$education_highschool_or_equivalent <- input_data$D8 == 2
+    input_data$education_some_college <- input_data$D8 == 3
+    input_data$education_2yr_degree <- input_data$D8 == 4
+    input_data$education_4yr_degree <- input_data$D8 == 5
+    input_data$education_masters <- input_data$D8 == 8
+    input_data$education_professional_degree <- input_data$D8 == 6
+    input_data$education_doctorate <- input_data$D8 == 7
+  } else {
+    input_data$education_less_than_highschool <- NA
+    input_data$education_highschool_or_equivalent <- NA
+    input_data$education_some_college <- NA
+    input_data$education_2yr_degree <- NA
+    input_data$education_4yr_degree <- NA
+    input_data$education_masters <- NA
+    input_data$education_professional_degree <- NA
+    input_data$education_doctorate <- NA
+  }
+
+  if ("D12" %in% names(input_data)) {
+    input_data$language_home_english <- input_data$D12 == 1
+    input_data$language_home_spanish <- input_data$D12 == 2
+    input_data$language_home_chinese <- input_data$D12 == 3
+    input_data$language_home_vietnamese <- input_data$D12 == 4
+    input_data$language_home_french <- input_data$D12 == 5
+    input_data$language_home_portugese <- input_data$D12 == 6
+    input_data$language_home_other <- input_data$D12 == 7
+  } else {
+    input_data$language_home_english <- NA
+    input_data$language_home_spanish <- NA
+    input_data$language_home_chinese <- NA
+    input_data$language_home_vietnamese <- NA
+    input_data$language_home_french <- NA
+    input_data$language_home_portugese <- NA
+    input_data$language_home_other <- NA
+  }
+
+  # Children by age
+  if (all(c("E1_1", "E1_2", "E1_3", "E1_4") %in% names(input_data))) {
+    # All subquestions coded as 1 = Yes, 2 = No, 5 = don't know
+    input_data$children_prek <- input_data$E1_1 == 1
+    input_data$children_gr1_5 <- input_data$E1_2 == 1
+    input_data$children_gr6_8 <- input_data$E1_3 == 1
+    input_data$children_gr9_12 <- input_data$E1_4 == 1
+  } else {
+    input_data$children_prek <- NA
+    input_data$children_gr1_5 <- NA
+    input_data$children_gr6_8 <- NA
+    input_data$children_gr9_12 <- NA
+  }
+
+  if ("E3" %in% names(input_data)) {
+    school_measures <- split_options(input_data$E3)
+
+    input_data$children_school_measure_mask_students <- is_selected(school_measures, "1")
+    input_data$children_school_measure_mask_teachers <- is_selected(school_measures, "2")
+    input_data$children_school_measure_same_teacher <- is_selected(school_measures, "3")
+    input_data$children_school_measure_same_students <- is_selected(school_measures, "4")
+    input_data$children_school_measure_outdoor <- is_selected(school_measures, "5")
+    input_data$children_school_measure_entry <- is_selected(school_measures, "6")
+    input_data$children_school_measure_class_size <- is_selected(school_measures, "7")
+    input_data$children_school_measure_cafeteria <- is_selected(school_measures, "8")
+    input_data$children_school_measure_playground <- is_selected(school_measures, "9")
+    input_data$children_school_measure_desk_shield <- is_selected(school_measures, "10")
+    input_data$children_school_measure_desk_space <- is_selected(school_measures, "11")
+    input_data$children_school_measure_extracurricular <- is_selected(school_measures, "12")
+    input_data$children_school_measure_supplies <- is_selected(school_measures, "14")
+    input_data$children_school_measure_screening <- is_selected(school_measures, "15")
+  } else {
+    input_data$children_school_measure_mask_students <- NA
+    input_data$children_school_measure_mask_teachers <- NA
+    input_data$children_school_measure_same_teacher <- NA
+    input_data$children_school_measure_same_students <- NA
+    input_data$children_school_measure_outdoor <- NA
+    input_data$children_school_measure_entry <- NA
+    input_data$children_school_measure_class_size <- NA
+    input_data$children_school_measure_cafeteria <- NA
+    input_data$children_school_measure_playground <- NA
+    input_data$children_school_measure_desk_shield <- NA
+    input_data$children_school_measure_desk_space <- NA
+    input_data$children_school_measure_extracurricular <- NA
+    input_data$children_school_measure_supplies <- NA
+    input_data$children_school_measure_screening <- NA
+  }
+
+  return(input_data)
+}
diff --git a/facebook/delphiFacebook/R/responses.R b/facebook/delphiFacebook/R/responses.R
index c5f4a8032..17167c3ee 100644
--- a/facebook/delphiFacebook/R/responses.R
+++ b/facebook/delphiFacebook/R/responses.R
@@ -235,6 +235,7 @@ load_response_one <- function(input_filename, params, contingency_run) {
     input_data <- code_occupation(input_data, wave)
     input_data <- code_education(input_data, wave)
     input_data <- code_vaccinated_breakdown(input_data, wave)
+    input_data <- code_addl_demographic(input_data, wave)
     
     # Indicators
     input_data <- code_addl_vaccines(input_data, wave)
diff --git a/facebook/delphiFacebook/man/code_addl_demographic.Rd b/facebook/delphiFacebook/man/code_addl_demographic.Rd
new file mode 100644
index 000000000..1cef0f91c
--- /dev/null
+++ b/facebook/delphiFacebook/man/code_addl_demographic.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contingency_variables.R
+\name{code_addl_demographic}
+\alias{code_addl_demographic}
+\title{Demographics}
+\usage{
+code_addl_demographic(input_data, wave)
+}
+\arguments{
+\item{input_data}{input data frame of raw survey data}
+
+\item{wave}{integer indicating survey version}
+}
+\value{
+augmented data frame
+}
+\description{
+Demographics
+}
diff --git a/facebook/delphiFacebook/man/code_addl_mental_health.Rd b/facebook/delphiFacebook/man/code_addl_mental_health.Rd
new file mode 100644
index 000000000..59dabcf00
--- /dev/null
+++ b/facebook/delphiFacebook/man/code_addl_mental_health.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contingency_variables.R
+\name{code_addl_mental_health}
+\alias{code_addl_mental_health}
+\title{Additional mental health indicators}
+\usage{
+code_addl_mental_health(input_data, wave)
+}
+\arguments{
+\item{input_data}{input data frame of raw survey data}
+
+\item{wave}{integer indicating survey version}
+}
+\value{
+augmented data frame
+}
+\description{
+Additional mental health indicators
+}
diff --git a/facebook/delphiFacebook/man/code_addl_symptoms.Rd b/facebook/delphiFacebook/man/code_addl_symptoms.Rd
index ac6d9abb5..0bb8fdf70 100644
--- a/facebook/delphiFacebook/man/code_addl_symptoms.Rd
+++ b/facebook/delphiFacebook/man/code_addl_symptoms.Rd
@@ -12,7 +12,7 @@ code_addl_symptoms(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with demographic grouping variables
+augmented data frame
 }
 \description{
 COVID symptoms with modifications for contingency tables
diff --git a/facebook/delphiFacebook/man/code_addl_vaccines.Rd b/facebook/delphiFacebook/man/code_addl_vaccines.Rd
index cfc498a30..429289f88 100644
--- a/facebook/delphiFacebook/man/code_addl_vaccines.Rd
+++ b/facebook/delphiFacebook/man/code_addl_vaccines.Rd
@@ -12,7 +12,7 @@ code_addl_vaccines(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with demographic grouping variables
+augmented data frame
 }
 \description{
 COVID vaccination variables with modifications for contingency tables
diff --git a/facebook/delphiFacebook/man/code_attempt_vaccine.Rd b/facebook/delphiFacebook/man/code_attempt_vaccine.Rd
index 985f3ef4f..92f35b877 100644
--- a/facebook/delphiFacebook/man/code_attempt_vaccine.Rd
+++ b/facebook/delphiFacebook/man/code_attempt_vaccine.Rd
@@ -12,7 +12,7 @@ code_attempt_vaccine(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with demographic grouping variables
+augmented data frame
 }
 \description{
 Attempts to get vaccinated
diff --git a/facebook/delphiFacebook/man/code_trust.Rd b/facebook/delphiFacebook/man/code_trust.Rd
index 016fff2af..6da5597bb 100644
--- a/facebook/delphiFacebook/man/code_trust.Rd
+++ b/facebook/delphiFacebook/man/code_trust.Rd
@@ -12,7 +12,7 @@ code_trust(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with demographic grouping variables
+augmented data frame
 }
 \description{
 Trust in various individuals and organizations for recommendations and info
diff --git a/facebook/delphiFacebook/man/code_vaccine_barriers.Rd b/facebook/delphiFacebook/man/code_vaccine_barriers.Rd
index 9a8838b72..5c45a8daa 100644
--- a/facebook/delphiFacebook/man/code_vaccine_barriers.Rd
+++ b/facebook/delphiFacebook/man/code_vaccine_barriers.Rd
@@ -12,7 +12,7 @@ code_vaccine_barriers(input_data, wave)
 \item{wave}{integer indicating survey version}
 }
 \value{
-data frame augmented with demographic grouping variables
+augmented data frame
 }
 \description{
 Vaccination barriers

From e29eac711d768a5ee0bb01be3fe5730a11d53366 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 21 Jun 2022 17:59:00 -0400
Subject: [PATCH 27/49] mean hh member by age from A5_123

---
 .../delphiFacebook/R/contingency_indicators.R | 11 ++++++-
 .../delphiFacebook/R/contingency_variables.R  | 31 +++++++++++++++++++
 2 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 5c7b936eb..579c47f13 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -557,7 +557,16 @@ get_aggs <- function() {
     # Means. No post-processing required.
     "mean_days_symptoms", "symp_n_days", compute_numeric_mean, I,
     "mean_ppl_symptoms_household", "hh_number_sick", compute_numeric_mean, I,
-    "mean_ppl_symptoms_community", "community_number_sick", compute_numeric_mean, I
+    "mean_ppl_symptoms_community", "community_number_sick", compute_numeric_mean, I,
+
+    "mean_hh_number_children", "hh_number_children", compute_numeric_mean, I,
+    "mean_hh_number_adults", "hh_number_adults", compute_numeric_mean, I,
+    "mean_hh_number_older", "hh_number_older", compute_numeric_mean, I,
+    "mean_hh_number_total", "hh_number_total", compute_numeric_mean, I,
+
+    "mean_children_in_household", "children_in_household", compute_numeric_mean, I,
+    "mean_adults_in_household", "adults_in_household", compute_numeric_mean, I,
+    "mean_olderadults_in_household", "older_in_household", compute_numeric_mean, I
   )
 
   aggs <- create_aggs_product(regions, groups, indicators)
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 34af08468..2905ce5dc 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1659,5 +1659,36 @@ code_addl_demographic <- function(input_data, wave) {
     input_data$children_school_measure_screening <- NA
   }
 
+  if ("A5_1" %in% names(input_data)) {
+    # This is Wave 4, where item A2b was replaced with 3 items asking about
+    # separate ages. Many respondents leave blank the categories that do not
+    # apply to their household, rather than entering 0, so if at least one of
+    # the three items has a response, we impute 0 for the remaining items.
+    suppressWarnings({
+      age18 <- as.integer(input_data$A5_1)
+      age1864 <- as.integer(input_data$A5_2)
+      age65 <- as.integer(input_data$A5_3)
+    })
+    input_data$hh_number_children <- ifelse(
+      is.na(age18) + is.na(age1864) + is.na(age65) < 3,
+      ifelse(is.na(age18), 0, age18),
+      NA_integer_
+    )
+    input_data$hh_number_adults <- ifelse(
+      is.na(age18) + is.na(age1864) + is.na(age65) < 3,
+      ifelse(is.na(age1864), 0, age1864),
+      NA_integer_
+    )
+    input_data$hh_number_older <- ifelse(
+      is.na(age18) + is.na(age1864) + is.na(age65) < 3,
+      ifelse(is.na(age65), 0, age65),
+      NA_integer_
+    )
+  } else {
+    input_data$hh_number_children <- NA_integer_
+    input_data$hh_number_adults <- NA_integer_
+    input_data$hh_number_older <- NA_integer_
+  }
+
   return(input_data)
 }

From 6aaec84877782e0bca7b8a3a39273b233cfa7e0f Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 17 Jun 2022 14:01:46 -0400
Subject: [PATCH 28/49] mean number of hh members from D3-5

---
 .../delphiFacebook/R/contingency_variables.R  | 54 ++++++++++++++++---
 1 file changed, 48 insertions(+), 6 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 2905ce5dc..e28f3efa2 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1669,25 +1669,67 @@ code_addl_demographic <- function(input_data, wave) {
       age1864 <- as.integer(input_data$A5_2)
       age65 <- as.integer(input_data$A5_3)
     })
-    input_data$hh_number_children <- ifelse(
+    input_data$ppl_in_household_children <- ifelse(
       is.na(age18) + is.na(age1864) + is.na(age65) < 3,
       ifelse(is.na(age18), 0, age18),
       NA_integer_
     )
-    input_data$hh_number_adults <- ifelse(
+    input_data$ppl_in_household_adults <- ifelse(
       is.na(age18) + is.na(age1864) + is.na(age65) < 3,
       ifelse(is.na(age1864), 0, age1864),
       NA_integer_
     )
-    input_data$hh_number_older <- ifelse(
+    input_data$ppl_in_household_older <- ifelse(
       is.na(age18) + is.na(age1864) + is.na(age65) < 3,
       ifelse(is.na(age65), 0, age65),
       NA_integer_
     )
   } else {
-    input_data$hh_number_children <- NA_integer_
-    input_data$hh_number_adults <- NA_integer_
-    input_data$hh_number_older <- NA_integer_
+    input_data$ppl_in_household_children <- NA_integer_
+    input_data$ppl_in_household_adults <- NA_integer_
+    input_data$ppl_in_household_older <- NA_integer_
+  }
+
+  if ("D3" %in% names(input_data)) {
+    # How many children younger than 18 currently stay in your household
+    # Free response
+    suppressWarnings({ D3_int <- as.integer(input_data$D3) })
+    input_data$children_in_household <- case_when(
+      D3_int < 0 ~ NA_integer_,
+      D3_int > 20 ~ NA_integer_,
+      is.na(D3_int) ~ NA_integer_,
+      TRUE ~ D3_int
+    )
+  } else {
+    input_data$children_in_household <- NA_integer_
+  }
+
+  if ("D4" %in% names(input_data)) {
+    # How many adults 18-65 currently stay in your household
+    # Free response
+    suppressWarnings({ D4_int <- as.integer(input_data$D4) })
+    input_data$adults_in_household <- case_when(
+      D4_int < 0 ~ NA_integer_,
+      D4_int > 20 ~ NA_integer_,
+      is.na(D4_int) ~ NA_integer_,
+      TRUE ~ D4_int
+    )
+  } else {
+    input_data$adults_in_household <- NA_integer_
+  }
+
+  if ("D5" %in% names(input_data)) {
+    # How many adults 65 or older currently stay in your household
+    # Free response
+    suppressWarnings({ D5_int <- as.integer(input_data$D5) })
+    input_data$older_in_household <- case_when(
+      D5_int < 0 ~ NA_integer_,
+      D5_int > 20 ~ NA_integer_,
+      is.na(D5_int) ~ NA_integer_,
+      TRUE ~ D5_int
+    )
+  } else {
+    input_data$older_in_household <- NA_integer_
   }
 
   return(input_data)

From 39b3400ec2aabbd1aa9ccc7a973bb1314f1082e3 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 16 Jun 2022 14:29:42 -0400
Subject: [PATCH 29/49] unknown gender; child age cuts

---
 .../delphiFacebook/R/contingency_indicators.R | 58 ++++++++++---------
 .../delphiFacebook/R/contingency_variables.R  | 31 +++++-----
 2 files changed, 49 insertions(+), 40 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index 579c47f13..bf00743fa 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -84,7 +84,7 @@ get_aggs <- function() {
 
     "pct_others_distanced_public", "c_others_distanced_public", compute_binary, jeffreys_binary,
     "pct_others_distanced_public_alt", "c_others_distanced_some_public", compute_binary, jeffreys_binary,
-    
+
     "pct_cli", "hh_p_cli", compute_household_binary, jeffreys_count,
     "pct_ili", "hh_p_ili", compute_household_binary, jeffreys_count,
     "pct_hh_cmnty_cli", "hh_community_yes", compute_binary, jeffreys_binary,
@@ -96,7 +96,7 @@ get_aggs <- function() {
 
