Merge branch 'main' into works_lab_fio2

docs/guide.rst

@@ -540,7 +540,9 @@ followup vaccination data is noisy and should be discarded.
 COVID-19 vaccine
 
 **vaccinated_covid19_dates**: List. Dates when subject received a COVID-19
-vaccine.
+vaccine. Dates are not necessarily inclusive of all doses; a single date will
+most often be the date of the most recent dose, but a single date does not preclude
+a subject from having recieved multiple doses.
 
 Visit
 -----
@@ -585,7 +587,7 @@ General drug types
 ~~~~~~~~~~~~~~~~~~
 
 The general drug categories *antiviral*, *antibiotic*, *corticosteroid*,
-*experimental_agent*, *antimalarial* and *delirium* all have a set of three
+*antimalarial* and *delirium* all have a set of three
 hierarchical attributes, e.g. for antivirals:
 
 + **treatment_antiviral**: Bool. If antivirals have been administered during the visit
@@ -675,7 +677,8 @@ delirium?
 monoclonal antibodies?
 
 **treatment_other**: Set. Any other treatments, or treatments recorded
-as free text fields, should be recorded here.
+as free text fields, should be recorded here. Can include drugs described
+as 'experimental agents'; trial drugs will be recorded in study metadata.
 
 **treatment_pacing**: Bool. Did the subject receive heart pacing during
 the visit?

isaric/parsers/brazil-followup.toml

@@ -211,6 +211,16 @@
   description = "Admission to an Intensive Care Unit (ICU / CTI)"
   ref = "Y/N"
 
+[subject.vaccinated_covid19]
+  field = "flw_cov_vacc"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [{ field = "flw_vacc_last_dose" }]
+  # context = ["Date of most recent dose"]
+
   # VISIT
   # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/ccp-cameroon.toml

@@ -272,6 +272,19 @@
     { field = "q14_treatment_outcome", if = { q1_treatment_outcome = 5 } },
   ]
 
+[subject.vaccinated_covid19]
+  field = "q1_vaccination"
+  values = { 1 = true, 0 = false }
+
+[subject.vaccinated_covid19_dates]
+  combinedType = "list"
+  excludeWhen = "none"
+  fields = [
+    { field = "q5_vaccination" },
+    { field = "q6_vaccination" },
+    { field = "q7_vaccination" },
+  ]
+
 [visit]
   country_iso3 = "CMR"
 
@@ -352,11 +365,6 @@
     { field = "q16_treatment", description = "16) Inotropes - vasopressors / 	Inotropes -vasopresseurrs?", ref = "Y/N" },
   ]
 
-[visit.treatment_experimental_agent]
-  field = "q15_medication"
-  description = "15) ELIXIR COVID and or ADSK COVID (Medication of Mgr Kleda)  / ELIXIR COVID et ou ADSAK COVID (Médicaments de MGR KLEDA) "
-  ref = "Y/N"
-
 [visit.treatment_dialysis]
   field = "q15_treatment"
   description = "15) Renal replacement therapy (RRT) or dialysis / 	Thérapie de substitution rénale (TRS) ou dialyse ?"
@@ -429,6 +437,7 @@
     { field = "q10_health_care" },
   ]
 
+
 [visit.outcome] # Q: Should we distinguish between not admitted (discharged before treatment) and discharged?
   # Q1_outcome and q1_treatment_outcome are present on different rows, so using "set" to get both (and therefore have 'discharged' vs ['hospitalised', 'discharged']) won't work.
   combinedType = "firstNonNull"

isaric/parsers/ccp-ghana.toml

@@ -4,6 +4,14 @@
   name = "ccp-ghana"
   description = "COVID-19 CCP Patient Data - ALERRT Ghana"
   defaultDateFormat = "%d/%m/%Y"
+  experimental_agents = [
+    'Chloroquine',
+    'Hydroxychloroquine',
+    'Remdesivir',
+    'IL6/IL1 inhibitors',
+    'Convalescent plasma',
+    'Tocilizumab',
+  ]
 
   [adtl.tables]
 
@@ -598,6 +606,7 @@
 
 [visit.treatment_antibiotics_type]
   combinedType = "set"
+  excludeWhen = "none"
   description = "Antibiotic given - free text field"
   fields = [{ field = "sup_antibiotic_agent" }]
 
@@ -607,9 +616,21 @@
   ref = "Y/N/NK"
 
 [visit.treatment_antimalarial]
-  field = "daily_antimal_cmyn"
-  description = "Antimalarial agent?"
