diff --git a/isaric/parsers/ccp-ghana.toml b/isaric/parsers/ccp-ghana.toml index cbbd5d7..e5ffb26 100644 --- a/isaric/parsers/ccp-ghana.toml +++ b/isaric/parsers/ccp-ghana.toml @@ -33,6 +33,7 @@ common = { visit_id = { field = "record_id", sensitive = true } } [adtl.defs] + checkbox = { values = { 1 = true } } "Y/N/NK" = { values = { 0 = false, 1 = true } } uid = { field = "record_id", sensitive = true } @@ -620,8 +621,8 @@ 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 } }, + { field = "daily_exper_cmtype___1", ref = "checkbox" }, + { field = "daily_exper_cmtype___2", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] @@ -715,7 +716,7 @@ excludeWhen = "none" fields = [ { field = "can_oxy_ther", description = "High-flow nasal canula oxygen therapy", ref = "Y/N/NK" }, - { field = "overall_oxygen_cmtype___2", description = "Oxygen therapy interface: HF nasal cannula", ref = "Y/N/NK" }, + { field = "overall_oxygen_cmtype___2", description = "Oxygen therapy interface: HF nasal cannula", ref = "checkbox" }, { field = "daily_oxygen_cmtype_1", description = "Oxygen therapy interface: HF nasal cannula", ref = "Y/N/NK" }, ] @@ -799,27 +800,27 @@ [[visit.treatment_oxygen_therapy.fields]] field = "overall_oxygen_cmtype___1" description = "Oxygen therapy?" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_oxygen_therapy.fields]] field = "overall_oxygen_cmtype___2" description = "Oxygen therapy?" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_oxygen_therapy.fields]] field = "overall_oxygen_cmtype___3" description = "Oxygen therapy?" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_oxygen_therapy.fields]] field = "overall_oxygen_cmtype___4" description = "Oxygen therapy?" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_oxygen_therapy.fields]] field = "overall_oxygen_cmtype___5" description = "Oxygen therapy?" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_oxygen_therapy.fields]] field = "daily_oxygen_cmtype_1" diff --git a/isaric/parsers/ccp-guinea.toml b/isaric/parsers/ccp-guinea.toml index a06f308..a2ce24b 100644 --- a/isaric/parsers/ccp-guinea.toml +++ b/isaric/parsers/ccp-guinea.toml @@ -32,6 +32,7 @@ [adtl.defs] "Y/N" = { values = { 1 = true, 2 = false } } + checkbox = { values = { 1 = true } } [adtl.defs.admissionDateHierarchy] combinedType = "firstNonNull" @@ -552,8 +553,8 @@ 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 } }, + { field = "daily_exper_cmtype___1", ref = "checkbox" }, + { field = "daily_exper_cmtype___2", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml index 17940e7..9609618 100644 --- a/isaric/parsers/ccp-uganda-v2.toml +++ b/isaric/parsers/ccp-uganda-v2.toml @@ -26,6 +26,9 @@ 1 = true 0 = false + [adtl.defs.checkbox.values] + 1 = true + [adtl.defs.admissionDateHierarchy] combinedType = "firstNonNull" fields = [ @@ -598,7 +601,7 @@ combinedType = "any" fields = [ { field = "cof", ref = "Y/N" }, - { field = "sick_symp___2", values = { 1 = true, 0 = false } }, + { field = "sick_symp___2", ref = "checkbox" }, ] [[observation]] @@ -640,7 +643,7 @@ ] } } duration_type = "event" phase = "admission" - is_present = { field = "sick_symp___3", values = { 1 = true, 0 = false } } + is_present = { field = "sick_symp___3", ref = "checkbox" } [[observation]] name = "diarrhoea" @@ -674,7 +677,7 @@ date = { field = "onset_date" } duration_type = "event" phase = "admission" - is_present = { field = "sick_symp___1", values = { 1 = true } } + is_present = { field = "sick_symp___1", ref = "checkbox" } [[observation]] name = "history_of_fever" diff --git a/isaric/parsers/cocoa_pediatrics.toml b/isaric/parsers/cocoa_pediatrics.toml index 0535be1..d96b5a4 100644 --- a/isaric/parsers/cocoa_pediatrics.toml +++ b/isaric/parsers/cocoa_pediatrics.toml @@ -24,6 +24,7 @@ [adtl.defs] "Y/N/NK" = { values = { 0 = false, 1 = true } } + checkbox = { values = { 1 = true } } [adtl.defs.admissionDateHierarchy] combinedType = "firstNonNull" @@ -376,7 +377,7 @@ name = "cough" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___2", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___2", ref = "checkbox" } [[observation]] name = "cough_dry" @@ -414,7 +415,7 @@ name = "diarrhoea" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___10", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___10", ref = "checkbox" } [[observation]] name = "diastolic_blood_pressure_mmHg" @@ -440,7 +441,7 @@ name = "hepatomegaly" phase = "admission" date = { field = "hostdat" } - is_present = { field = "cardiac_failure___4", values = { 1 = true } } + is_present = { field = "cardiac_failure___4", ref = "checkbox" } [[observation]] name = "history_of_fever" @@ -454,7 +455,7 @@ name = "history_of_fever" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___1", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___1", ref = "checkbox" } [[observation]] name = "fatigue_malaise" @@ -480,7 +481,7 @@ name = "feeding_intolerance_pediatrics" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___11", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___11", ref = "checkbox" } [[observation]] name = "inability_to_walk" @@ -556,8 +557,8 @@ combinedType = "any" excludeWhen = "none" fields = [ - { field = "myalgia_ceoccur_v2", values = { 1 = true } }, - { field = "jointpain_ceoccur_v2", values = { 1 = true } }, + { field = "myalgia_ceoccur_v2", ref = "checkbox" }, + { field = "jointpain_ceoccur_v2", ref = "checkbox" }, ] [[observation]] @@ -660,7 +661,7 @@ name = "shortness_of_breath" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___3", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___3", ref = "checkbox" } [[observation]] name = "skin_rash" @@ -674,7 +675,7 @@ name = "skin_rash" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___5", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___5", ref = "checkbox" } [[observation]] name = "skin_ulcers" @@ -740,7 +741,7 @@ name = "vomiting_nausea" phase = "followup" date = { field = "date" } - is_present = { field = "ongoing_symptoms___9", values = { 1 = true } } + is_present = { field = "ongoing_symptoms___9", ref = "checkbox" } [[observation]] name = "blantyre_coma_score" diff --git a/isaric/parsers/datcov-southafrica.toml b/isaric/parsers/datcov-southafrica.toml index 65b4cd4..70040cd 100644 --- a/isaric/parsers/datcov-southafrica.toml +++ b/isaric/parsers/datcov-southafrica.toml @@ -22,6 +22,9 @@ 1 = true 0 = false + [adtl.defs.checkbox.values] + 1 = true + [adtl.defs.subjectId] combinedType = "firstNonNull" fields = [{ field = "PatientId" }, { field = "NICDCaseID" }] @@ -135,35 +138,35 @@ [subject.has_chronic_hematologic_disease] field = "flw_ongoing_chronic_list___12" description = "Diagnosed, ongoing condition before COVID-19 diagnosis: Blood disorder" - ref = "Y/N/NK" + ref = "checkbox" [subject.has_asplenia] field = "flw_ongoing_chronic_list___10" - ref = "Y/N/NK" + ref = "checkbox" description = "Asplenia" [subject.has_tuberculosis] combinedType = "any" fields = [ { field = "Tuberculosis Active", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan] - { field = "flw_ongoing_chronic_list___20", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___20", ref = "checkbox" }, ] [subject.has_dementia] field = "flw_ongoing_chronic_list___15" - ref = "Y/N/NK" + ref = "checkbox" description = "Dementia" [subject.has_rheumatologic_disorder] field = "flw_ongoing_chronic_list___13" - ref = "Y/N/NK" + ref = "checkbox" description = "Rhemumatologic disorder" [subject.has_hiv] combinedType = "any" fields = [ { field = "HIV Positive", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', nan]} - { field = "flw_ongoing_chronic_list___16", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___16", ref = "checkbox" }, ] [subject.has_obesity] @@ -175,14 +178,14 @@ combinedType = "any" fields = [ { field = "Hypertension", values = { 'Yes' = true, 'No' = false } }, - { field = "flw_ongoing_chronic_list___2", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___2", ref = "checkbox" }, ] [subject.has_malignant_neoplasm] combinedType = "any" fields = [ { field = "Malignancy", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan] - { field = "flw_ongoing_chronic_list___11", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___11", ref = "checkbox" }, ] [subject.has_smoking] @@ -196,30 +199,30 @@ combinedType = "any" fields = [ { field = "Asthma", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan] - { field = "flw_ongoing_chronic_list___3", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___3", ref = "checkbox" }, ] [subject.has_chronic_cardiac_disease] combinedType = "any" fields = [ { field = "Cardiac Disease", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan] - { field = "flw_ongoing_chronic_list___1", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___1", ref = "checkbox" }, ] [subject.has_chronic_kidney_disease] combinedType = "any" fields = [ { field = "Chronic Renal Failure", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan] } - { field = "flw_ongoing_chronic_list___8", ref = "Y/N/NK" }, + { field = "flw_ongoing_chronic_list___8", ref = "checkbox" }, ] [subject.has_diabetes] combinedType = "any" fields = [ - { field = "Diabetes", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan] - { field = "flw_ongoing_chronic_list___5", ref = "Y/N/NK", description = "Diabetes Type 1" }, - { field = "flw_ongoing_chronic_list___6", ref = "Y/N/NK", description = "Diabetes Type 2" }, - { field = "flw_ongoing_chronic_list___7", ref = "Y/N/NK", description = "Diabetes Gestational" }, + { field = "Diabetes", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan] + { field = "flw_ongoing_chronic_list___5", ref = "checkbox", description = "Diabetes Type 1" }, + { field = "flw_ongoing_chronic_list___6", ref = "checkbox", description = "Diabetes Type 2" }, + { field = "flw_ongoing_chronic_list___7", ref = "checkbox", description = "Diabetes Gestational" }, ] # can we assume diabetes as a disease was there before COVID? and so the followup data applies here? @@ -233,14 +236,9 @@ [subject.has_liver_disease] field = "flw_ongoing_chronic_list___9" - ref = "Y/N/NK" + ref = "checkbox" description = "Liver disease" - # [subject.has_hiv_viral_suppression] - # field = "HIV Viral Suppression" - # values = { 'Yes' = true, 'No' = false } - # # values = [nan, 'No', 'Unknown', 'Yes'] - [subject.has_tuberculosis_past] field = "Tuberculosis Past" values = { 'Yes' = true, 'No' = false } diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml index 8a2cfae..16e7f8c 100644 --- a/isaric/parsers/isaric-ccpuk.toml +++ b/isaric/parsers/isaric-ccpuk.toml @@ -13,6 +13,9 @@ 1 = true 2 = false + [adtl.defs.checkbox.values] + 1 = true + [adtl.defs.admissionDateHierarchy] combinedType = "firstNonNull" fields = [ @@ -445,7 +448,7 @@ [visit.treatment_antimalarial] field = "antiviral_cmtrt___7" - values = { 1 = true } + ref = "checkbox" [visit.treatment_antimalarial_type] combinedType = "set" diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml index 44b554e..adff30b 100644 --- a/isaric/parsers/isaric-rapid.toml +++ b/isaric/parsers/isaric-rapid.toml @@ -627,14 +627,14 @@ { field = "overall_antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent?" }, { field = "daily_antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent?" }, { field = "antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent on the first day of admission?" }, - { fieldPattern = ".*exper_cmtype___1", values = { 1 = true } }, - { fieldPattern = ".*exper_cmtype___2", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___1", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___2", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___3", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___4", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___5", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___6", values = { 1 = true } }, + { fieldPattern = ".