     "pct_avoid_contact", "c_avoid_contact", compute_binary, jeffreys_binary,
     "pct_avoid_contact_7d", "c_avoid_contact_7d", compute_binary, jeffreys_binary,
-    
+
     # symptoms
     "pct_taken_temp", "t_taken_temp", compute_binary, jeffreys_binary,
 
@@ -122,7 +122,7 @@ get_aggs <- function() {
     "pct_symp_headache", "symp_headache", compute_binary, jeffreys_binary,
     "pct_symp_sleep_changes", "symp_sleep_changes", compute_binary, jeffreys_binary,
     "pct_symp_stuffy_nose", "symp_stuffy_nose", compute_binary, jeffreys_binary,
-    
+
     # unusual symptoms
     "pct_symp_fever_unusual", "symp_fever_unusual", compute_binary, jeffreys_binary,
     "pct_symp_cough_unusual", "symp_cough_unusual", compute_binary, jeffreys_binary,
@@ -142,7 +142,7 @@ get_aggs <- function() {
     "pct_symp_headache_unusual", "symp_headache_unusual", compute_binary, jeffreys_binary,
     "pct_symp_sleep_changes_unusual", "symp_sleep_changes_unusual", compute_binary, jeffreys_binary,
     "pct_symp_stuffy_nose_unusual", "symp_stuffy_nose_unusual", compute_binary, jeffreys_binary,
-    
+
     # vaccines
     "pct_vaccinated", "v_covid_vaccinated", compute_binary, jeffreys_binary,
     "pct_received_2_vaccine_doses", "v_received_2_vaccine_doses", compute_binary, jeffreys_binary,
@@ -156,10 +156,10 @@ get_aggs <- function() {
 
     "pct_covid_vaccinated_friends", "v_covid_vaccinated_friends", compute_binary, jeffreys_binary,
     "pct_covid_vaccinated_friends_alt", "v_covid_vaccinated_some_friends", compute_binary, jeffreys_binary,
-    
+
     "pct_vaccinate_children", "v_vaccinate_children", compute_binary, jeffreys_binary,
     "pct_vaccinate_child_oldest", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
-    
+
     "pct_child_vaccine_already", "v_child_vaccine_already", compute_binary, jeffreys_multinomial_factory(5),
     "pct_child_vaccine_yes_def", "v_child_vaccine_yes_def", compute_binary, jeffreys_multinomial_factory(5),
     "pct_child_vaccine_yes_prob", "v_child_vaccine_yes_prob", compute_binary, jeffreys_multinomial_factory(5),
@@ -174,19 +174,19 @@ get_aggs <- function() {
     "pct_accept_vaccine_no_appointment_probyes", "v_accept_vaccine_no_appointment_probyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_accept_vaccine_no_appointment_probno", "v_accept_vaccine_no_appointment_probno", compute_binary, jeffreys_multinomial_factory(4),
     "pct_accept_vaccine_no_appointment_defno", "v_accept_vaccine_no_appointment_defno", compute_binary, jeffreys_multinomial_factory(4),
-    
+
     "pct_initial_dose_one_of_one", "v_initial_dose_one_of_one", compute_binary, jeffreys_multinomial_factory(4),
     "pct_initial_dose_one_of_two", "v_initial_dose_one_of_two", compute_binary, jeffreys_multinomial_factory(4),
     "pct_initial_dose_two_of_two", "v_initial_dose_two_of_two", compute_binary, jeffreys_multinomial_factory(4),
-    
+
     "pct_vaccinated_one_booster", "v_vaccinated_one_booster", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_two_or_more_boosters", "v_vaccinated_two_or_more_boosters", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_no_booster", "v_vaccinated_no_booster", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_at_least_one_booster", "v_vaccinated_at_least_one_booster", compute_binary, jeffreys_binary,
-    
+
     "pct_vaccinated_booster_accept", "v_vaccinated_booster_accept", compute_binary, jeffreys_binary,
     "pct_vaccinated_booster_hesitant", "v_vaccinated_booster_hesitant", compute_binary, jeffreys_binary,
-    
+
     "pct_vaccinated_booster_defyes", "v_vaccinated_booster_defyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_booster_probyes", "v_vaccinated_booster_probyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_booster_probno", "v_vaccinated_booster_probno", compute_binary, jeffreys_multinomial_factory(4),
@@ -198,8 +198,8 @@ get_aggs <- function() {
     "pct_flu_vaccine_june_2020", "v_flu_vaccinated_june_2020", compute_binary, jeffreys_binary,
     "pct_flu_vaccine_july_2020", "v_flu_vaccinated_july_2020", compute_binary, jeffreys_binary,
     "pct_flu_vaccinated_2021", "v_flu_vaccinated_2021", compute_binary, jeffreys_binary,
-    
-    
+
+
     # vaccine timing
     "pct_vaccine_timing_weeks", "v_vaccine_timing_weeks", compute_binary, jeffreys_multinomial_factory(7),
     "pct_vaccine_timing_onemonth", "v_vaccine_timing_onemonth", compute_binary, jeffreys_multinomial_factory(7),
@@ -207,7 +207,7 @@ get_aggs <- function() {
     "pct_vaccine_timing_sixmonths", "v_vaccine_timing_sixmonths", compute_binary, jeffreys_multinomial_factory(7),
     "pct_vaccine_timing_morethansix", "v_vaccine_timing_morethansix", compute_binary, jeffreys_multinomial_factory(7),
     "pct_vaccine_timing_dontknow", "v_vaccine_timing_dontknow", compute_binary, jeffreys_multinomial_factory(7),
-    
+
     # vaccine influences
     "pct_vaccine_likely_friends", "v_vaccine_likely_friends", compute_binary, jeffreys_binary,
     "pct_vaccine_likely_local_health", "v_vaccine_likely_local_health", compute_binary, jeffreys_binary,
@@ -223,7 +223,7 @@ get_aggs <- function() {
     "pct_trust_covid_info_journalists", "i_trust_covid_info_journalists", compute_binary, jeffreys_binary,
     "pct_trust_covid_info_friends", "i_trust_covid_info_friends", compute_binary, jeffreys_binary,
     "pct_trust_covid_info_religious", "i_trust_covid_info_religious", compute_binary, jeffreys_binary,
-    
+
     "pct_worried_vaccine_sideeffects", "v_worried_vaccine_side_effects", compute_binary, jeffreys_binary,
     "pct_hesitant_worried_vaccine_sideeffects", "v_hesitant_worried_vaccine_sideeffects", compute_binary, jeffreys_binary,
 
@@ -241,7 +241,7 @@ get_aggs <- function() {
     "pct_hesitant_trust_covid_info_journalists", "i_hesitant_trust_covid_info_journalists", compute_binary, jeffreys_binary,
     "pct_hesitant_trust_covid_info_friends", "i_hesitant_trust_covid_info_friends", compute_binary, jeffreys_binary,
     "pct_hesitant_trust_covid_info_religious", "i_hesitant_trust_covid_info_religious", compute_binary, jeffreys_binary,
-    
+
     # vaccine worries
     "pct_hesitant_barrier_sideeffects", "v_hesitant_barrier_sideeffects", compute_binary, jeffreys_binary,
     "pct_hesitant_barrier_allergic", "v_hesitant_barrier_allergic", compute_binary, jeffreys_binary,
@@ -259,7 +259,7 @@ get_aggs <- function() {
     "pct_hesitant_barrier_pregnant", "v_hesitant_barrier_pregnant", compute_binary, jeffreys_binary,
     "pct_hesitant_barrier_other", "v_hesitant_barrier_other", compute_binary, jeffreys_binary,
     "pct_hesitant_barrier_dislike_vaccines_generally", "v_hesitant_barrier_dislike_vaccines_generally", compute_binary, jeffreys_binary,
-    
+
     "pct_hesitant_dontneed_reason_had_covid", "v_hesitant_dontneed_reason_had_covid", compute_binary, jeffreys_binary,
     "pct_hesitant_dontneed_reason_dont_spend_time", "v_hesitant_dontneed_reason_dont_spend_time", compute_binary, jeffreys_binary,
     "pct_hesitant_dontneed_reason_not_high_risk", "v_hesitant_dontneed_reason_not_high_risk", compute_binary, jeffreys_binary,
@@ -267,7 +267,7 @@ get_aggs <- function() {
     "pct_hesitant_dontneed_reason_not_serious", "v_hesitant_dontneed_reason_not_serious", compute_binary, jeffreys_binary,
     "pct_hesitant_dontneed_reason_not_beneficial", "v_hesitant_dontneed_reason_not_beneficial", compute_binary, jeffreys_binary,
     "pct_hesitant_dontneed_reason_other", "v_hesitant_dontneed_reason_other", compute_binary, jeffreys_binary,
-    
+
     "pct_barrier_sideeffects", "v_hesitancy_reason_sideeffects", compute_binary, jeffreys_binary,
     "pct_barrier_allergic", "v_hesitancy_reason_allergic", compute_binary, jeffreys_binary,
     "pct_barrier_ineffective", "v_hesitancy_reason_ineffective", compute_binary, jeffreys_binary,
@@ -284,7 +284,7 @@ get_aggs <- function() {
     "pct_barrier_pregnant", "v_hesitancy_reason_pregnant", compute_binary, jeffreys_binary,
     "pct_barrier_other", "v_hesitancy_reason_other", compute_binary, jeffreys_binary,
     "pct_barrier_dislike_vaccines_generally", "v_hesitancy_reason_dislike_vaccines_generally", compute_binary, jeffreys_binary,
-    
+
     # vaccine incomplete reasons
     "pct_vaccine_incomplete_sideeffect", "v_vaccine_incomplete_sideeffect", compute_binary, jeffreys_binary,
     "pct_vaccine_incomplete_allergic", "v_vaccine_incomplete_allergic", compute_binary, jeffreys_binary,
@@ -310,7 +310,7 @@ get_aggs <- function() {
     "pct_dontneed_reason_not_serious", "v_dontneed_reason_not_serious_5abc_6", compute_binary, jeffreys_binary,
     "pct_dontneed_reason_not_beneficial", "v_dontneed_reason_not_beneficial_5abc_6", compute_binary, jeffreys_binary,
     "pct_dontneed_reason_other", "v_dontneed_reason_other_5abc_6", compute_binary, jeffreys_binary,
-    
+
     "pct_defno_barrier_sideeffects", "v_defno_barrier_sideeffects", compute_binary, jeffreys_binary,
     "pct_defno_barrier_allergic", "v_defno_barrier_allergic", compute_binary, jeffreys_binary,
     "pct_defno_barrier_ineffective", "v_defno_barrier_ineffective", compute_binary, jeffreys_binary,
@@ -327,7 +327,7 @@ get_aggs <- function() {
     "pct_defno_barrier_pregnant", "v_defno_barrier_pregnant", compute_binary, jeffreys_binary,
     "pct_defno_barrier_other", "v_defno_barrier_other", compute_binary, jeffreys_binary,
     "pct_defno_barrier_dislike_vaccines_generally", "v_defno_barrier_dislike_vaccines_generally", compute_binary, jeffreys_binary,
-    
+
     "pct_defno_dontneed_reason_had_covid", "v_defno_dontneed_reason_had_covid", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_dont_spend_time", "v_defno_dontneed_reason_dont_spend_time", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_not_high_risk", "v_defno_dontneed_reason_not_high_risk", compute_binary, jeffreys_binary,
@@ -335,7 +335,7 @@ get_aggs <- function() {
     "pct_defno_dontneed_reason_not_serious", "v_defno_dontneed_reason_not_serious", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_not_beneficial", "v_defno_dontneed_reason_not_beneficial", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_other", "v_defno_dontneed_reason_other", compute_binary, jeffreys_binary,
-    
+
     "pct_informed_access", "v_informed_access", compute_binary, jeffreys_binary,
     
     # appointments
@@ -571,7 +571,6 @@ get_aggs <- function() {
 
   aggs <- create_aggs_product(regions, groups, indicators)
 
-
   monthly_indicators <- tribble(
     ~name, ~metric, ~compute_fn, ~post_fn,
     "pct_child_school_public", "s_child_school_public", compute_binary, jeffreys_multinomial_factory(5),
@@ -641,9 +640,10 @@ get_aggs <- function() {
   demo_groups <- list(c())
   demo_indicators <- tribble(
     ~name, ~metric, ~compute_fn, ~post_fn,
-    "pct_gender_male", "gender_male", compute_binary, jeffreys_multinomial_factory(3),
-    "pct_gender_female", "gender_female", compute_binary, jeffreys_multinomial_factory(3),
-    "pct_gender_nonbinary_other", "gender_nonbinary_other", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_gender_male", "gender_male", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_gender_female", "gender_female", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_gender_nonbinary_other", "gender_nonbinary_other", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_gender_unknown", "gender_unknown", compute_binary, jeffreys_multinomial_factory(4),
 
     "pct_age_18_24", "age_18_24", compute_binary, jeffreys_multinomial_factory(7),
     "pct_age_25_34", "age_25_34", compute_binary, jeffreys_multinomial_factory(7),
@@ -748,9 +748,15 @@ get_aggs <- function() {
     demo_indicators
   )
 
+
+  ## Parenting cuts
+  parent_groups <- list(c("child_age"))
+  parent_indicators <- tribble()
+  parent_aggs <- create_aggs_product(regions, parent_groups, parent_indicators)
+
   weekly_aggs <- rbind(aggs, demo_aggs)
   monthly_aggs <- rbind(aggs, monthly_aggs, demo_aggs)
-  
+
   return(list("week"=weekly_aggs, "month"=monthly_aggs))
 }
 
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index e28f3efa2..4435d8266 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1512,28 +1512,19 @@ code_addl_activities <- function(input_data, wave) {
 code_addl_demographic <- function(input_data, wave) {
   if ("D1" %in% names(input_data)) {
     # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = no answer
-    input_data$gender_male <- case_when(
-      input_data$D1 == 1 ~ 1,
-      input_data$D1 %in% c(2, 3, 4) ~ 0,
-      input_data$D1 == 5 ~ NA_real_,
-      TRUE ~ NA_real_
-    )
-    input_data$gender_female <- case_when(
-      input_data$D1 == 2 ~ 1,
-      input_data$D1 %in% c(1, 3, 4) ~ 0,
-      input_data$D1 == 5 ~ NA_real_,
-      TRUE ~ NA_real_
-    )
+    input_data$gender_male <- input_data$D1 == 1
+    input_data$gender_female <- input_data$D1 == 2
     input_data$gender_nonbinary_other <- case_when(
       input_data$D1 %in% c(3, 4) ~ 1,
-      input_data$D1 %in% c(1, 2) ~ 0,
-      input_data$D1 == 5 ~ NA_real_,
+      input_data$D1 %in% c(1, 2, 5) ~ 0,
       TRUE ~ NA_real_
     )
+    input_data$gender_unknown <- input_data$D1 == 5
   } else {
     input_data$gender_male <- NA_real_
     input_data$gender_female <- NA_real_
     input_data$gender_nonbinary_other <- NA_real_
+    input_data$gender_unknown <- NA_real_
   }
 
   if ("D2" %in% names(input_data)) {
@@ -1659,6 +1650,18 @@ code_addl_demographic <- function(input_data, wave) {
     input_data$children_school_measure_screening <- NA
   }
 
+  if ("P2" %in% names(input_data)) {
+    input_data$child_age <- case_when(
+      input_data$P2 == 1 ~ "less than 5 years",
+      input_data$P2 == 2 ~ "5-11 years",
+      input_data$P2 == 3 ~ "12-15 years",
+      input_data$P2 == 4 ~ "16-17 years",
+      TRUE ~ NA_character_
+    )
+  } else {
+    input_data$child_age <- NA_character_
+  }
+
   if ("A5_1" %in% names(input_data)) {
     # This is Wave 4, where item A2b was replaced with 3 items asking about
     # separate ages. Many respondents leave blank the categories that do not

From aecf0fd2e0aa534498659dbda3ae65e928b9deeb Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Tue, 21 Jun 2022 18:26:34 -0400
Subject: [PATCH 30/49] add overall county indicators; remove monthly-only

---
 .../delphiFacebook/R/contingency_indicators.R     | 15 ++++-----------
 facebook/delphiFacebook/R/contingency_write.R     | 11 ++++++-----
 .../man/write_contingency_tables.Rd               |  2 +-
 3 files changed, 11 insertions(+), 17 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index bf00743fa..e0bfc0d8e 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -569,17 +569,10 @@ get_aggs <- function() {
     "mean_olderadults_in_household", "older_in_household", compute_numeric_mean, I
   )
 