-  ref = "Y/N/NK"
+  combinedType = "any"
+  excludeWhen = "none"
+  fields = [
+    { field = "daily_antimal_cmyn", description = "Antimalarial agent?", ref = "Y/N/NK" },
+    { field = "daily_exper_cmtype___1", values = { 1 = true } },
+    { field = "daily_exper_cmtype___2", values = { 1 = true } },
+  ]
+
+[visit.treatment_antimalarial_type]
+  combinedType = "set"
+  excludeWhen = "none"
+  fields = [
+    { field = "daily_exper_cmtype___1", values = { 1 = "Chloroquine" } },
+    { field = "daily_exper_cmtype___2", values = { 1 = "Hydroxychloroquine" } },
+  ]
 
 [visit.treatment_antivirals]
   combinedType = "any"
@@ -634,6 +655,7 @@
 
 [visit.treatment_antiviral_type_other]
   combinedType = "set"
+  excludeWhen = "none"
   description = "Antiviral agent = other - free text field"
   fields = [{ field = "daily_antiviral_cmoth" }]
 
@@ -688,32 +710,6 @@
     { field = "ecls", ref = "Y/N/NK" },
   ]
 
-
-[visit.treatment_experimental_agent]
-  field = "daily_exper_cmyn"
-  description = "Experimental agent?"
-  ref = "Y/N/NK"
-
-[visit.treatment_experimental_agent_type]
-  description = "Experimental agent - if 'Other' experimental agent, specify"
-  combinedType = "set"
-  excludeWhen = "none"
-  fields = [
-    { field = "daily_exper_cmtype___1", values = { 1 = "Chloroquine" } },
-    { field = "daily_exper_cmtype___2", values = { 1 = "Hydroxychloroquine" } },
-    { field = "daily_exper_cmtype___3", values = { 1 = "Remdesivir" } },
-    { field = "daily_exper_cmtype___4", values = { 1 = "IL6 inhibitor" } },
-    { field = "daily_exper_cmtype___5", values = { 1 = "IL1 inhibitor" } },
-    { field = "daily_exper_cmtype___6", values = { 1 = "Convalescent plasma" } },
-    { field = "daily_exper_cmtype___7", values = { 1 = "Other" } },
-    { field = "disx251s", values = { 3 = "Tocilizumab" } },
-  ]
-
-[visit.treatment_experimental_agent_type_other]
-  combinedType = "set"
-  description = "Experimental agent = other - free text field"
-  fields = [{ field = "daily_exper_cmoth" }]
-
 [visit.treatment_high_flow_nasal_cannula]
   combinedType = "any"
   excludeWhen = "none"
@@ -736,7 +732,6 @@
     { field = "vaso_or_inot", description = "Any vasopressor/inotropic support?", ref = "Y/N/NK" },
   ]
 
-
 [visit.treatment_intravenous_fluids]
   field = "daily_iv_fluids_cmyn"
   description = "Intravenous fluids?"
