#32 first draft of combined metadata

inst/templates/ad_advs.R

@@ -0,0 +1,130 @@
+# Name: ADVS
+#
+# Label: Vital Signs Analysis Dataset
+#
+# Input: adsl, vs
+library(admiral)
+library(pharmaversesdtm) # Contains example datasets from the CDISC pilot project
+library(dplyr)
+library(lubridate)
+library(stringr)
+
+#Modified ADVS template to be added here
+#
+#
+#
+#
+
+
+# Creation of the Growth metadata combining WHO and CDC
+# Default reference sources: WHO for children <2 yrs old (<730 days),
+# and CDC for children >=2 yrs old (>= 730.5 days)
+# Load WHO and CDC metadata datasets ----
+
+message("Please be aware that our default reference source is in our metadata :
+        WHO for <2 yrs old children, and CDC for >=2 yrs old children.
+The user could replace these metadata with their own chosen metadata")
+
+## BMI for age
+data(WHO_bmi_for_age_boys)
+data(WHO_bmi_for_age_girls)
+data(cdc_bmiage)
+
+bmi_for_age <- who_bmi_for_age_boys %>%
+  filter(Day <= 729) %>%
+  mutate(SEX = "M") %>%
+  rbind(who_bmi_for_age_girls %>%
+    filter(Day <= 729) %>%
+    mutate(SEX = "F")) %>%
+  rename(AGE = Day) %>%
+  rbind(cdc_bmiage %>%
+    mutate(
+      SEX = case_when(
+        SEX == 1 ~ "M",
+        SEX == 2 ~ "F",
+        TRUE ~ NA_character_
+      ),
+      AGE = AGE * 30.4375
+    )) %>%
+  arrange(AGE, SEX)
+
+## HEIGHT for age
+data(who_lgth_ht_for_age_boys)
+data(who_lgth_ht_for_age_girls)
+data(cdc_htage)
+
+height_for_age <- who_lgth_ht_for_age_boys %>%
+  filter(Day <= 729) %>%
+  mutate(SEX = "M") %>%
+  rbind(who_lgth_ht_for_age_girls %>%
+    filter(Day <= 729) %>%
+    mutate(SEX = "F")) %>%
+  rename(AGE = Day) %>%
+  rbind(cdc_htage %>%
+    mutate(
+      SEX = case_when(
+        SEX == 1 ~ "M",
+        SEX == 2 ~ "F",
+        TRUE ~ NA_character_
+      ),
+      AGE = AGE * 30.4375
+    )) %>%
+  arrange(AGE, SEX)
+
+## WEIGHT for age
+data(who_wt_for_age_boys)
+data(who_wt_for_age_girls)
+data(cdc_wtage)
+
+weight_for_age <- who_wt_for_age_boys %>%
+  filter(Day <= 729) %>%
+  mutate(SEX = "M") %>%
+  rbind(who_wt_for_age_girls %>%
+    filter(Day <= 729) %>%
+    mutate(SEX = "F")) %>%
+  rename(AGE = Day) %>%
+  rbind(cdc_wtage %>%
+    mutate(
+      SEX = case_when(
+        SEX == 1 ~ "M",
+        SEX == 2 ~ "F",
+        TRUE ~ NA_character_
+      ),
+      AGE = AGE * 30.4375
+    )) %>%
+  arrange(AGE, SEX)
+
+
+## WHO - HEAD CIRCUMFERENCE for age
+data(who_hc_for_age_boys)
+data(who_hc_for_age_girls)
+
+who_hc_for_age <- who_hc_for_age_boys %>%
+  filter(Day <= 729) %>%
+  mutate(SEX = "M") %>%
+  rbind(who_hc_for_age_girls %>%
+    filter(Day <= 729) %>%
+    mutate(SEX = "F")) %>%
+  rename(AGE = Day) %>%
+  arrange(AGE, SEX)
+
+## WHO - WEIGHT/HEIGHT
+data(who_wt_for_ht_boys)
+data(who_wt_for_ht_girls)
+data(who_wt_for_lgth_boys)
+data(who_wt_for_lgth_girls)
+
+who_wt_for_ht_lgth <- who_wt_for_ht_boys %>%
+  mutate(SEX = "M") %>%
+  rbind(who_wt_for_ht_girls %>%
+    mutate(SEX = "F")) %>%
+  mutate(MEASURE = "HEIGHT") %>%
+  rename(HEIGHT_LENGTH = Height) %>%
+  rbind(who_wt_for_lgth_boys %>%
+    mutate(SEX = "M") %>%
+    rbind(who_wt_for_lgth_girls %>%
+      mutate(SEX = "F")) %>%
+    mutate(MEASURE = "LENGTH") %>%
+    rename(HEIGHT_LENGTH = Length))
+
+