-  aggs <- create_aggs_product(regions, groups, indicators)
-
-  monthly_indicators <- tribble(
-    ~name, ~metric, ~compute_fn, ~post_fn,
-    "pct_child_school_public", "s_child_school_public", compute_binary, jeffreys_multinomial_factory(5),
-    "pct_child_school_private", "s_child_school_private", compute_binary, jeffreys_multinomial_factory(5),
-    "pct_child_school_homeschool", "s_child_school_homeschool", compute_binary, jeffreys_multinomial_factory(5),
-    "pct_child_school_not", "s_child_school_not", compute_binary, jeffreys_multinomial_factory(5),
-    "pct_child_school_other", "s_child_school_other", compute_binary, jeffreys_multinomial_factory(5)
+  aggs <- rbind(
+    create_aggs_product(regions, groups, indicators),
+    create_aggs_product(list("county"), list(c()), indicators)
   )
-  monthly_aggs <- create_aggs_product(regions, groups, monthly_indicators)
 
   ### Include handful of original public tables not already covered by set above
   common_group <- c("agefull", "gender", "race", "hispanic")
@@ -755,7 +748,7 @@ get_aggs <- function() {
   parent_aggs <- create_aggs_product(regions, parent_groups, parent_indicators)
 
   weekly_aggs <- rbind(aggs, demo_aggs)
-  monthly_aggs <- rbind(aggs, monthly_aggs, demo_aggs)
+  monthly_aggs <- rbind(aggs, demo_aggs)
 
   return(list("week"=weekly_aggs, "month"=monthly_aggs))
 }
diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index 4ae4c4cf3..58aca8a92 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -21,8 +21,7 @@
 #' @importFrom stringi stri_trim
 #'
 #' @export
-write_contingency_tables <- function(data, params, geo_type, groupby_vars)
-{
+write_contingency_tables <- function(data, params, geo_type, groupby_vars, theme = NULL) {
   if (!is.null(data) && nrow(data) != 0) {
     
     # Reorder the group-by columns and sort the dataset by them.
@@ -43,7 +42,7 @@ write_contingency_tables <- function(data, params, geo_type, groupby_vars)
     
     create_dir_not_exist(params$export_dir)
     
-    file_name <- get_file_name(params, geo_type, groupby_vars)
+    file_name <- get_file_name(params, geo_type, groupby_vars, theme)
     msg_df(sprintf("saving contingency table data to %-35s", file_name), data)
     # Automatically uses gzip compression based on output file name.
     write_csv(data, file.path(params$export_dir, file_name))
@@ -109,6 +108,8 @@ add_geo_vars <- function(data, params, geo_type) {
         .data$county,
         .data$county_fips
       )
+  } else if (geo_type == "county") {
+    warning("county metadata not supported")
   }
   
   geo_vars <- bind_cols(first, rest)
@@ -154,8 +155,7 @@ add_metadata_vars <- function(data, params, geo_type, groupby_vars) {
 
 #' Get the file name for the given parameters, geography, and set of group-by variables.
 #' @noRd
-get_file_name <- function(params, geo_type, groupby_vars) {
-  
+get_file_name <- function(params, geo_type, groupby_vars, theme = NULL) {
   aggregation_type <- sort(setdiff(groupby_vars, "geo_id"))
   if (length(aggregation_type) == 0) aggregation_type <- "overall"
   
@@ -164,6 +164,7 @@ get_file_name <- function(params, geo_type, groupby_vars) {
     format(params$end_date, "%Y%m%d"),
     get_period_type(params$aggregate_range),
     geo_type,
+    ifelse(is.null(theme), "all_indicators", paste("theme", theme, sep = "_")),
     paste(aggregation_type, collapse = "_"),
     sep = "_"
   )
diff --git a/facebook/delphiFacebook/man/write_contingency_tables.Rd b/facebook/delphiFacebook/man/write_contingency_tables.Rd
index ce687becd..fcdd8bd6f 100644
--- a/facebook/delphiFacebook/man/write_contingency_tables.Rd
+++ b/facebook/delphiFacebook/man/write_contingency_tables.Rd
@@ -4,7 +4,7 @@
 \alias{write_contingency_tables}
 \title{Write csv file for sharing with researchers.}
 \usage{
-write_contingency_tables(data, params, geo_type, groupby_vars)
+write_contingency_tables(data, params, geo_type, groupby_vars, theme = NULL)
 }
 \arguments{
 \item{data}{a data frame to save; must contain the columns in

From 85564ccfd58d37e80e58e70f406763faf4009899 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 16 Jun 2022 12:35:27 -0400
Subject: [PATCH 31/49] make theme tables

---
 facebook/delphiFacebook/DESCRIPTION           |   1 +
 facebook/delphiFacebook/NAMESPACE             |   1 +
 .../delphiFacebook/R/contingency_aggregate.R  |  12 +
 .../delphiFacebook/R/contingency_indicators.R | 692 ++++++++++++++++--
 .../delphiFacebook/R/contingency_variables.R  | 142 ++--
 5 files changed, 761 insertions(+), 87 deletions(-)