@@ -785,8 +780,12 @@
     { field = "other_meds", description = "Other Medication" },
     { field = "other_meds_3", description = "Other Medication" },
     { field = "other_meds_2", description = "Other Medication" },
-    # { field = "premeds_other_meds1", description = "Other Medications (1)" }, - preadmission medications
-    # { field = "premeds_other_meds2", description = "Other Medications (2)" },
+    { field = "daily_exper_cmtype___3", values = { 1 = "Remdesivir" } },
+    { field = "daily_exper_cmtype___4", values = { 1 = "IL6 inhibitor" } },
+    { field = "daily_exper_cmtype___5", values = { 1 = "IL1 inhibitor" } },
+    { field = "daily_exper_cmtype___6", values = { 1 = "Convalescent plasma" } },
+    { field = "disx251s", values = { 3 = "Tocilizumab" } },
+    { field = "daily_exper_cmoth" },
   ]
 
 [visit.treatment_oxygen_therapy]

isaric/parsers/ccp-guinea.toml

@@ -4,6 +4,13 @@
   name = "ccp-guinea"
   description = "ccp-guinea"
   defaultDateFormat = "%d/%m/%Y"
+  experimental_agents = [
+    'Chloroquine',
+    'Hydroxychloroquine',
+    'Remdesivir',
+    'IL6/IL1 inhibitors',
+    'Convalescent plasma',
+  ]
 
   [adtl.tables.subject]
     kind = "groupBy"
@@ -521,6 +528,7 @@
 
 [visit.treatment_antibiotics_type]
   combinedType = "set"
+  excludeWhen = "none"
   description = "Antibiotic given - free text field"
   fields = [{ field = "daily_antibiot_cmyn_name" }]
 
@@ -540,9 +548,21 @@
   values = { 1 = true, 0 = false }
 
 [visit.treatment_antimalarial]
-  field = "daily_antimal_cmyn"
-  description = "Antimalarials?"
-  values = { 1 = true, 0 = false }
+  combinedType = "any"
+  excludeWhen = "none"
+  fields = [
+    { field = "daily_antimal_cmyn", description = "Antimalarials?", values = { 1 = true, 0 = false } },
+    { field = "daily_exper_cmtype___1", values = { 1 = true } },
+    { field = "daily_exper_cmtype___2", values = { 1 = true } },
+  ]
+
+[visit.treatment_antimalarial_type]
+  combinedType = "set"
+  excludeWhen = "none"
+  fields = [
+    { field = "daily_exper_cmtype___1", values = { 1 = "Chloroquine" } },
+    { field = "daily_exper_cmtype___2", values = { 1 = "Hydroxychloroquine" } },
+  ]
 
 [visit.treatment_antiviral_type]
   description = "Type of antiviral agent used"
@@ -608,28 +628,6 @@
     { field = "vaso_or_inot", description = "Any administration of vasopressor/inotrope?", ref = "Y/N" },
   ]
 
-[visit.treatment_experimental_agent]
-  field = "daily_exper_cmyn"
-  values = { 1 = true, 0 = false }
-
-[visit.treatment_experimental_agent_type]
-  combinedType = "set"
-  excludeWhen = "none"
-  fields = [
-    { field = "daily_exper_cmtype___1", values = { 1 = "Chloroquine" } },
-    { field = "daily_exper_cmtype___2", values = { 1 = "Hydroxychloroquine" } },
-    { field = "daily_exper_cmtype___3", values = { 1 = "Remdesivir" } },
-    { field = "daily_exper_cmtype___4", values = { 1 = "IL6 inhibitor" } },
-    { field = "daily_exper_cmtype___5", values = { 1 = "IL1 inhibitor" } },
-    { field = "daily_exper_cmtype___6", values = { 1 = "Convalescent plasma" } },
-    { field = "daily_exper_cmtype___7", values = { 1 = "Other" } },
-  ]
-
-[visit.treatment_experimental_agent_type_other]
-  combinedType = "set"
-  description = "Experimental agent = other - free text field"
-  fields = [{ field = "daily_exper_cmoth" }]
-
 [visit.treatment_inotropes_vasopressors]
   field = "vaso_or_inot"
   description = "Any administration of vasopressor/inotrope?"