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index 51ad1e74b..c42da0224 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -15,6 +15,7 @@ Imports:
     rlang,
     readr,
     dplyr,
+    tidyr,
     stringi,
     jsonlite,
     lubridate,
diff --git a/facebook/delphiFacebook/NAMESPACE b/facebook/delphiFacebook/NAMESPACE
index 7846002a4..cfef1c937 100644
--- a/facebook/delphiFacebook/NAMESPACE
+++ b/facebook/delphiFacebook/NAMESPACE
@@ -127,5 +127,6 @@ importFrom(survey,svymean)
 importFrom(survey,svyvar)
 importFrom(tibble,add_column)
 importFrom(tibble,tribble)
+importFrom(tidyr,drop_na)
 importFrom(utils,tail)
 useDynLib(delphiFacebook, .registration = TRUE)
diff --git a/facebook/delphiFacebook/R/contingency_aggregate.R b/facebook/delphiFacebook/R/contingency_aggregate.R
index fb2b8fe98..054b980b0 100644
--- a/facebook/delphiFacebook/R/contingency_aggregate.R
+++ b/facebook/delphiFacebook/R/contingency_aggregate.R
@@ -26,6 +26,7 @@
 #' @import data.table
 #' @importFrom dplyr full_join %>% select all_of
 #' @importFrom purrr reduce
+#' @importFrom tidyr drop_na
 #'
 #' @export
 produce_aggregates <- function(df, aggregations, cw_list, params) {
@@ -95,6 +96,17 @@ produce_aggregates <- function(df, aggregations, cw_list, params) {
     if ( length(dfs_out) != 0 ) {
       df_out <- dfs_out %>% reduce(full_join, by=agg_group, suff=c("", ""))
       write_contingency_tables(df_out, params, geo_level, agg_group)
+      
+      for (theme in names(THEME_GROUPS)) {
+        theme_out <- select(df_out, agg_group, contains(THEME_GROUPS[[theme]]))
+        # Drop any rows that are completely `NA`. Grouping variables are always
+        # defined, so need to ignore those.
+        theme_out <- drop_na(theme_out, !!setdiff(names(theme_out), agg_group))
+        
+        if ( nrow(theme_out) != 0 && ncol(theme_out) != 0 ) {
+          write_contingency_tables(theme_out, params, geo_level, agg_group, theme)  
+        }
+      }
     }
   }
 }
diff --git a/facebook/delphiFacebook/R/contingency_indicators.R b/facebook/delphiFacebook/R/contingency_indicators.R
index e0bfc0d8e..d00df791d 100644
--- a/facebook/delphiFacebook/R/contingency_indicators.R
+++ b/facebook/delphiFacebook/R/contingency_indicators.R
@@ -1,3 +1,559 @@
+THEME_GROUPS <- list(
+  "sociodemographics" = c(
+    "pct_age_18_24",
+    "pct_age_25_34",
+    "pct_age_35_44",
+    "pct_age_45_54",
+    "pct_age_55_64",
+    "pct_age_65_74",
+    "pct_age_75_older",
+    "pct_condition_asthma",
+    "pct_condition_cancer",
+    "pct_condition_cvd",
+    "pct_condition_diabetes",
+    "pct_condition_hbp",
+    "pct_condition_immune",
+    "pct_condition_kidney",
+    "pct_condition_lung",
+    "pct_condition_none",
+    "pct_condition_obesity",
+    "pct_education_2yr_degree",
+    "pct_education_4yr_degree",
+    "pct_education_doctorate",
+    "pct_education_highschool_or_equivalent",
+    "pct_education_less_than_highschool",
+    "pct_education_masters",
+    "pct_education_professional_degree",
+    "pct_education_some_college",
+    "pct_gender_female",
+    "pct_gender_male",
+    "pct_gender_nonbinary_other",
+    "pct_gender_unknown",
+    "pct_hispanic_latino",
+    "pct_language_home_chinese",
+    "pct_language_home_english",
+    "pct_language_home_french",
+    "pct_language_home_other",
+    "pct_language_home_portuguese",
+    "pct_language_home_spanish",
+    "pct_language_home_vietnamese",
+    "pct_occ_4w_admin",
+    "pct_occ_4w_arts",
+    "pct_occ_4w_building",
+    "pct_occ_4w_construction",
+    "pct_occ_4w_education",
+    "pct_occ_4w_food",
+    "pct_occ_4w_health_prac",
+    "pct_occ_4w_health_support",
+    "pct_occ_4w_maintenance",
+    "pct_occ_4w_other",
+    "pct_occ_4w_personal",
+    "pct_occ_4w_production",
+    "pct_occ_4w_protective",
+    "pct_occ_4w_sales",
+    "pct_occ_4w_social",
+    "pct_occ_4w_transportation",
+    "pct_pregnant",
+    "pct_race_american_indian_alaska_native",
+    "pct_race_asian",
+    "pct_race_black_african_american",
+    "pct_race_native_hawaiian_pacific_islander",
+    "pct_race_multiple_other",
+    "pct_race_white",
+    "pct_smoke",
+    "pct_work_for_pay_4w",
+    "pct_work_for_pay_outside_home_4w",
+    "mean_adults_in_household",
+    "mean_children_in_household",
+    "mean_olderadults_in_household",
+    "mean_ppl_in_household",
+    "mean_ppl_in_household_adults",
+    "mean_ppl_in_household_children",
+    "mean_ppl_in_household_olderadults"
+  ),
+  "vaccines" = c(
+    "pct_accept_vaccine",
+    "pct_accept_vaccine_no_appointment",
+    "pct_accept_vaccine_defno",
+    "pct_accept_vaccine_defyes",
+    "pct_accept_vaccine_no_appointment_defno",
+    "pct_accept_vaccine_no_appointment_defyes",
+    "pct_accept_vaccine_no_appointment_probno",
+    "pct_accept_vaccine_no_appointment_probyes",
+    "pct_accept_vaccine_probno",
+    "pct_accept_vaccine_probyes",
+    "pct_appointment_have",
+    "pct_appointment_not_vaccinated",
+    "pct_appointment_or_accept_vaccine",
+    "pct_appointment_tried",
+    "pct_barrier_allergic",
+    "pct_barrier_cost",
+    "pct_barrier_dislike_vaccines",
+    "pct_barrier_dislike_vaccines_generally",
+    "pct_barrier_distrust_govt",
+    "pct_barrier_distrust_vaccines",
+    "pct_barrier_dontneed",
+    "pct_barrier_health_condition",
+    "pct_barrier_ineffective",
+    "pct_barrier_low_priority",
+    "pct_barrier_not_recommended",
+    "pct_barrier_other",
+    "pct_barrier_pregnant",
+    "pct_barrier_reason_allergic",
+    "pct_barrier_reason_cost",
+    "pct_barrier_reason_not_recommended",
+    "pct_barrier_reason_dontbelieve",
+    "pct_barrier_reason_dontlike",
+    "pct_barrier_reason_distrust_gov",
+    "pct_barrier_reason_health",
+    "pct_barrier_reason_other",
+    "pct_barrier_reason_otherpeople",
+    "pct_barrier_reason_pregnant",
+    "pct_barrier_reason_religion",
+    "pct_barrier_reason_sideeffect",
+    "pct_barrier_reason_distrust_vaccine",
+    "pct_barrier_reason_wait",
+    "pct_barrier_reason_wontwork",
+    "pct_barrier_religious",
+    "pct_barrier_sideeffects",
+    "pct_barrier_wait_safety",
+    "pct_defno_barrier_allergic",
+    "pct_defno_barrier_cost",
+    "pct_defno_barrier_dislike_vaccines",
+    "pct_defno_barrier_dislike_vaccines_generally",
+    "pct_defno_barrier_distrust_govt",
+    "pct_defno_barrier_distrust_vaccines",
+    "pct_defno_barrier_dontneed",
+    "pct_defno_barrier_health_condition",
+    "pct_defno_barrier_ineffective",
+    "pct_defno_barrier_low_priority",
+    "pct_defno_barrier_not_recommended",
+    "pct_defno_barrier_other",
+    "pct_defno_barrier_pregnant",
+    "pct_defno_barrier_religious",
+    "pct_defno_barrier_sideeffects",
+    "pct_defno_barrier_wait_safety",
+    "pct_defno_dontneed_reason_dont_spend_time",
+    "pct_defno_dontneed_reason_had_covid",
+    "pct_defno_dontneed_reason_not_beneficial",
+    "pct_defno_dontneed_reason_not_high_risk",
+    "pct_defno_dontneed_reason_not_serious",
+    "pct_defno_dontneed_reason_other",
+    "pct_defno_dontneed_reason_precautions",
+    "pct_dontneed_reason_dont_spend_time",
+    "pct_dontneed_reason_had_covid",
+    "pct_dontneed_reason_not_beneficial",
+    "pct_dontneed_reason_not_high_risk",
+    "pct_dontneed_reason_not_serious",
+    "pct_dontneed_reason_other",
+    "pct_dontneed_reason_precautions",
+    "pct_hesitant_barrier_allergic",
+    "pct_hesitant_barrier_cost",
+    "pct_hesitant_barrier_dislike_vaccines",
+    "pct_hesitant_barrier_dislike_vaccines_generally",
+    "pct_hesitant_barrier_distrust_govt",
+    "pct_hesitant_barrier_distrust_vaccines",
+    "pct_hesitant_barrier_dontneed",
+    "pct_hesitant_barrier_health_condition",
+    "pct_hesitant_barrier_ineffective",
+    "pct_hesitant_barrier_low_priority",
+    "pct_hesitant_barrier_not_recommended",
+    "pct_hesitant_barrier_other",
+    "pct_hesitant_barrier_pregnant",
+    "pct_hesitant_barrier_religious",
+    "pct_hesitant_barrier_sideeffects",
+    "pct_hesitant_barrier_wait_safety",
+    "pct_hesitant_dontneed_reason_dont_spend_time",
+    "pct_hesitant_dontneed_reason_had_covid",
+    "pct_hesitant_dontneed_reason_not_beneficial",
+    "pct_hesitant_dontneed_reason_not_high_risk",
+    "pct_hesitant_dontneed_reason_not_serious",
+    "pct_hesitant_dontneed_reason_other",
+    "pct_hesitant_dontneed_reason_precautions",
+    "pct_hesitant_trust_covid_info_cdc",
+    "pct_hesitant_trust_covid_info_doctors",
+    "pct_hesitant_trust_covid_info_experts",
+    "pct_hesitant_trust_covid_info_friends",
+    "pct_hesitant_trust_covid_info_govt_health",
+    "pct_hesitant_trust_covid_info_journalists",
+    "pct_hesitant_trust_covid_info_politicians",
+    "pct_hesitant_trust_covid_info_religious",
+    "pct_hesitant_vaccine",
+    "pct_hesitant_vaccine_likely_doctors",
+    "pct_hesitant_vaccine_likely_friends",
+    "pct_hesitant_vaccine_likely_govt",
+    "pct_hesitant_vaccine_likely_local_health",
+    "pct_hesitant_vaccine_likely_politicians",
+    "pct_hesitant_vaccine_likely_who",
+    "pct_hesitant_worried_vaccine_sideeffects",
+    "pct_informed_access",
+    "pct_initial_dose_one_of_one",
+    "pct_initial_dose_one_of_two",
+    "pct_initial_dose_two_of_two",
+    "pct_receive_all_doses_noplan",
+    "pct_receive_all_doses_plan",
+    "pct_receive_all_doses_yes",
+    "pct_received_2_vaccine_doses",
+    "pct_trust_covid_info_cdc",
+    "pct_trust_covid_info_doctors",
+    "pct_trust_covid_info_experts",
+    "pct_trust_covid_info_friends",
+    "pct_trust_covid_info_govt_health",
+    "pct_trust_covid_info_journalists",
+    "pct_trust_covid_info_politicians",
+    "pct_trust_covid_info_religious",
+    "pct_vaccinate_children",
+    "pct_child_vaccine_vaccinated_or_accept",
+    "pct_vaccinated",
+    "pct_vaccinated_appointment_or_accept",
+    "pct_vaccinated_at_least_one_booster",
+    "pct_vaccinated_booster_accept",
+    "pct_vaccinated_booster_defno",
+    "pct_vaccinated_booster_defyes",
+    "pct_vaccinated_booster_hesitant",
+    "pct_vaccinated_booster_probno",
+    "pct_vaccinated_booster_probyes",
+    "pct_vaccinated_no_booster",
+    "pct_vaccinated_one_booster",
+    "pct_vaccinated_or_accept",
+    "pct_vaccinated_two_or_more_boosters",
+    "pct_vaccine_barrier_appointment_location",
+    "pct_vaccine_barrier_appointment_location_has",
+    "pct_vaccine_barrier_appointment_location_tried",
+    "pct_vaccine_barrier_appointment_time",
+    "pct_vaccine_barrier_appointment_time_has",
+    "pct_vaccine_barrier_appointment_time_tried",
+    "pct_vaccine_barrier_childcare",
+    "pct_vaccine_barrier_childcare_has",
+    "pct_vaccine_barrier_childcare_tried",
+    "pct_vaccine_barrier_document",
+    "pct_vaccine_barrier_document_has",
+    "pct_vaccine_barrier_document_tried",
+    "pct_vaccine_barrier_eligible",
+    "pct_vaccine_barrier_eligible_has",
+    "pct_vaccine_barrier_eligible_tried",
+    "pct_vaccine_barrier_language",
+    "pct_vaccine_barrier_language_has",
+    "pct_vaccine_barrier_language_tried",
+    "pct_vaccine_barrier_no_appointments",
+    "pct_vaccine_barrier_no_appointments_has",
+    "pct_vaccine_barrier_no_appointments_tried",
+    "pct_vaccine_barrier_none",
+    "pct_vaccine_barrier_none_has",
+    "pct_vaccine_barrier_none_tried",
+    "pct_vaccine_barrier_other",
+    "pct_vaccine_barrier_other_has",
+    "pct_vaccine_barrier_other_tried",
+    "pct_vaccine_barrier_technical_difficulties",
+    "pct_vaccine_barrier_technical_difficulties_has",
+    "pct_vaccine_barrier_technical_difficulties_tried",
+    "pct_vaccine_barrier_technology_access",
+    "pct_vaccine_barrier_technology_access_has",
+    "pct_vaccine_barrier_technology_access_tried",
+    "pct_vaccine_barrier_time",
+    "pct_vaccine_barrier_time_has",
+    "pct_vaccine_barrier_time_tried",
+    "pct_vaccine_barrier_travel",
+    "pct_vaccine_barrier_travel_has",
+    "pct_vaccine_barrier_travel_tried",
+    "pct_vaccine_barrier_type",
+    "pct_vaccine_barrier_type_has",
+    "pct_vaccine_barrier_type_tried",
+    "pct_vaccine_likely_doctors",
+    "pct_vaccine_likely_friends",
+    "pct_vaccine_likely_govt_health",
+    "pct_vaccine_likely_local_health",
+    "pct_vaccine_likely_politicians",
+    "pct_vaccine_likely_who",
+    "pct_vaccine_timing_dontknow",
+    "pct_vaccine_timing_morethansix",
+    "pct_vaccine_timing_onemonth",
+    "pct_vaccine_timing_sixmonths",
+    "pct_vaccine_timing_threemonths",
+    "pct_vaccine_timing_weeks",
+    "pct_vaccine_tried",
+    "pct_worried_vaccine_sideeffects",
+    "pct_flu_shot_1y",
+    "pct_flu_vaccine_july_2020",
+    "pct_flu_vaccine_june_2020",
+    "pct_flu_vaccinated_2021",
+    "pct_overall_vaccine_hesitancy",
+    "pct_overall_vaccine_hesitancy",
+    "pct_vaccine_incomplete_allergic",
+    "pct_vaccine_incomplete_cost",
+    "pct_vaccine_incomplete_distrust_gov",
+    "pct_vaccine_incomplete_distrust_vaccine",
+    "pct_vaccine_incomplete_dontbelieve",
+    "pct_vaccine_incomplete_dontlike",
+    "pct_vaccine_incomplete_health",
+    "pct_vaccine_incomplete_not_recommended",
+    "pct_vaccine_incomplete_other",
+    "pct_vaccine_incomplete_otherpeople",
+    "pct_vaccine_incomplete_pregnant",
+    "pct_vaccine_incomplete_religion",
+    "pct_vaccine_incomplete_sideeffect",
+    "pct_vaccine_incomplete_wait",
+    "pct_vaccine_incomplete_wontwork"
+  ),
+  "symptoms_and_testing" = c(
+    "pct_symp_anosmia",
+    "pct_had_covid_ever",
+    "pct_had_covid_ever",
+    "pct_symp_sore_throat",
+    "pct_cli",
+    "pct_ever_tested",
+    "pct_ever_tested_positive",
+    "pct_hh_cmnty_cli",
+    "pct_ili",
+    "pct_test_reason_contact",
+    "pct_test_reason_medical",
+    "pct_test_reason_none",
+    "pct_test_reason_required",
+    "pct_test_reason_sick",
+    "pct_test_reason_travel",
+    "pct_test_reason_visit",
+    "pct_test_reason_large_event",
+    "pct_test_reason_crowd",
+    "pct_tested_14d",
+    "pct_tested_positive_14d",
+    "pct_wanted_test_14d",
+    "pct_cough_mucus",
+    "mean_days_symptoms",
+    "pct_hh_cmnty_cli",
+    "pct_nohh_cmnty_cli",
+    "mean_ppl_symptoms_community",
+    "mean_ppl_symptoms_household",
+    "pct_reason_not_tested_appointment",
+    "pct_reason_not_tested_cost",
+    "pct_reason_not_tested_location",
+    "pct_reason_not_tested_stigma",
+    "pct_reason_not_tested_time",
+    "pct_reason_not_tested_travel",
+    "pct_reason_not_tested_tried",
+    "pct_reason_not_tested_none",
+    "pct_taken_temp",
+    "pct_symp_aches",
+    "pct_symp_chest_pain",
+    "pct_symp_chills",
+    "pct_symp_cough",
+    "pct_symp_diarrhea",
+    "pct_symp_diff_breathing",
+    "pct_symp_eye_pain",
+    "pct_symp_fatigue",
+    "pct_symp_fever",
+    "pct_symp_headache",
+    "pct_symp_nasal_congestion",
+    "pct_symp_nausea",
+    "pct_symp_none",
+    "pct_symp_other",
+    "pct_symp_runny_nose",
+    "pct_symp_shortness_breath",
+    "pct_symp_sleep_changes",
+    "pct_symp_stuffy_nose",
+    "pct_symp_unusual_given_fever",
+    "pct_symp_unusual_given_cough",
+    "pct_symp_unusual_given_shortness_breath",
+    "pct_symp_unusual_given_diff_breathing",
+    "pct_symp_unusual_given_fatigue",
+    "pct_symp_unusual_given_nasal_congestion",
+    "pct_symp_unusual_given_runny_nose",
+    "pct_symp_unusual_given_aches",
+    "pct_symp_unusual_given_sore_throat",
+    "pct_symp_unusual_given_chest_pain",
+    "pct_symp_unusual_given_nausea",
+    "pct_symp_unusual_given_diarrhea",
+    "pct_symp_unusual_given_anosmia",
+    "pct_symp_unusual_given_other",
+    "pct_symp_unusual_given_eye_pain",
+    "pct_symp_unusual_given_chills",
+    "pct_symp_unusual_given_headache",
+    "pct_symp_unusual_given_sleep_changes",
+    "pct_symp_unusual_given_stuffy_nose",
+    "pct_unusual_symptom_fever",
+    "pct_unusual_symptom_cough",
+    "pct_unusual_symptom_shortness_breath",
+    "pct_unusual_symptom_breathing",
+    "pct_unusual_symptom_tired",
+    "pct_unusual_symptom_congestion",
+    "pct_unusual_symptom_runnynose",
+    "pct_unusual_symptom_muscle",
+    "pct_unusual_symptom_sorethroat",
+    "pct_unusual_symptom_chestpain",
+    "pct_unusual_symptom_nausea",
+    "pct_unusual_symptom_diarrhea",
+    "pct_unusual_symptom_anosmia",
+    "pct_unusual_symptom_eyepain",
+    "pct_unusual_symptom_chills",
+    "pct_unusual_symptom_headache",
+    "pct_unusual_symptom_sleep_changes",
+    "pct_unusual_symptom_stuffy_nose",
+    "pct_unusual_symptom_other",
+    "pct_unusual_symptom_hospital",
+    "pct_unusual_symptom_hospital_tried",
+    "pct_unusual_symptom_medical_care_called_doctor",
+    "pct_unusual_symptom_medical_care_telemedicine",
+    "pct_unusual_symptom_medical_care_visited_doctor",
+    "pct_unusual_symptom_medical_care_urgent_care",
+    "pct_unusual_symptom_medical_care_er",
+    "pct_unusual_symptom_medical_care_hospital",
+    "pct_unusual_symptom_medical_care_tried",
+    "pct_unusual_symptom_tested",
+    "pct_unusual_symptom_tested_positive"
+  ),
+  "behavior_and_mental_health" = c(
+    "pct_large_event_1d",
+    "pct_mask_large_event_1d",
+    "pct_mask_public_transit_1d",
+    "pct_mask_restaurant_1d",
+    "pct_mask_shop_1d",
+    "pct_mask_spent_time_1d",
+    "pct_mask_shop_indoors_1d",
+    "pct_mask_restaurant_indoors_1d",
+    "pct_mask_spent_time_indoors_1d",
+    "pct_mask_large_event_indoors_1d",
+    "pct_mask_work_outside_home_1d",
+    "pct_mask_work_outside_home_indoors_1d",
+    "pct_public_transit_1d",
+    "pct_shop_1d",
+    "pct_spent_time_1d",
+    "pct_restaurant_1d",
+    "pct_shop_indoors_1d",
+    "pct_restaurant_indoors_1d",
+    "pct_spent_time_indoors_1d",
+    "pct_large_event_indoors_1d",
+    "pct_travel_outside_state_5d",
+    "pct_travel_outside_state_7d",
+    "pct_work_outside_home_1d",
+    "pct_work_outside_home_indoors_1d",
+    "pct_work_outside_home_5d",
+    "pct_anxious_5d",
+    "pct_anxious_5d_alt",
+    "pct_anxious_7d",
+    "pct_anxious_7d_alt",
+    "pct_depressed_5d",
+    "pct_depressed_5d_alt",
+    "pct_depressed_7d",
+    "pct_depressed_7d_alt",
+    "pct_felt_isolated_5d",
+    "pct_felt_isolated_5d_alt",
+    "pct_felt_isolated_7d",
+    "pct_felt_isolated_7d_alt",
+    "pct_delayed_care_cost",
+    "pct_race_treated_fairly_healthcare",
+    "pct_worried_become_ill",
+    "pct_direct_contact",
+    "pct_finance",
+    "pct_wearing_mask_5d",
+    "pct_wearing_mask_5d_alt",
+    "pct_wearing_mask_7d",
+    "pct_wearing_mask_7d_alt",
+    "pct_others_masked",
+    "pct_others_masked_alt",
+    "pct_avoid_contact",
+    "pct_avoid_contact_7d",
+    "pct_covid_vaccinated_friends_alt",
+    "pct_depressed_7d_alt",
+    "pct_direct_contact_covid",
+    "pct_direct_contact_covid_hh",
+    "pct_finance_alt",
+    "pct_financial_threat",
+    "pct_others_distanced_public_alt",
+    "pct_others_masked_public",
+    "pct_others_masked_public_alt",
+    "pct_wearing_mask_7d_alt",
+    "pct_work_healthcare_5d",
+    "pct_work_nursing_home_5d",
+    "pct_work_outside_home_4w",
+    "pct_work_outside_home_5d"
+  ),
+  "norms_information_beliefs" = c(
+    "pct_belief_children_immune",
+    "pct_belief_created_small_group",
+    "pct_belief_distancing_effective",
+    "pct_belief_govt_exploitation",
+    "pct_belief_masking_effective",
+    "pct_belief_vaccinated_mask_unnecessary",
+    "pct_covid_vaccinated_friends",
+    "pct_others_distanced_public",
+    "pct_others_masked_public",
+    "pct_received_news_experts",
+    "pct_received_news_friends",
+    "pct_received_news_govt_health",
+    "pct_received_news_journalists",
+    "pct_received_news_local_health",
+    "pct_received_news_none",
+    "pct_received_news_politicians",
+    "pct_received_news_religious",
+    "pct_received_news_cdc",
+    "pct_want_info_children_education",
+    "pct_want_info_covid_treatment",
+    "pct_want_info_covid_variants",
+    "pct_want_info_employment",
+    "pct_want_info_mental_health",
+    "pct_want_info_none",
+    "pct_want_info_relationships",
+    "pct_want_info_vaccine_access",
+    "pct_want_info_vaccine_types",
+    "pct_worried_catch_covid"
+  ),
+  "parenting" = c(
+    "pct_child_school_homeschool",
+    "pct_child_school_not",
+    "pct_child_school_other",
+    "pct_child_school_private",
+    "pct_child_school_public",
+    "pct_child_vaccine_already",
+    "pct_child_vaccine_no_def",
+    "pct_child_vaccine_no_prob",
+    "pct_child_vaccine_vaccinated_or_accept",
+    "pct_child_vaccine_yes_def",
+    "pct_child_vaccine_yes_prob",
+    "pct_has_child_under_18",
+    "pct_oldest_child_under_5",
+    "pct_oldest_child_12_to_15",
+    "pct_oldest_child_16_to_17",
+    "pct_oldest_child_5_to_11",
+    "pct_children_gr1_5",
+    "pct_children_gr6_8",
+    "pct_children_gr9_12",
+    "pct_children_prek",
+    "pct_children_school_measure_cafeteria",
+    "pct_children_school_measure_class_size",
+    "pct_children_school_measure_desk_shield",
+    "pct_children_school_measure_desk_space",
+    "pct_children_school_measure_entry",
+    "pct_children_school_measure_extracurricular",
+    "pct_children_school_measure_mask_students",
+    "pct_children_school_measure_mask_teachers",
+    "pct_children_school_measure_outdoor",
+    "pct_children_school_measure_playground",
+    "pct_children_school_measure_same_students",
+    "pct_children_school_measure_same_teacher",
+    "pct_children_school_measure_screening",
+    "pct_children_school_measure_supplies",
+    "pct_inperson_school_fulltime",
+    "pct_inperson_school_parttime",
+    "pct_school_safety_measures_mask_students",
+    "pct_school_safety_measures_mask_teachers",
+    "pct_school_safety_measures_restricted_entry",
+    "pct_school_safety_measures_separators",
+    "pct_school_safety_measures_extracurricular",
+    "pct_school_safety_measures_symptom_screen",
+    "pct_school_safety_measures_ventilation",
+    "pct_school_safety_measures_testing_staff",
+    "pct_school_safety_measures_testing_students",
+    "pct_school_safety_measures_vaccine_staff",
+    "pct_school_safety_measures_vaccine_students",
+    "pct_school_safety_measures_cafeteria",
+    "pct_school_safety_measures_dont_know",
+    "pct_remote_school_fulltime_oldest",
+    "pct_inperson_school_fulltime_oldest",
+    "pct_inperson_school_parttime_oldest",
+    "pct_vaccinate_children",
+    "pct_child_vaccine_vaccinated_or_accept"
+  )
+)
+
 #' Make tables specifying aggregations to output
 #'
 #' Each row represents one aggregate to report. `name` is the aggregate's base
@@ -114,7 +670,7 @@ get_aggs <- function() {
     "pct_symp_chest_pain", "symp_chest_pain", compute_binary, jeffreys_binary,
     "pct_symp_nausea", "symp_nausea", compute_binary, jeffreys_binary,
     "pct_symp_diarrhea", "symp_diarrhea", compute_binary, jeffreys_binary,
-    "pct_anosmia", "symp_loss_smell_taste", compute_binary, jeffreys_binary,
+    "pct_symp_anosmia", "symp_loss_smell_taste", compute_binary, jeffreys_binary,
     "pct_symp_other", "symp_other", compute_binary, jeffreys_binary,
     "pct_symp_none", "symp_none", compute_binary, jeffreys_binary,
     "pct_symp_eye_pain", "symp_eye_pain", compute_binary, jeffreys_binary,
@@ -124,24 +680,45 @@ get_aggs <- function() {
     "pct_symp_stuffy_nose", "symp_stuffy_nose", compute_binary, jeffreys_binary,
 
     # unusual symptoms
-    "pct_symp_fever_unusual", "symp_fever_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_cough_unusual", "symp_cough_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_shortness_breath_unusual", "symp_shortness_breath_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_diff_breathing_unusual", "symp_diff_breathing_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_fatigue_unusual", "symp_fatigue_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_nasal_congestion_unusual", "symp_nasal_congestion_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_runny_nose_unusual", "symp_runny_nose_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_aches_unusual", "symp_aches_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_sore_throat_unusual", "symp_sore_throat_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_chest_pain_unusual", "symp_chest_pain_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_nausea_unusual", "symp_nausea_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_diarrhea_unusual", "symp_diarrhea_unusual", compute_binary, jeffreys_binary,
-    "pct_anosmia_unusual", "symp_loss_smell_taste_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_eye_pain_unusual", "symp_eye_pain_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_chills_unusual", "symp_chills_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_headache_unusual", "symp_headache_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_sleep_changes_unusual", "symp_sleep_changes_unusual", compute_binary, jeffreys_binary,
-    "pct_symp_stuffy_nose_unusual", "symp_stuffy_nose_unusual", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_fever", "symp_unusual_given_fever", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_cough", "symp_unusual_given_cough", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_shortness_breath", "symp_unusual_given_shortness_breath", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_diff_breathing", "symp_unusual_given_diff_breathing", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_fatigue", "symp_unusual_given_fatigue", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_nasal_congestion", "symp_unusual_given_nasal_congestion", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_runny_nose", "symp_unusual_given_runny_nose", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_aches", "symp_unusual_given_aches", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_sore_throat", "symp_unusual_given_sore_throat", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_chest_pain", "symp_unusual_given_chest_pain", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_nausea", "symp_unusual_given_nausea", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_diarrhea", "symp_unusual_given_diarrhea", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_anosmia", "symp_unusual_given_loss_smell_taste", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_other", "symp_unusual_given_other", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_eye_pain", "symp_unusual_given_eye_pain", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_chills", "symp_unusual_given_chills", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_headache", "symp_unusual_given_headache", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_sleep_changes", "symp_unusual_given_sleep_changes", compute_binary, jeffreys_binary,
+    "pct_symp_unusual_given_stuffy_nose", "symp_unusual_given_stuffy_nose", compute_binary, jeffreys_binary,
+
+    "pct_unusual_symptom_fever", "symp_fever_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_cough", "symp_cough_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_shortness_breath", "symp_shortness_breath_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_breathing", "symp_diff_breathing_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_tired", "symp_fatigue_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_congestion", "symp_nasal_congestion_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_runnynose", "symp_runny_nose_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_muscle", "symp_aches_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_sorethroat", "symp_sore_throat_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_chestpain", "symp_chest_pain_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_nausea", "symp_nausea_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_diarrhea", "symp_diarrhea_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_anosmia", "symp_loss_smell_taste_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_eyepain", "symp_eye_pain_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_chills", "symp_chills_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_headache", "symp_headache_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_sleep_changes", "symp_sleep_changes_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_stuffy_nose", "symp_stuffy_nose_unusual", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_other", "symp_other_unusual", compute_binary, jeffreys_binary,
 
     # vaccines
     "pct_vaccinated", "v_covid_vaccinated", compute_binary, jeffreys_binary,
@@ -158,7 +735,7 @@ get_aggs <- function() {
     "pct_covid_vaccinated_friends_alt", "v_covid_vaccinated_some_friends", compute_binary, jeffreys_binary,
 
     "pct_vaccinate_children", "v_vaccinate_children", compute_binary, jeffreys_binary,
-    "pct_vaccinate_child_oldest", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
+    "pct_child_vaccine_vaccinated_or_accept", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
 
     "pct_child_vaccine_already", "v_child_vaccine_already", compute_binary, jeffreys_multinomial_factory(5),
     "pct_child_vaccine_yes_def", "v_child_vaccine_yes_def", compute_binary, jeffreys_multinomial_factory(5),
@@ -192,7 +769,9 @@ get_aggs <- function() {
     "pct_vaccinated_booster_probno", "v_vaccinated_booster_probno", compute_binary, jeffreys_multinomial_factory(4),
     "pct_vaccinated_booster_defno", "v_vaccinated_booster_defno", compute_binary, jeffreys_multinomial_factory(4),
 
-    "pct_vaccine_all_doses", "v_received_all_doses", compute_binary, jeffreys_binary,
+    "pct_receive_all_doses_yes", "v_receive_all_doses_yes", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_receive_all_doses_plan", "v_receive_all_doses_plan", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_receive_all_doses_noplan", "v_receive_all_doses_noplan", compute_binary, jeffreys_multinomial_factory(3),
 
     "pct_flu_shot_1y", "v_flu_vaccinated_1y", compute_binary, jeffreys_binary,
     "pct_flu_vaccine_june_2020", "v_flu_vaccinated_june_2020", compute_binary, jeffreys_binary,
@@ -336,6 +915,23 @@ get_aggs <- function() {
     "pct_defno_dontneed_reason_not_beneficial", "v_defno_dontneed_reason_not_beneficial", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_other", "v_defno_dontneed_reason_other", compute_binary, jeffreys_binary,
 
+    # Combined (V5abcd) barriers to vaccination
+    "pct_barrier_reason_sideeffect", "v_overall_barrier_reason_sideeffect", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_allergic", "v_overall_barrier_reason_allergic", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_wontwork", "v_overall_barrier_reason_wontwork", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_dontbelieve", "v_overall_barrier_reason_dontbelieve", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_dontlike", "v_overall_barrier_reason_dontlike", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_not_recommended", "v_overall_barrier_reason_not_recommended", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_wait", "v_overall_barrier_reason_wait", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_otherpeople", "v_overall_barrier_reason_otherpeople", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_cost", "v_overall_barrier_reason_cost", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_distrust_vaccine", "v_overall_barrier_reason_distrust_vaccine", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_distrust_gov", "v_overall_barrier_reason_distrust_gov", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_health", "v_overall_barrier_reason_health", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_other", "v_overall_barrier_reason_other", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_pregnant", "v_overall_barrier_reason_pregnant", compute_binary, jeffreys_binary,
+    "pct_barrier_reason_religion", "v_overall_barrier_reason_religion", compute_binary, jeffreys_binary,
+
     "pct_informed_access", "v_informed_access", compute_binary, jeffreys_binary,
     
     # appointments
@@ -401,10 +997,12 @@ get_aggs <- function() {
     "pct_tested_positive_14d", "t_tested_positive_14d", compute_binary, jeffreys_binary,
     "pct_wanted_test_14d", "t_wanted_test_14d", compute_binary, jeffreys_binary,
     "pct_ever_tested", "t_ever_tested", compute_binary, jeffreys_binary,
+    "pct_ever_tested_positive", "t_ever_tested_positive", compute_binary, jeffreys_binary,
 
     "pct_unusual_symptom_tested", "t_unusual_symptom_tested", compute_binary, jeffreys_binary,
     "pct_unusual_symptom_tested_positive", "t_unusual_symptom_tested_positive", compute_binary, jeffreys_binary,
     "pct_unusual_symptom_hospital", "t_unusual_symptom_hospital", compute_binary, jeffreys_binary,
+    "pct_unusual_symptom_hospital_tried", "t_unusual_symptom_hospital_tried", compute_binary, jeffreys_binary,
 
     "pct_unusual_symptom_medical_care_called_doctor", "unusual_symptom_medical_care_called_doctor", compute_binary, jeffreys_binary,
     "pct_unusual_symptom_medical_care_telemedicine", "unusual_symptom_medical_care_telemedicine", compute_binary, jeffreys_binary,
@@ -454,9 +1052,9 @@ get_aggs <- function() {
     "pct_depressed_7d_alt", "mh_some_depressed_7d", compute_binary, jeffreys_binary,
 
     "pct_felt_isolated_5d", "mh_isolated", compute_binary, jeffreys_binary,
-    "pct_isolated_5d_alt", "mh_some_isolated", compute_binary, jeffreys_binary,
+    "pct_felt_isolated_5d_alt", "mh_some_isolated", compute_binary, jeffreys_binary,
     "pct_felt_isolated_7d", "mh_isolated_7d", compute_binary, jeffreys_binary,
-    "pct_isolated_7d_alt", "mh_some_isolated_7d", compute_binary, jeffreys_binary,
+    "pct_felt_isolated_7d_alt", "mh_some_isolated_7d", compute_binary, jeffreys_binary,
     
     # travel outside state
     # pre-wave 10
@@ -554,15 +1152,30 @@ get_aggs <- function() {
     "pct_school_safety_measures_cafeteria", "s_school_safety_measures_cafeteria", compute_binary, jeffreys_binary,
     "pct_school_safety_measures_dont_know", "s_school_safety_measures_dont_know", compute_binary, jeffreys_binary,
 
+    # Schooling types
+    "pct_child_school_public", "s_child_school_public", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_private", "s_child_school_private", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_homeschool", "s_child_school_homeschool", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_not", "s_child_school_not", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_other", "s_child_school_other", compute_binary, jeffreys_multinomial_factory(5),
+
+    # Children ages
+    "pct_oldest_child_under_5", "ch_oldest_child_under_5", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_oldest_child_5_to_11", "ch_oldest_child_5_to_11", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_oldest_child_12_to_15", "ch_oldest_child_12_to_15", compute_binary, jeffreys_multinomial_factory(4),
+    "pct_oldest_child_16_to_17", "ch_oldest_child_16_to_17", compute_binary, jeffreys_multinomial_factory(4),
+
+    "pct_has_child_under_18", "ch_has_child_under_18", compute_binary, jeffreys_multinomial_factory(4),
+
     # Means. No post-processing required.
     "mean_days_symptoms", "symp_n_days", compute_numeric_mean, I,
     "mean_ppl_symptoms_household", "hh_number_sick", compute_numeric_mean, I,
     "mean_ppl_symptoms_community", "community_number_sick", compute_numeric_mean, I,
 
-    "mean_hh_number_children", "hh_number_children", compute_numeric_mean, I,
-    "mean_hh_number_adults", "hh_number_adults", compute_numeric_mean, I,
-    "mean_hh_number_older", "hh_number_older", compute_numeric_mean, I,
-    "mean_hh_number_total", "hh_number_total", compute_numeric_mean, I,
+    "mean_ppl_in_household_children", "ppl_in_household_children", compute_numeric_mean, I,
+    "mean_ppl_in_household_adults", "ppl_in_household_adults", compute_numeric_mean, I,
+    "mean_ppl_in_household_olderadults", "ppl_in_household_older", compute_numeric_mean, I,
+    "mean_ppl_in_household", "hh_number_total", compute_numeric_mean, I,
 
     "mean_children_in_household", "children_in_household", compute_numeric_mean, I,
     "mean_adults_in_household", "adults_in_household", compute_numeric_mean, I,
@@ -694,13 +1307,6 @@ get_aggs <- function() {
     "pct_children_gr6_8", "children_gr6_8", compute_binary, jeffreys_binary,
     "pct_children_gr9_12", "children_gr9_12", compute_binary, jeffreys_binary,
 
-    # Already in main grouping, including "overall". Just need to make sure to include in demo/parenting tables.
-    # "pct_inperson_school_fulltime", "s_inperson_school_fulltime", compute_binary, jeffreys_binary,
-    # "pct_inperson_school_parttime", "s_inperson_school_parttime", compute_binary, jeffreys_binary,
-    # "pct_inperson_school_fulltime_oldest", "s_inperson_school_fulltime_oldest", compute_binary, jeffreys_binary,
-    # "pct_remote_school_fulltime_oldest", "s_remote_school_fulltime_oldest", compute_binary, jeffreys_binary,
-    # "pct_inperson_school_parttime_oldest", "s_inperson_school_parttime_oldest", compute_binary, jeffreys_binary,
-
     "pct_children_school_measure_mask_students", "children_school_measure_mask_students", compute_binary, jeffreys_binary,
     "pct_children_school_measure_mask_teachers", "children_school_measure_mask_teachers", compute_binary, jeffreys_binary,
     "pct_children_school_measure_same_teacher", "children_school_measure_same_teacher", compute_binary, jeffreys_binary,
@@ -731,24 +1337,20 @@ get_aggs <- function() {
     "pct_occ_4w_maintenance", "occ_4w_maintenance", compute_binary, jeffreys_multinomial_factory(16),
     "pct_occ_4w_production", "occ_4w_production", compute_binary, jeffreys_multinomial_factory(16),
     "pct_occ_4w_transportation", "occ_4w_transportation", compute_binary, jeffreys_multinomial_factory(16),
-    "pct_occ_4w_other", "occ_4w_other", compute_binary, jeffreys_multinomial_factory(16),
-
-    "pct_", "", compute_binary, jeffreys_binary,
+    "pct_occ_4w_other", "occ_4w_other", compute_binary, jeffreys_multinomial_factory(16)
   )
-  demo_aggs <- create_aggs_product(
-    regsions,
-    demo_groups,
-    demo_indicators
+  demo_aggs <- rbind(
+    create_aggs_product(regions, demo_groups, demo_indicators),
+    create_aggs_product(list("county"), list(c()), demo_indicators)
   )
 
-
   ## Parenting cuts
   parent_groups <- list(c("child_age"))
-  parent_indicators <- tribble()
+  parent_indicators <- filter(indicators, name %in% THEME_GROUPS[["parenting"]])
   parent_aggs <- create_aggs_product(regions, parent_groups, parent_indicators)
 
-  weekly_aggs <- rbind(aggs, demo_aggs)
-  monthly_aggs <- rbind(aggs, demo_aggs)
+  weekly_aggs <- rbind(aggs, demo_aggs, parent_aggs)
+  monthly_aggs <- rbind(aggs, demo_aggs, parent_aggs)
 
   return(list("week"=weekly_aggs, "month"=monthly_aggs))
 }
diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 4435d8266..99771ecc8 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -257,14 +257,13 @@ code_addl_vaccines <- function(input_data, wave) {
   if ("V2a" %in% names(input_data)) {
     # coded as 1 = Yes, received all recommended doses, 2 = Plan to receive all recommended doses,
     # 3 = Don't plan to receive all recommended doses.
-    input_data$v_received_all_doses <- case_when(
-      input_data$V2a == 1 ~ 1,
-      input_data$V2a == 2 ~ 0,
-      input_data$V2a == 3 ~ 0,
-      TRUE ~ NA_real_
-    )
+    input_data$v_receive_all_doses_yes <- input_data$V2a == 1
+    input_data$v_receive_all_doses_plan <- input_data$V2a == 2
+    input_data$v_receive_all_doses_noplan <- input_data$V2a == 3
   } else {
-    input_data$v_received_all_doses <- NA_real_
+    input_data$v_receive_all_doses_yes <- NA_real_
+    input_data$v_receive_all_doses_plan <- NA_real_
+    input_data$v_receive_all_doses_noplan <- NA_real_
   }
 
   # hesitant_vaccine
@@ -342,6 +341,13 @@ code_addl_vaccines <- function(input_data, wave) {
   } else {
     input_data$t_ever_tested <- NA
   }
+
+  if ("B11" %in% names(input_data)) {
+    # Coded as 1 = Yes, 2 = No, 3 = don't know.
+    input_data$t_ever_tested_positive <- input_data$B11 == 1
+  } else {
+    input_data$t_ever_tested_positive <- NA
+  }
   
   if ("B5" %in% names(input_data)) {
     # Coded as 1 = "tested and COVID+", 2 = "tested and COVID-",
@@ -362,8 +368,10 @@ code_addl_vaccines <- function(input_data, wave) {
 
   if ("B6" %in% names(input_data)) {
     input_data$t_unusual_symptom_hospital <- input_data$B6 == 1
+    input_data$t_unusual_symptom_hospital_tried <- input_data$B6 == 1 | input_data$B6 == 3
   } else {
     input_data$t_unusual_symptom_hospital <- NA
+    input_data$t_unusual_symptom_hospital_tried <- NA
   }
 
   if ("B7" %in% names(input_data)) {
@@ -447,7 +455,24 @@ if ("V5d" %in% names(input_data)) {
     input_data$v_vaccine_incomplete_religion <- NA_real_
   }
 