@@ -650,6 +648,11 @@
     { field = "other_meds_1", description = "Other treatment" },
     { field = "other_meds_2", description = "Other treatment" },
     { field = "other_intervs_specify" },
+    { field = "daily_exper_cmtype___3", values = { 1 = "Remdesivir" } },
+    { field = "daily_exper_cmtype___4", values = { 1 = "IL6 inhibitor" } },
+    { field = "daily_exper_cmtype___5", values = { 1 = "IL1 inhibitor" } },
+    { field = "daily_exper_cmtype___6", values = { 1 = "Convalescent plasma" } },
+    { field = "daily_exper_cmoth" },
   ]
 
 [visit.treatment_oxygen_therapy]

isaric/parsers/ccp-senegal.toml

@@ -4,6 +4,7 @@
   name = "ccp-senegal"
   description = "CCP Senegal"
   defaultDateFormat = "%d/%m/%Y"
+  experimental_agents = ['Hydroxychloroquine']
 
   [adtl.tables.subject]
     kind = "groupBy"
@@ -340,13 +341,21 @@
 
 [visit.treatment_antimalarial]
   combinedType = "any"
+  excludeWhen = "none"
 
   [[visit.treatment_antimalarial.fields]]
     fieldPattern = "tmt_pdthosp_nom.*"
 
     [visit.treatment_antimalarial.fields.values]
       HYDROXYCHLOROQUINE = true
 
+[visit.treatment_antimalarial_type]
+  combinedType = "set"
+  excludeWhen = "none"
+  fields = [
+    { fieldPattern = "tmt_pdthosp_nom.*", values = { HYDROXYCHLOROQUINE = "Hydroxychloroquine" } },
+  ]
+
 [visit.treatment_antibiotics]
   combinedType = "any"
 
@@ -370,6 +379,7 @@
 
 [visit.treatment_antibiotics_type]
   combinedType = "set"
+  excludeWhen = "none"
 
   [[visit.treatment_antibiotics_type.fields]]
     fieldPattern = "tmt_pdthosp_nom.*"
@@ -389,13 +399,6 @@
       TINIDAZOLE = "Tinidazole"
       "TOBREX COLLYRE" = "Tobramycin"
 
-[visit.treatment_experimental_agent_type]
-  combinedType = "set"
-  excludeWhen = "none"
-  fields = [
-    { fieldPattern = "tmt_pdthosp_nom.*", values = { HYDROXYCHLOROQUINE = "Hydroxychloroquine" } },
-  ]
-
 [visit.treatment_antifungal_agent]
   combinedType = "any"
 

isaric/parsers/ccp-uganda-v2.toml

@@ -244,6 +244,15 @@
       { field = "icu_date", apply = { function = "isNotNull" } },
     ]
 
+  [subject.vaccinated_covid19]
+    field = "vaccin_covid"
+    values = { 1 = true, 0 = false }
+
+  [subject.vaccinated_covid19_dates]
+    combinedType = "list"
+    excludeWhen = "none"
+    fields = [{ field = "vaccin_date" }]
+
     # VISIT
     # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"
 

isaric/parsers/cocoa_pediatrics.toml

@@ -269,11 +269,6 @@
     description = "Renal replacement therapy (RRT) or dialysis?"
     ref = "Y/N/NK"
 
-  [visit.treatment_experimental_agent]
-    field = "exprmntl_cmyn_v2"
-    description = "Experimental agent?"
-    ref = "Y/N/NK"
-
   [visit.treatment_inotropes_vasopressors]
     field = "inotrop_prtrt_v3"
     description = "Inotropes / vasopressors?"

isaric/parsers/datcov-southafrica.toml

@@ -291,6 +291,19 @@
       { field = "flw_icu", description = "If ever admitted to hospital, were you admitted to intensive care (ICU/ITU)?", values = { 0 = false, 1 = true } },
     ]
 
+  [subject.vaccinated_covid19]
+    field = "Vaccinated"
+    values = { 1 = true, 0 = false }
+
+  [subject.vaccinated_covid19_dates]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "First Dose Date" },
+      { field = "Second Dose Date" },
+      { field = "Booster Dose Date" },
+    ]
+
 [visit]
   country_iso3 = "ZAF"