-if ("C2" %in% names(input_data)) {
+  # Overall barriers to vaccination from V5abcd.
+  input_data$v_overall_barrier_reason_sideeffect <- input_data$v_hesitancy_reason_sideeffects | input_data$v_vaccine_incomplete_sideeffect
+  input_data$v_overall_barrier_reason_allergic <- input_data$v_hesitancy_reason_allergic | input_data$v_vaccine_incomplete_allergic
+  input_data$v_overall_barrier_reason_wontwork <- input_data$v_hesitancy_reason_ineffective | input_data$v_vaccine_incomplete_wontwork
+  input_data$v_overall_barrier_reason_dontbelieve <- input_data$v_hesitancy_reason_unnecessary | input_data$v_vaccine_incomplete_dontbelieve
+  input_data$v_overall_barrier_reason_dontlike <- input_data$v_hesitancy_reason_dislike_vaccines | input_data$v_vaccine_incomplete_dontlike
+  input_data$v_overall_barrier_reason_not_recommended <- input_data$v_hesitancy_reason_not_recommended | input_data$v_vaccine_incomplete_not_recommended
+  input_data$v_overall_barrier_reason_wait <- input_data$v_hesitancy_reason_wait_safety | input_data$v_vaccine_incomplete_wait
+  input_data$v_overall_barrier_reason_otherpeople <- input_data$v_hesitancy_reason_low_priority | input_data$v_vaccine_incomplete_otherpeople
+  input_data$v_overall_barrier_reason_cost <- input_data$v_hesitancy_reason_cost | input_data$v_vaccine_incomplete_cost
+  input_data$v_overall_barrier_reason_distrust_vaccine <- input_data$v_hesitancy_reason_distrust_vaccines | input_data$v_vaccine_incomplete_distrust_vaccine
+  input_data$v_overall_barrier_reason_distrust_gov <- input_data$v_hesitancy_reason_distrust_gov | input_data$v_vaccine_incomplete_distrust_gov
+  input_data$v_overall_barrier_reason_health <- input_data$v_hesitancy_reason_health_condition | input_data$v_vaccine_incomplete_health
+  input_data$v_overall_barrier_reason_other <- input_data$v_hesitancy_reason_other | input_data$v_vaccine_incomplete_other
+  input_data$v_overall_barrier_reason_pregnant <- input_data$v_hesitancy_reason_pregnant | input_data$v_vaccine_incomplete_pregnant
+  input_data$v_overall_barrier_reason_religion <- input_data$v_hesitancy_reason_religious | input_data$v_vaccine_incomplete_religion
+
+  if ("C2" %in% names(input_data)) {
     # Coded as 1 = "Yes", 2 = "No"
     input_data$v_flu_vaccinated_1y <- input_data$C2 == 1
   } else {
@@ -1156,62 +1181,105 @@ code_addl_symptoms <- function(input_data, wave) {
   
   if ("B2c" %in% names(input_data)) {
     symptoms <- split_options(input_data$B2c)
+
+    input_data$symp_fever_unusual <- is_selected(symptoms, "1")
+    input_data$symp_cough_unusual <- is_selected(symptoms, "2")
+    input_data$symp_shortness_breath_unusual <- is_selected(symptoms, "3")
+    input_data$symp_diff_breathing_unusual <- is_selected(symptoms, "4")
+    input_data$symp_fatigue_unusual <- is_selected(symptoms, "5")
+    input_data$symp_nasal_congestion_unusual <- is_selected(symptoms, "6")
+    input_data$symp_runny_nose_unusual <- is_selected(symptoms, "7")
+    input_data$symp_aches_unusual <- is_selected(symptoms, "8")
+    input_data$symp_sore_throat_unusual <- is_selected(symptoms, "9")
+    input_data$symp_chest_pain_unusual <- is_selected(symptoms, "10")
+    input_data$symp_nausea_unusual <- is_selected(symptoms, "11")
+    input_data$symp_diarrhea_unusual <- is_selected(symptoms, "12")
+    input_data$symp_loss_smell_taste_unusual <- is_selected(symptoms, "13")
+    input_data$symp_loss_smell_taste_unusual <- is_selected(symptoms, "14")
+    input_data$symp_eye_pain_unusual <- is_selected(symptoms, "16")
+    input_data$symp_chills_unusual <- is_selected(symptoms, "17")
+    input_data$symp_headache_unusual <- is_selected(symptoms, "18")
+    input_data$symp_sleep_changes_unusual <- is_selected(symptoms, "19")
+    input_data$symp_stuffy_nose_unusual <- is_selected(symptoms, "20")
     
-    input_data$symp_fever_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_fever <- calc_unusual_given_symptom(
       input_data$symp_fever, is_selected(symptoms, "1")
     )
-    input_data$symp_cough_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_cough <- calc_unusual_given_symptom(
       input_data$symp_cough, is_selected(symptoms, "2")
     )
-    input_data$symp_shortness_breath_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_shortness_breath <- calc_unusual_given_symptom(
       input_data$symp_shortness_breath, is_selected(symptoms, "3")
     )
-    input_data$symp_diff_breathing_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_diff_breathing <- calc_unusual_given_symptom(
       input_data$symp_diff_breathing, is_selected(symptoms, "4")
     )
-    input_data$symp_fatigue_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_fatigue <- calc_unusual_given_symptom(
       input_data$symp_fatigue, is_selected(symptoms, "5")
     )
-    input_data$symp_nasal_congestion_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_nasal_congestion <- calc_unusual_given_symptom(
       input_data$symp_nasal_congestion, is_selected(symptoms, "6")
     )
-    input_data$symp_runny_nose_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_runny_nose <- calc_unusual_given_symptom(
       input_data$symp_runny_nose, is_selected(symptoms, "7")
     )
-    input_data$symp_aches_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_aches <- calc_unusual_given_symptom(
       input_data$symp_aches, is_selected(symptoms, "8")
     )
-    input_data$symp_sore_throat_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_sore_throat <- calc_unusual_given_symptom(
       input_data$symp_sore_throat, is_selected(symptoms, "9")
     )
-    input_data$symp_chest_pain_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_chest_pain <- calc_unusual_given_symptom(
       input_data$symp_chest_pain, is_selected(symptoms, "10")
     )
-    input_data$symp_nausea_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_nausea <- calc_unusual_given_symptom(
       input_data$symp_nausea, is_selected(symptoms, "11")
     )
-    input_data$symp_diarrhea_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_diarrhea <- calc_unusual_given_symptom(
       input_data$symp_diarrhea, is_selected(symptoms, "12")
     )
-    input_data$symp_loss_smell_taste_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_loss_smell_taste <- calc_unusual_given_symptom(
       input_data$symp_loss_smell_taste, is_selected(symptoms, "13")
     )
-    input_data$symp_eye_pain_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_other <- calc_unusual_given_symptom(
+      input_data$symp_other, is_selected(symptoms, "14")
+    )
+    input_data$symp_unusual_given_eye_pain <- calc_unusual_given_symptom(
       input_data$symp_eye_pain, is_selected(symptoms, "16")
     )
-    input_data$symp_chills_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_chills <- calc_unusual_given_symptom(
       input_data$symp_chills, is_selected(symptoms, "17")
     )
-    input_data$symp_headache_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_headache <- calc_unusual_given_symptom(
       input_data$symp_headache, is_selected(symptoms, "18")
     )
-    input_data$symp_sleep_changes_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_sleep_changes <- calc_unusual_given_symptom(
       input_data$symp_sleep_changes, is_selected(symptoms, "19")
     )
-    input_data$symp_stuffy_nose_unusual <- calc_unusual_given_symptom(
+    input_data$symp_unusual_given_stuffy_nose <- calc_unusual_given_symptom(
       input_data$symp_stuffy_nose, is_selected(symptoms, "20")
     )
   } else {
+    input_data$symp_unusual_given_fever <- NA
+    input_data$symp_unusual_given_cough <- NA
+    input_data$symp_unusual_given_shortness_breath <- NA
+    input_data$symp_unusual_given_diff_breathing <- NA
+    input_data$symp_unusual_given_fatigue <- NA
+    input_data$symp_unusual_given_nasal_congestion <- NA
+    input_data$symp_unusual_given_runny_nose <- NA
+    input_data$symp_unusual_given_aches <- NA
+    input_data$symp_unusual_given_sore_throat <- NA
+    input_data$symp_unusual_given_chest_pain <- NA
+    input_data$symp_unusual_given_nausea <- NA
+    input_data$symp_unusual_given_diarrhea <- NA
+    input_data$symp_unusual_given_loss_smell_taste <- NA
+    input_data$symp_unusual_given_other <- NA
+    input_data$symp_unusual_given_eye_pain <- NA
+    input_data$symp_unusual_given_chills <- NA
+    input_data$symp_unusual_given_headache <- NA
+    input_data$symp_unusual_given_sleep_changes <- NA
+    input_data$symp_unusual_given_stuffy_nose <- NA
+
     input_data$symp_fever_unusual <- NA
     input_data$symp_cough_unusual <- NA
     input_data$symp_shortness_breath_unusual <- NA
@@ -1230,6 +1298,7 @@ code_addl_symptoms <- function(input_data, wave) {
     input_data$symp_headache_unusual <- NA
     input_data$symp_sleep_changes_unusual <- NA
     input_data$symp_stuffy_nose_unusual <- NA
+    input_data$symp_stuffy_nose_unusual <- NA
   }
 
   if ("B4" %in% names(input_data)) {
@@ -1270,23 +1339,15 @@ code_behaviors <- function(input_data, wave) {
   if ("C11" %in% names(input_data)) {
     # Had "direct contact" with someone COVID-positive in the last 24 hours
     # Coded as 1 = Yes, 2 = No
-    input_data$c_direct_contact_covid <- case_when(
-      input_data$C11 == 1 ~ 1,
-      input_data$C11 == 2 ~ 0,
-      TRUE ~ NA_real_
-    )
+    input_data$c_direct_contact_covid <- input_data$C11 == 1
   } else {
     input_data$c_direct_contact_covid <- NA_real_
   }
 
-  if (all(c("C11", "C12") %in% names(input_data))) {
+  if ("C12" %in% names(input_data)) {
     # C12: was the person in C11 a member of your household
     # Coded as 1 = Yes, 2 = No
-    input_data$c_direct_contact_covid_hh <- case_when(
-      input_data$C11 == 1 & input_data$C12 == 1 ~ 1,
-      input_data$C11 == 2 | input_data$C12 == 2 ~ 0,
-      TRUE ~ NA_real_
-    )
+    input_data$c_direct_contact_covid_hh <- input_data$C12 == 1
   } else {
     input_data$c_direct_contact_covid_hh <- NA_real_
   }
@@ -1364,10 +1425,7 @@ code_addl_mental_health <- function(input_data, wave) {
   if ("Q36" %in% names(input_data)) {
     # Included in waves 1, 2, 3. Coded as 1 = substantial threat,
     # 2 = moderate threat, 3 = not much of a threat, 4 = not a threat at all
-    input_data$mh_financial_threat <- case_when(
-      is.na(input_data$Q36) ~ NA,
-      input_data$Q36 == 1 ~ TRUE,
-      TRUE ~ FALSE)
+    input_data$mh_financial_threat <- input_data$Q36 == 1
   } else {
     input_data$mh_financial_threat <- NA
   }
@@ -1511,7 +1569,7 @@ code_addl_activities <- function(input_data, wave) {
 #' @return augmented data frame
 code_addl_demographic <- function(input_data, wave) {
   if ("D1" %in% names(input_data)) {
-    # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = no answer
+    # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = prefer not to answer
     input_data$gender_male <- input_data$D1 == 1
     input_data$gender_female <- input_data$D1 == 2
     input_data$gender_nonbinary_other <- case_when(

From 0a981e52f072fca79e43439bef76843ff7c436dd Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 17 Jun 2022 12:34:14 -0400
Subject: [PATCH 32/49] county metadata

---
 facebook/delphiFacebook/DESCRIPTION           |  2 +-
 facebook/delphiFacebook/NAMESPACE             |  2 +
 facebook/delphiFacebook/R/contingency_write.R | 50 +++++++++++++++++--
 3 files changed, 48 insertions(+), 6 deletions(-)

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index c42da0224..beda72167 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -30,5 +30,5 @@ Suggests:
     testthat (>= 1.0.1),
     covr (>= 2.2.2)
 LinkingTo: Rcpp
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Encoding: UTF-8
diff --git a/facebook/delphiFacebook/NAMESPACE b/facebook/delphiFacebook/NAMESPACE
index cfef1c937..4416f8e45 100644
--- a/facebook/delphiFacebook/NAMESPACE
+++ b/facebook/delphiFacebook/NAMESPACE
@@ -69,6 +69,7 @@ importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,coalesce)
 importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
@@ -121,6 +122,7 @@ importFrom(stringi,stri_split)
 importFrom(stringi,stri_sub)
 importFrom(stringi,stri_trans_tolower)
 importFrom(stringi,stri_trim)
+importFrom(stringr,str_pad)
 importFrom(survey,oldsvyquantile)
 importFrom(survey,svydesign)
 importFrom(survey,svymean)
diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index 58aca8a92..da2d33d1b 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -23,7 +23,6 @@
 #' @export
 write_contingency_tables <- function(data, params, geo_type, groupby_vars, theme = NULL) {
   if (!is.null(data) && nrow(data) != 0) {
-    
     # Reorder the group-by columns and sort the dataset by them.
     groupby_vars <- c("geo_id", sort(setdiff(groupby_vars, "geo_id")))
     data <- data %>%
@@ -61,8 +60,9 @@ write_contingency_tables <- function(data, params, geo_type, groupby_vars, theme
 #' @param params A parameters object with the `static_dir` resources folder.
 #' @param geo_type "nation", "state".
 #' 
-#' @importFrom dplyr bind_cols left_join select
+#' @importFrom dplyr bind_cols left_join select distinct mutate
 #' @importFrom readr read_csv cols
+#' @importFrom stringr str_pad
 #' @noRd
 add_geo_vars <- function(data, params, geo_type) {
   
@@ -75,7 +75,6 @@ add_geo_vars <- function(data, params, geo_type) {
   )
   
   if (geo_type == "nation") {
-    
     rest <- data.frame(
       region = overall,
       GID_1 = NA_character_,
@@ -86,7 +85,6 @@ add_geo_vars <- function(data, params, geo_type) {
     )
     
   } else if (geo_type == "state") {
-    
     states <- read_csv(
       file.path(params$static_dir, "state_list.csv"),
       col_types = cols(.default = "c")
@@ -109,7 +107,49 @@ add_geo_vars <- function(data, params, geo_type) {
         .data$county_fips
       )
   } else if (geo_type == "county") {
-    warning("county metadata not supported")
+    counties <- read_csv(
+      file.path(params$static_dir, "02_20_uszips.csv"),
+      col_types = cols(.default = "c")
+    ) %>% 
+      mutate(
+        fips = str_pad(.data$fips, 5, pad="0")
+      ) %>%
+      select(fips, county_name, state_id, state_name) %>% 
+      distinct()
+
+    rest <- data.frame(
+      county_fips = data$geo_id
+    )
+
+    rest <- left_join(rest, counties, by = c("county_fips" = "fips")) %>%
+      mutate(
+        region = .data$state_id,
+        state = .data$state_id,
+        county = .data$county_name,
+        county_fips = .data$county_fips
+      ) %>% 
+      select(
+        .data$region,
+        .data$state,
+        .data$county,
+        .data$county_fips
+      )
+    
+    # Fill in state fips and GID_1
+    states <- read_csv(
+      file.path(params$static_dir, "state_list.csv"),
+      col_types = cols(.default = "c")
+    )
+    
+    rest <- left_join(rest, states, by = "state") %>%
+      select(
+        .data$region,
+        .data$GID_1,
+        .data$state,
+        .data$state_fips,
+        .data$county,
+        .data$county_fips
+      )
   }
   
   geo_vars <- bind_cols(first, rest)

From dd384ffb6e0bcbe0a62052bde71b9a6996da2046 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 22 Jun 2022 17:01:12 -0400
Subject: [PATCH 33/49] swap stringr for stringi

---
 facebook/delphiFacebook/NAMESPACE             | 2 +-
 facebook/delphiFacebook/R/contingency_write.R | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/facebook/delphiFacebook/NAMESPACE b/facebook/delphiFacebook/NAMESPACE
index 4416f8e45..1890f72ee 100644
--- a/facebook/delphiFacebook/NAMESPACE
+++ b/facebook/delphiFacebook/NAMESPACE
@@ -116,13 +116,13 @@ importFrom(stats,setNames)
 importFrom(stats,weighted.mean)
 importFrom(stringi,stri_extract)
 importFrom(stringi,stri_extract_first)
+importFrom(stringi,stri_pad)
 importFrom(stringi,stri_replace)
 importFrom(stringi,stri_replace_all)
 importFrom(stringi,stri_split)
 importFrom(stringi,stri_sub)
 importFrom(stringi,stri_trans_tolower)
 importFrom(stringi,stri_trim)
-importFrom(stringr,str_pad)
 importFrom(survey,oldsvyquantile)
 importFrom(survey,svydesign)
 importFrom(survey,svymean)
diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index da2d33d1b..01f2346a2 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -62,7 +62,7 @@ write_contingency_tables <- function(data, params, geo_type, groupby_vars, theme
 #' 
 #' @importFrom dplyr bind_cols left_join select distinct mutate
 #' @importFrom readr read_csv cols
-#' @importFrom stringr str_pad
+#' @importFrom stringi stri_pad
 #' @noRd
 add_geo_vars <- function(data, params, geo_type) {
   
@@ -112,7 +112,7 @@ add_geo_vars <- function(data, params, geo_type) {
       col_types = cols(.default = "c")
     ) %>% 
       mutate(
-        fips = str_pad(.data$fips, 5, pad="0")
+        fips = stri_pad(.data$fips, 5, pad="0")
       ) %>%
       select(fips, county_name, state_id, state_name) %>% 
       distinct()

From c653918e6155b435b964211a33d325e63a3d15e3 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 22 Jun 2022 17:08:52 -0400
Subject: [PATCH 34/49] tests

---
 facebook/delphiFacebook/DESCRIPTION                       | 2 +-
 facebook/delphiFacebook/R/contingency_write.R             | 2 ++
 facebook/delphiFacebook/man/write_contingency_tables.Rd   | 2 ++
 .../unit-tests/testthat/test-contingency-write.R          | 8 ++++----
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index c42da0224..beda72167 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -30,5 +30,5 @@ Suggests:
     testthat (>= 1.0.1),
     covr (>= 2.2.2)
 LinkingTo: Rcpp
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Encoding: UTF-8
diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index 58aca8a92..9ccf0241b 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -15,6 +15,8 @@
 #' @param geo_type       name of the geographic level; used for naming the output file
 #' @param groupby_vars   character vector of column names used for grouping to
 #'                       calculate aggregations; used for naming the output file
+#' @param theme          string indicating theme group (topic) indicators
+#                        belong to according to THEME_GROUPS, or NULL
 #'
 #' @importFrom readr write_csv
 #' @importFrom dplyr arrange across everything
diff --git a/facebook/delphiFacebook/man/write_contingency_tables.Rd b/facebook/delphiFacebook/man/write_contingency_tables.Rd
index fcdd8bd6f..339c5ffd1 100644
--- a/facebook/delphiFacebook/man/write_contingency_tables.Rd
+++ b/facebook/delphiFacebook/man/write_contingency_tables.Rd
@@ -21,6 +21,8 @@ write_contingency_tables(data, params, geo_type, groupby_vars, theme = NULL)
 
 \item{groupby_vars}{character vector of column names used for grouping to
 calculate aggregations; used for naming the output file}
+
+\item{theme}{string indicating theme group (topic) indicators}
 }
 \description{
 CSV name includes date specifying start of time period aggregated, geo level,
diff --git a/facebook/delphiFacebook/unit-tests/testthat/test-contingency-write.R b/facebook/delphiFacebook/unit-tests/testthat/test-contingency-write.R
index b479b8d95..2551f86c9 100644
--- a/facebook/delphiFacebook/unit-tests/testthat/test-contingency-write.R
+++ b/facebook/delphiFacebook/unit-tests/testthat/test-contingency-write.R
@@ -45,9 +45,9 @@ test_that("testing write_contingency_tables command", {
                                          aggregate_range = "week"), 
                            "state", 
                            c("geo_id", "tested"))
-  expect_setequal(!!dir(tdir), c("20200510_20200516_weekly_state_tested.csv.gz"))
+  expect_setequal(!!dir(tdir), c("20200510_20200516_weekly_state_all_indicators_tested.csv.gz"))
   
-  df <- read_csv(file.path(tdir, "20200510_20200516_weekly_state_tested.csv.gz"))
+  df <- read_csv(file.path(tdir, "20200510_20200516_weekly_state_all_indicators_tested.csv.gz"))
   expect_equivalent(df, test_data)
 })
 
@@ -59,13 +59,13 @@ test_that("testing command to create output filenames", {
     end_date=as.Date("2021-01-02")
   )
   out <- get_file_name(params, "nation", c("gender"))
-  expected <- "DebugOn-DoNotShare_20210101_20210102_monthly_nation_gender.csv.gz"
+  expected <- "DebugOn-DoNotShare_20210101_20210102_monthly_nation_all_indicators_gender.csv.gz"
   
   expect_equal(out, expected)
   
   params$debug <- FALSE
   out <- get_file_name(params, "nation", c("gender", "race", "ethnicity"))
-  expected <- "20210101_20210102_monthly_nation_ethnicity_gender_race.csv.gz"
+  expected <- "20210101_20210102_monthly_nation_all_indicators_ethnicity_gender_race.csv.gz"
   
   expect_equal(out, expected)
 })

From 4785af5f2fc360f792b557d7933dfc7e330f0995 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 23 Jun 2022 11:47:19 -0400
Subject: [PATCH 35/49] lower overall sample size threshold

---
 facebook/delphiFacebook/R/contingency_utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_utils.R b/facebook/delphiFacebook/R/contingency_utils.R
index b0f3368ec..5a5cfd5fe 100644
--- a/facebook/delphiFacebook/R/contingency_utils.R
+++ b/facebook/delphiFacebook/R/contingency_utils.R
@@ -36,7 +36,7 @@ read_contingency_params <- function(path = "params.json", template_path = "param
     }
   }
   
-  contingency_params$num_filter <- if_else(contingency_params$debug, 2L, 100L)
+  contingency_params$num_filter <- if_else(contingency_params$debug, 2L, 40L)
   contingency_params$s_weight <- if_else(contingency_params$debug, 1.00, 0.01)
   contingency_params$s_mix_coef <- if_else(contingency_params$debug, 0.05, 0.05)
   contingency_params$use_input_asis <- if_else(

From 0ccfaa85e6009083ee2203412b4ac0596f4114b1 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 23 Jun 2022 12:01:03 -0400
Subject: [PATCH 36/49] raise n thres only for county

---
 facebook/delphiFacebook/R/contingency_aggregate.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/facebook/delphiFacebook/R/contingency_aggregate.R b/facebook/delphiFacebook/R/contingency_aggregate.R
index 054b980b0..1527fdfe8 100644
--- a/facebook/delphiFacebook/R/contingency_aggregate.R
+++ b/facebook/delphiFacebook/R/contingency_aggregate.R
@@ -66,6 +66,12 @@ produce_aggregates <- function(df, aggregations, cw_list, params) {
     geo_level <- agg_groups$geo_level[group_ind]
     geo_crosswalk <- cw_list[[geo_level]]
 
+    if (geo_level == "county") {
+      # Raise sample size threshold to 100.
+      old_thresh <- params$num_filter
+      params$num_filter <- 100L
+    }
+
     # Subset aggregations to keep only those grouping by the current agg_group
     # and with the current geo_level. `setequal` ignores differences in
     # ordering and only looks at unique elements.
@@ -108,6 +114,11 @@ produce_aggregates <- function(df, aggregations, cw_list, params) {
         }
       }
     }
+
+    if (geo_level == "county") {
+      # Restore old sample size threshold
+      params$num_filter <- old_thresh
+    }
   }
 }
 

From a51df29a9df0d89cc2afb4334e3ff0cabd056dc3 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 23 Jun 2022 12:14:27 -0400
Subject: [PATCH 37/49] round all sample sizes

---
 facebook/delphiFacebook/DESCRIPTION            |  1 +
 facebook/delphiFacebook/NAMESPACE              |  1 +
 .../delphiFacebook/R/contingency_aggregate.R   |  6 +++++-
 .../delphiFacebook/R/contingency_privacy.R     | 18 ++++++++++++++++--
 .../man/apply_privacy_censoring.Rd             |  4 ++--
 facebook/delphiFacebook/man/round_n.Rd         | 17 +++++++++++++++++
 6 files changed, 42 insertions(+), 5 deletions(-)
 create mode 100644 facebook/delphiFacebook/man/round_n.Rd

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index beda72167..875d9dcde 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -15,6 +15,7 @@ Imports:
     rlang,
     readr,
     dplyr,
+    plyr,
     tidyr,
     stringi,
     jsonlite,
diff --git a/facebook/delphiFacebook/NAMESPACE b/facebook/delphiFacebook/NAMESPACE
index cfef1c937..b3ce270d7 100644
--- a/facebook/delphiFacebook/NAMESPACE
+++ b/facebook/delphiFacebook/NAMESPACE
@@ -98,6 +98,7 @@ importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
 importFrom(parallel,detectCores)
 importFrom(parallel,mclapply)
+importFrom(plyr,round_any)
 importFrom(purrr,reduce)
 importFrom(readr,col_character)
 importFrom(readr,col_integer)
diff --git a/facebook/delphiFacebook/R/contingency_aggregate.R b/facebook/delphiFacebook/R/contingency_aggregate.R
index 1527fdfe8..beb25493a 100644
--- a/facebook/delphiFacebook/R/contingency_aggregate.R
+++ b/facebook/delphiFacebook/R/contingency_aggregate.R
@@ -318,10 +318,14 @@ summarize_aggs <- function(df, crosswalk_data, aggregations, geo_level, params)
       rowSums(is.na(dfs_out[[aggregation]][, c("val", "sample_size")])) == 0,
     ]
 
+    # Censor rows with low sample size
     dfs_out[[aggregation]] <- apply_privacy_censoring(dfs_out[[aggregation]], params)
 
-    ## Apply the post-function
+    # Apply the post-function
     dfs_out[[aggregation]] <- post_fn(dfs_out[[aggregation]])
+
+    # Round sample sizes
+    dfs_out[[aggregation]] <- round_n(dfs_out[[aggregation]], params)
   }
 
   return(dfs_out)
diff --git a/facebook/delphiFacebook/R/contingency_privacy.R b/facebook/delphiFacebook/R/contingency_privacy.R
index 81b764da9..3a122a751 100644
--- a/facebook/delphiFacebook/R/contingency_privacy.R
+++ b/facebook/delphiFacebook/R/contingency_privacy.R
@@ -1,7 +1,7 @@
 #' Censor aggregates to ensure privacy.
 #'
-#' Currently done in simple, static way: Rows with sample size less than 100 are
-#' removed; no noise is added.
+#' Currently done in simple, static way: Rows with sample size less than num_filter
+#' are removed; no noise is added.
 #'
 #' @param df a data frame of summarized response data
 #' @param params a named list with entries "s_weight", "s_mix_coef",
@@ -16,3 +16,17 @@ apply_privacy_censoring <- function(df, params) {
                 .data$sample_size >= params$num_filter,
                 .data$effective_sample_size >= params$num_filter))
 }
+
+#' Round sample sizes to nearest 5.
+#'
+#' @param df a data frame of summarized response data
+#' @param params a named list with entries "s_weight", "s_mix_coef",
+#'   "num_filter"
+#'
+#' @importFrom plyr round_any
+round_n <- function(df, params) {
+  return(mutate(df,
+                sample_size = round_any(.data$sample_size, 5),
+                effective_sample_size = round_any(.data$effective_sample_size, 5)
+        ))
+}
diff --git a/facebook/delphiFacebook/man/apply_privacy_censoring.Rd b/facebook/delphiFacebook/man/apply_privacy_censoring.Rd
index 0f83c7d4b..405e0ea13 100644
--- a/facebook/delphiFacebook/man/apply_privacy_censoring.Rd
+++ b/facebook/delphiFacebook/man/apply_privacy_censoring.Rd
@@ -13,6 +13,6 @@ apply_privacy_censoring(df, params)
 "num_filter"}
 }
 \description{
-Currently done in simple, static way: Rows with sample size less than 100 are
-removed; no noise is added.
+Currently done in simple, static way: Rows with sample size less than num_filter
+are removed; no noise is added.
 }
diff --git a/facebook/delphiFacebook/man/round_n.Rd b/facebook/delphiFacebook/man/round_n.Rd
new file mode 100644
index 000000000..b310116f2
--- /dev/null
+++ b/facebook/delphiFacebook/man/round_n.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contingency_privacy.R
+\name{round_n}
+\alias{round_n}
+\title{Round sample sizes to nearest 5.}
+\usage{
+round_n(df, params)
+}
+\arguments{
+\item{df}{a data frame of summarized response data}
+
+\item{params}{a named list with entries "s_weight", "s_mix_coef",
+"num_filter"}
+}
+\description{
+Round sample sizes to nearest 5.
+}

From 1d396fb3a2f6869da8c511b97625a2d86289745f Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Thu, 23 Jun 2022 11:55:18 -0400
Subject: [PATCH 38/49] tests missing theme tables

---
 .../testthat/test-contingency-run.R           | 34 ++++++++++++++++---
 .../testthat/test-integration.R               |  6 ++--
 2 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/facebook/delphiFacebook/integration-tests/testthat/test-contingency-run.R b/facebook/delphiFacebook/integration-tests/testthat/test-contingency-run.R
index e17b897bc..06955ae1e 100644
--- a/facebook/delphiFacebook/integration-tests/testthat/test-contingency-run.R
+++ b/facebook/delphiFacebook/integration-tests/testthat/test-contingency-run.R
@@ -67,11 +67,19 @@ test_that("small dataset produces no output", {
 ### This test relies on `setup-run.R` to run the full pipeline and tests basic
 ### properties of the output.
 test_that("full synthetic dataset produces expected output format", {
-  expected_files <- c("20200501_20200531_monthly_nation_gender.csv.gz")
+  expected_files <- c(
+    "20200501_20200531_monthly_nation_all_indicators_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_behavior_and_mental_health_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_norms_information_beliefs_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_parenting_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_sociodemographics_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_symptoms_and_testing_gender.csv.gz",
+    "20200501_20200531_monthly_nation_theme_vaccines_gender.csv.gz"
+  )
   actual_files <- dir(test_path("receiving_contingency_full"))
   
-  out <- read.csv(file.path(params$export_dir, "20200501_20200531_monthly_nation_gender.csv.gz"))
-  
+  out <- read.csv(file.path(params$export_dir, "20200501_20200531_monthly_nation_all_indicators_gender.csv.gz"))
+
   expect_setequal(expected_files, actual_files)
   expect_equal(dir.exists(test_path("receiving_contingency_full")), TRUE)
   expect_equal(nrow(out) > 0, TRUE)
@@ -98,6 +106,7 @@ test_that("simple equal-weight dataset produces correct percents", {
   local_mock("delphiFacebook::load_archive" = mock_load_archive)
   local_mock("delphiFacebook::add_geo_vars" = mock_geo_vars)
   local_mock("delphiFacebook::add_metadata_vars" = mock_metadata)
+
   run_contingency_tables_many_periods(params, base_aggs[2,])
 
   # Expected files
@@ -228,7 +237,24 @@ test_that("production of historical CSVs for range of dates", {
 
   run_contingency_tables_many_periods(params, base_aggs[2,])
   # Expected files
-  expect_equal(!!dir(params$export_dir), c("20200503_20200509_weekly_nation_gender.csv.gz", "20200510_20200516_weekly_nation_gender.csv.gz"))
+  expect_equal(!!dir(params$export_dir),
+               c(
+                 "20200503_20200509_weekly_nation_all_indicators_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_behavior_and_mental_health_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_norms_information_beliefs_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_parenting_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_sociodemographics_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_symptoms_and_testing_gender.csv.gz",
+                 "20200503_20200509_weekly_nation_theme_vaccines_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_all_indicators_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_behavior_and_mental_health_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_norms_information_beliefs_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_parenting_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_sociodemographics_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_symptoms_and_testing_gender.csv.gz",
+                 "20200510_20200516_weekly_nation_theme_vaccines_gender.csv.gz"
+               )
+  )
 })
 
 
diff --git a/facebook/delphiFacebook/integration-tests/testthat/test-integration.R b/facebook/delphiFacebook/integration-tests/testthat/test-integration.R
index f111175c0..64993c6b8 100644
--- a/facebook/delphiFacebook/integration-tests/testthat/test-integration.R
+++ b/facebook/delphiFacebook/integration-tests/testthat/test-integration.R
@@ -24,8 +24,8 @@ metrics <- c("raw_cli", "raw_ili", "raw_hh_cmnty_cli", "raw_nohh_cmnty_cli",
 
              # work outside home
              # pre-wave-4
-             "wip_smoothed_work_outside_home_5d",
-             "wip_smoothed_wwork_outside_home_5d"
+             "smoothed_work_outside_home_5d",
+             "smoothed_wwork_outside_home_5d"
              )
 
 test_that("testing existence of csv files", {
@@ -70,7 +70,7 @@ test_that("testing geo files contain correct number of lines", {
 
   dt <- lapply(fnames, read_csv)
   dt_nrow <- sapply(dt, nrow)
-
+  
   expect_true(all(dt_nrow[grid$dates == "20200510"] == 1L))
   expect_true(all(dt_nrow[grid$dates == "20200511"] == 1L))
   expect_true(all(dt_nrow[grid$dates == "20200512" & grid$geo_levels != "nation"] == 2L))

From a98d4bd0f0265b1d91f559c35bde2df6769f393e Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 24 Jun 2022 10:51:03 -0400
Subject: [PATCH 39/49] filter out gender self-described responses

---
 facebook/delphiFacebook/DESCRIPTION           |  2 +-
 facebook/delphiFacebook/R/contingency_run.R   |  1 +
 facebook/delphiFacebook/R/responses.R         | 16 ++++++++++++++++
 .../man/code_addl_mental_health.Rd            | 19 +++++++++++++++++++
 .../man/filter_data_for_contingency.Rd        | 14 ++++++++++++++
 5 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 facebook/delphiFacebook/man/code_addl_mental_health.Rd
 create mode 100644 facebook/delphiFacebook/man/filter_data_for_contingency.Rd

diff --git a/facebook/delphiFacebook/DESCRIPTION b/facebook/delphiFacebook/DESCRIPTION
index 51ad1e74b..a8be617fe 100644
--- a/facebook/delphiFacebook/DESCRIPTION
+++ b/facebook/delphiFacebook/DESCRIPTION
@@ -29,5 +29,5 @@ Suggests:
     testthat (>= 1.0.1),
     covr (>= 2.2.2)
 LinkingTo: Rcpp
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Encoding: UTF-8
diff --git a/facebook/delphiFacebook/R/contingency_run.R b/facebook/delphiFacebook/R/contingency_run.R
index 9ea1edfba..e5defbd37 100644
--- a/facebook/delphiFacebook/R/contingency_run.R
+++ b/facebook/delphiFacebook/R/contingency_run.R
@@ -137,6 +137,7 @@ run_contingency_tables_one_period <- function(params, aggregations)
     data_agg <- create_data_for_aggregation(input_data)
     data_agg <- filter_data_for_aggregation(data_agg, params,
                                               lead_days = params$backfill_days)
+    data_agg <- filter_data_for_contingency(data_agg)
 
     if (nrow(data_agg) == 0) {
       msg_plain(sprintf("no data available in the desired date range %s- to %s",
diff --git a/facebook/delphiFacebook/R/responses.R b/facebook/delphiFacebook/R/responses.R
index c5f4a8032..e9d53936d 100644
--- a/facebook/delphiFacebook/R/responses.R
+++ b/facebook/delphiFacebook/R/responses.R
@@ -394,6 +394,22 @@ filter_data_for_aggregation <- function(df, params, lead_days = 12L)
   return(df)
 }
 
+#' Filter out low-quality data for contingency tables
+#'
+#' @param df data frame of responses
+#'
+#' @importFrom dplyr filter
+filter_data_for_contingency <- function(df)
+{
+  if ("D1" %in% names(df)) {
+    # What is your gender?
+    # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = prefer not to answer
+    # Self-describe responses are usually bad faith responses, so drop them.
+    df <- filter(df, .data$D1 != 4)
+  }
+  return(df)
+}
+
 #' Fix translation error in Wave 6.
 #'
 #' In Wave 6's first deployment, some of the translations swapped the order of
diff --git a/facebook/delphiFacebook/man/code_addl_mental_health.Rd b/facebook/delphiFacebook/man/code_addl_mental_health.Rd
new file mode 100644
index 000000000..59dabcf00
--- /dev/null
+++ b/facebook/delphiFacebook/man/code_addl_mental_health.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contingency_variables.R
+\name{code_addl_mental_health}
+\alias{code_addl_mental_health}
+\title{Additional mental health indicators}
+\usage{
+code_addl_mental_health(input_data, wave)
+}
+\arguments{
+\item{input_data}{input data frame of raw survey data}
+
+\item{wave}{integer indicating survey version}
+}
+\value{
+augmented data frame
+}
+\description{
+Additional mental health indicators
+}
diff --git a/facebook/delphiFacebook/man/filter_data_for_contingency.Rd b/facebook/delphiFacebook/man/filter_data_for_contingency.Rd
new file mode 100644
index 000000000..7f961c5c3
--- /dev/null
+++ b/facebook/delphiFacebook/man/filter_data_for_contingency.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/responses.R
+\name{filter_data_for_contingency}
+\alias{filter_data_for_contingency}
+\title{Filter out low-quality data for contingency tables}
+\usage{
+filter_data_for_contingency(df)
+}
+\arguments{
+\item{df}{data frame of responses}
+}
+\description{
+Filter out low-quality data for contingency tables
+}

From 7885d0bad1cc38c7ae091d8307ec299ede15a4ed Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 24 Jun 2022 17:31:05 -0400
Subject: [PATCH 40/49] return empty result if n=1 to avoid svydesign error

---
 .../delphiFacebook/R/contingency_calculate.R  | 35 ++++++++++++++-----
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_calculate.R b/facebook/delphiFacebook/R/contingency_calculate.R
index a5ff70676..d9e9dc208 100644
--- a/facebook/delphiFacebook/R/contingency_calculate.R
+++ b/facebook/delphiFacebook/R/contingency_calculate.R
@@ -125,15 +125,32 @@ post_convert_count_to_pct <- function(df) {
 compute_numeric_mean <- function(response, weight, sample_size, total_represented) {
   assert(length(response) == length(weight))
   
+  if (length(response) == 1) {
+    # svydesign complains if given only one response, so return an empty df
+    # instead. This group will be dropped anyway.
+    return(list(
+      val = NA_real_,
+      se = NA_real_,
+      sd = NA_real_,
+      p25 = NA_real_,
+      p50 = NA_real_,
+      p75 = NA_real_,
+      sample_size = NA_real_,
+      effective_sample_size = NA_real_,
+      represented = NA_real_
+    ))
+  }
+  
   design <- svydesign(id = ~1, weight = ~weight, data = data.frame(response, weight))
-  return(list(val = as.data.frame(svymean(~response, na.rm = TRUE, design = design))[,"mean"],
-              se = NA_real_,
-              sd = as.data.frame(sqrt(svyvar(~response, na.rm = TRUE, design = design)))[,"variance"],
-              p25 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.25))[,"0.25"],
-              p50 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.5))[,"0.5"],
-              p75 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.75))[,"0.75"],
-              sample_size = sample_size,
-              effective_sample_size = sample_size,
-              represented = total_represented
+  return(list(
+    val = as.data.frame(svymean(~response, na.rm = TRUE, design = design))[,"mean"],
+    se = NA_real_,
+    sd = as.data.frame(sqrt(svyvar(~response, na.rm = TRUE, design = design)))[,"variance"],
+    p25 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.25))[,"0.25"],
+    p50 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.5))[,"0.5"],
+    p75 = as.data.frame(oldsvyquantile(~response, na.rm = TRUE, design = design, quantiles = 0.75))[,"0.75"],
+    sample_size = sample_size,
+    effective_sample_size = sample_size,
+    represented = total_represented
   ))
 }

From c72d452898e2571ff37612a53781697e3b1a685f Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 24 Jun 2022 17:31:23 -0400
Subject: [PATCH 41/49] respect parallel_max_cores

---
 facebook/delphiFacebook/R/contingency_run.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_run.R b/facebook/delphiFacebook/R/contingency_run.R
index 9ea1edfba..104dbef22 100644
--- a/facebook/delphiFacebook/R/contingency_run.R
+++ b/facebook/delphiFacebook/R/contingency_run.R
@@ -23,7 +23,7 @@ run_contingency_tables <- function(params) {
       warning("Could not detect the number of CPU cores; parallel mode disabled")
       params$parallel <- FALSE
     } else {
-      options(mc.cores = cores)
+      options(mc.cores = min(params$parallel_max_cores, cores))
       msg_plain(paste0("Running on ", cores, " cores"))
     }
   }

From 6760ce3ec7f0917fcb20f054a806b0fe78aa4435 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Fri, 24 Jun 2022 18:43:36 -0400
Subject: [PATCH 42/49] retain field names when adding geo info

---
 facebook/delphiFacebook/R/contingency_write.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index 01f2346a2..93ebe5d4a 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -157,7 +157,12 @@ add_geo_vars <- function(data, params, geo_type) {
   # Insert the geographic variables in place of the "geo_id" variable.
   index <- which(names(data) == "geo_id")
   before <- if (index > 1) data[, 1:(index-1)] else NULL
-  after <- data[, (index+1):ncol(data)]
+  
+  if (ncol(data) == 1) {
+    after <- NULL
+  } else {
+    after <- select(data, (index+1):ncol(data))
+  }
   result <- bind_cols(before, geo_vars, after)
   
   return(result)

From ebcb8a4116c2763c3f872813db22304f5193b232 Mon Sep 17 00:00:00 2001
From: nmdefries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 27 Jun 2022 16:02:42 -0400
Subject: [PATCH 43/49] Update facebook/delphiFacebook/R/responses.R

Co-authored-by: Alex Reinhart <alex@refsmmat.com>
---
 facebook/delphiFacebook/R/responses.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/responses.R b/facebook/delphiFacebook/R/responses.R
index e9d53936d..61919f76e 100644
--- a/facebook/delphiFacebook/R/responses.R
+++ b/facebook/delphiFacebook/R/responses.R
@@ -405,7 +405,7 @@ filter_data_for_contingency <- function(df)
     # What is your gender?
     # Coded as 1 = male, 2 = female, 3 = non-binary, 4 = self-describe, 5 = prefer not to answer
     # Self-describe responses are usually bad faith responses, so drop them.
-    df <- filter(df, .data$D1 != 4)
+    df <- filter(df, is.na(.data$D1) | .data$D1 != 4)
   }
   return(df)
 }

From 78c8d4d78fd52709ec84fac82c30b47dea708e65 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 27 Jun 2022 16:13:27 -0400
Subject: [PATCH 44/49] combine select and mutate

---
 facebook/delphiFacebook/R/contingency_write.R | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_write.R b/facebook/delphiFacebook/R/contingency_write.R
index 93ebe5d4a..eb6c2ec89 100644
--- a/facebook/delphiFacebook/R/contingency_write.R
+++ b/facebook/delphiFacebook/R/contingency_write.R
@@ -122,17 +122,11 @@ add_geo_vars <- function(data, params, geo_type) {
     )
 
     rest <- left_join(rest, counties, by = c("county_fips" = "fips")) %>%
-      mutate(
+      select(
         region = .data$state_id,
         state = .data$state_id,
         county = .data$county_name,
         county_fips = .data$county_fips
-      ) %>% 
-      select(
-        .data$region,
-        .data$state,
-        .data$county,
-        .data$county_fips
       )
     
     # Fill in state fips and GID_1

From a558503f631c5a926927286c3bd98e0e6cf62c9c Mon Sep 17 00:00:00 2001
From: nmdefries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 11 Jul 2022 13:05:16 -0700
Subject: [PATCH 45/49] High blood pressure code

Co-authored-by: Alex Reinhart <alex@refsmmat.com>
---
 facebook/delphiFacebook/R/contingency_variables.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 99771ecc8..0101e580b 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -151,7 +151,7 @@ code_health <- function(input_data, wave) {
     comorbidities <- split_options(input_data$C1)
     
     input_data$comorbidheartdisease <- is_selected(comorbidities, "3")
-    input_data$comorbid_high_blood_pressure <- is_selected(comorbidities, "5")
+    input_data$comorbid_high_blood_pressure <- is_selected(comorbidities, "4")
     input_data$comorbid_asthma <- is_selected(comorbidities, "5")
     input_data$comorbidcancer <- is_selected(comorbidities, "2")
     input_data$comorbidkidneydisease <- is_selected(comorbidities, "7")

From 135efce2dffd090b113115a992f6a1bfa0310a53 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 11 Jul 2022 16:27:33 -0400
Subject: [PATCH 46/49] name symp_other_unusual

---
 facebook/delphiFacebook/R/contingency_variables.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index 0101e580b..d4d59052a 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1195,7 +1195,7 @@ code_addl_symptoms <- function(input_data, wave) {
     input_data$symp_nausea_unusual <- is_selected(symptoms, "11")
     input_data$symp_diarrhea_unusual <- is_selected(symptoms, "12")
     input_data$symp_loss_smell_taste_unusual <- is_selected(symptoms, "13")
-    input_data$symp_loss_smell_taste_unusual <- is_selected(symptoms, "14")
+    input_data$symp_other_unusual <- is_selected(symptoms, "14")
     input_data$symp_eye_pain_unusual <- is_selected(symptoms, "16")
     input_data$symp_chills_unusual <- is_selected(symptoms, "17")
     input_data$symp_headache_unusual <- is_selected(symptoms, "18")
@@ -1293,12 +1293,12 @@ code_addl_symptoms <- function(input_data, wave) {
     input_data$symp_nausea_unusual <- NA
     input_data$symp_diarrhea_unusual <- NA
     input_data$symp_loss_smell_taste_unusual <- NA
+    input_data$symp_other_unusual <- NA
     input_data$symp_eye_pain_unusual <- NA
     input_data$symp_chills_unusual <- NA
     input_data$symp_headache_unusual <- NA
     input_data$symp_sleep_changes_unusual <- NA
     input_data$symp_stuffy_nose_unusual <- NA
-    input_data$symp_stuffy_nose_unusual <- NA
   }
 
   if ("B4" %in% names(input_data)) {

From e39c044eb65d146f2322c91dce8726a5f597d824 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 11 Jul 2022 18:52:28 -0400
Subject: [PATCH 47/49] make hh_direct_contact out of all respondents

---
 facebook/delphiFacebook/R/contingency_variables.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index d4d59052a..bf85322c8 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1344,10 +1344,14 @@ code_behaviors <- function(input_data, wave) {
     input_data$c_direct_contact_covid <- NA_real_
   }
 
-  if ("C12" %in% names(input_data)) {
+  if (all(c("C11", "C12") %in% names(input_data))) {
     # C12: was the person in C11 a member of your household
     # Coded as 1 = Yes, 2 = No
-    input_data$c_direct_contact_covid_hh <- input_data$C12 == 1
+    input_data$c_direct_contact_covid_hh <- case_when(
+      input_data$C11 == 1 & input_data$C12 == 1 ~ 1,
+      input_data$C11 == 2 | input_data$C12 == 2 ~ 0,
+      TRUE ~ NA_real_
+    )
   } else {
     input_data$c_direct_contact_covid_hh <- NA_real_
   }

From 5044a06466f03ee9011b808d218cccd59d042d85 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Mon, 11 Jul 2022 19:06:04 -0400
Subject: [PATCH 48/49] ignore idk from E3 school measures

---
 facebook/delphiFacebook/R/contingency_variables.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index bf85322c8..a00bdd7d9 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -1679,7 +1679,10 @@ code_addl_demographic <- function(input_data, wave) {
   }
 
   if ("E3" %in% names(input_data)) {
-    school_measures <- split_options(input_data$E3)
+    school_measures <- input_data$E3
+    # Remove "I don't know" responses.
+    school_measures  <- ifelse(school_measures == "16", NA_character_, school_measures)
+    school_measures <- split_options(school_measures)
 
     input_data$children_school_measure_mask_students <- is_selected(school_measures, "1")
     input_data$children_school_measure_mask_teachers <- is_selected(school_measures, "2")

From 07eceff21c46b357c091eb1b6f4ddb6de6809463 Mon Sep 17 00:00:00 2001
From: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Date: Wed, 13 Jul 2022 19:36:53 -0400
Subject: [PATCH 49/49] ignore B7 in wave 10

---
 facebook/delphiFacebook/R/contingency_variables.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/facebook/delphiFacebook/R/contingency_variables.R b/facebook/delphiFacebook/R/contingency_variables.R
index c3bd1d1eb..01ce19117 100644
--- a/facebook/delphiFacebook/R/contingency_variables.R
+++ b/facebook/delphiFacebook/R/contingency_variables.R
@@ -324,7 +324,13 @@ code_addl_vaccines <- function(input_data, wave) {
     input_data$t_unusual_symptom_hospital <- NA
   }
 
-  if ("B7" %in% names(input_data)) {
+  if ("B7" %in% names(input_data) && wave != 10) {
+    # Before Wave 10, B7 was asked of respondents who selected > 0 items for B2c ("are 
+    # any of your symptoms unusual?"). In Wave 10, the display logic changed so that B7 
+    # is only shown when exactly 0 items (not even "none of the above") are selected on 
+    # B2 ("do you have any of these symptoms?"), meaning the respondent left the question 
+    # entirely blank. Discard these responses.
+    # 
     # Coded as 8 = no medical care sought, 1-6 = various types of medical care sought,
     # 7 = care sought but not received
     unusual_symptoms_care <- split_options(input_data$B7)