*exper_cmtype___1", ref = "checkbox" }, + { fieldPattern = ".*exper_cmtype___2", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___1", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___2", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___3", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___4", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___5", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___6", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] @@ -659,7 +659,7 @@ { field = "overall_antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent?" }, { field = "daily_antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent?" }, { field = "antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent on the first day of admission?" }, - { fieldPattern = ".*exper_cmtype___3", values = { 1 = true } }, + { fieldPattern = ".*exper_cmtype___3", ref = "checkbox" }, ] [visit.treatment_antiviral_type] @@ -866,7 +866,7 @@ { fieldPattern = ".*oxygen_cmoccur", ref = "Y/N/NK", description = "Oxygen therepy?" }, { field = "ccm_a_fi02_lbyn", ref = "Y/N/NK", description = "Any supplemental oxygen?" }, { field = "ccm_b_hhfnc_prtrt", ref = "Y/N/NK", description = "Humidified high flow nasal cannula (HHFNC)?" }, - { fieldPattern = "overall_oxygen_cmtype.*", values = { 1 = true }, description = "Oxygen therapy? (interface)" }, + { fieldPattern = "overall_oxygen_cmtype.*", ref = "checkbox", description = "Oxygen therapy? (interface)" }, { fieldPattern = ".*oxygen_cmtype", values = { 1 = true, 2 = true, 3 = true, 4 = true }, description = "Oxygen therapy? (interface)" }, { fieldPattern = ".*invasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, { field = "ccm_b_invasive_prtrt", ref = "Y/N/NK", description = "Invasive ventilation?" }, @@ -902,7 +902,7 @@ excludeWhen = "none" fields = [ { field = "ccm_b_hhfnc_prtrt", ref = "Y/N/NK", description = "Humidified high flow nasal cannula (HHFNC)?" }, - { field = "overall_oxygen_cmtype___2", values = { 1 = true }, description = "Oxygen therapy? (interface)" }, + { field = "overall_oxygen_cmtype___2", ref = "checkbox", description = "Oxygen therapy? (interface)" }, { field = "daily_oxygen_cmtype", values = { 2 = true }, description = "Oxygen therapy? (interface)" }, { field = "oxygen_cmtype", values = { 2 = true }, description = "Oxygen therapy? (interface)" }, ] @@ -910,9 +910,9 @@ [visit.treatment_oxygen_mask_prongs] combinedType = "any" fields = [ - { field = "overall_oxygen_cmtype___1", values = { 1 = true }, description = "Nasal prongs" }, - { field = "overall_oxygen_cmtype___3", values = { 1 = true }, description = "Mask" }, - { field = "overall_oxygen_cmtype___4", values = { 1 = true }, description = "Mask with reservoir" }, + { field = "overall_oxygen_cmtype___1", ref = "checkbox", description = "Nasal prongs" }, + { field = "overall_oxygen_cmtype___3", ref = "checkbox", description = "Mask" }, + { field = "overall_oxygen_cmtype___4", ref = "checkbox", description = "Mask with reservoir" }, { field = "oxygen_cmtype", values = { 1 = true, 3 = true, 4 = true }, description = "Oxygen therapy? (interface)" }, { field = "daily_oxygen_cmtype", values = { 1 = true, 3 = true, 4 = true }, description = "Oxygen therapy? (interface)" }, ] diff --git a/isaric/parsers/isaric_washington.toml b/isaric/parsers/isaric_washington.toml index 666686f..a45b8b3 100644 --- a/isaric/parsers/isaric_washington.toml +++ b/isaric/parsers/isaric_washington.toml @@ -24,6 +24,7 @@ [adtl.defs] "Y/N" = { values = { 0 = false, 1 = true } } + checkbox = { values = { 1 = true } } [adtl.defs.countryMap.values] 1 = "USA" @@ -97,30 +98,30 @@ [subject.has_tuberculosis] field = "any_other_pos___4" - values = { 1 = true } + ref = "checkbox" [subject.has_dementia] field = "comorbidities___34" - values = { 1 = true } + ref = "checkbox" [subject.has_obesity] field = "comorbidities___30" - values = { 1 = true } + ref = "checkbox" [subject.has_hiv] combinedType = "any" fields = [ - { field = "comorbidities___22", values = { 1 = true } }, - { field = "any_other_pos___1", values = { 1 = true } }, + { field = "comorbidities___22", ref = "checkbox" }, + { field = "any_other_pos___1", ref = "checkbox" }, ] [subject.has_hypertension] field = "comorbidities___3" - values = { 1 = true } + ref = "checkbox" [subject.has_malignant_neoplasm] field = "comorbidities___20" - values = { 1 = true } + ref = "checkbox" [subject.has_smoking] combinedType = "firstNonNull" @@ -132,40 +133,40 @@ [subject.has_asthma] field = "comorbidities___8" - values = { 1 = true } + ref = "checkbox" [subject.has_chronic_kidney_disease] field = "comorbidities___10" - values = { 1 = true } + ref = "checkbox" [subject.has_chronic_cardiac_disease] combinedType = "any" fields = [ - { field = "comorbidities___2", values = { 1 = true }, description = "Coronary artery disease" }, - { field = "comorbidities___4", values = { 1 = true }, description = "Cardiac arrhythmia" }, - { field = "comorbidities___5", values = { 1 = true }, description = "Congestive heart failure" }, - { field = "comorbidities___6", values = { 1 = true }, description = "Valvular heart disease" }, + { field = "comorbidities___2", ref = "checkbox", description = "Coronary artery disease" }, + { field = "comorbidities___4", ref = "checkbox", description = "Cardiac arrhythmia" }, + { field = "comorbidities___5", ref = "checkbox", description = "Congestive heart failure" }, + { field = "comorbidities___6", ref = "checkbox", description = "Valvular heart disease" }, ] [subject.has_chronic_respiratory_disease] combinedType = "any" fields = [ - { field = "comorbidities___7", values = { 1 = true } }, - { field = "comorbidities___9", values = { 1 = true } }, + { field = "comorbidities___7", ref = "checkbox" }, + { field = "comorbidities___9", ref = "checkbox" }, ] [subject.has_chronic_hematologic_disease] field = "comorbidities___19" - values = { 1 = true } + ref = "checkbox" description = "hematologic malignancy" [subject.has_rheumatologic_disorder] field = "comorbidities___25" - values = { 1 = true } + ref = "checkbox" [subject.has_diabetes] field = "comorbidities___12" - values = { 1 = true } + ref = "checkbox" [subject.diabetes_type] combinedType = "firstNonNull" @@ -178,27 +179,27 @@ [subject.has_liver_disease] combinedType = "any" fields = [ - { field = "comorbidities___14", values = { 1 = true } }, - { field = "comorbidities___15", values = { 1 = true }, description = "Hep B" }, - { field = "comorbidities___16", values = { 1 = true }, description = "Hep C" }, + { field = "comorbidities___14", ref = "checkbox" }, + { field = "comorbidities___15", ref = "checkbox", description = "Hep B" }, + { field = "comorbidities___16", ref = "checkbox", description = "Hep C" }, ] [subject.has_malnutrition] field = "comorbidities___29" - values = { 1 = true } + ref = "checkbox" [subject.has_solid_organ_transplant] field = "comorbidities___21" - values = { 1 = true } + ref = "checkbox" [subject.has_hiv_art] field = "pre_hospital_medication___3" - values = { 1 = true } + ref = "checkbox" [subject.has_immunosuppression] field = "comorbidities___22" - values = { 1 = true } + ref = "checkbox" [subject.has_comorbidity_other] combinedType = "set" @@ -220,8 +221,8 @@ [subject.icu_admitted] combinedType = "any" fields = [ - { field = "admitted_to_icu", values = { 1 = true } }, - { field = "is_patient_admitted_to_icu", values = { 1 = true } }, + { field = "admitted_to_icu", ref = "checkbox" }, + { field = "is_patient_admitted_to_icu", ref = "checkbox" }, ] @@ -247,8 +248,8 @@ [visit.icu_admission] combinedType = "any" fields = [ - { field = "admitted_to_icu", values = { 1 = true } }, - { field = "is_patient_admitted_to_icu", values = { 1 = true } }, + { field = "admitted_to_icu", ref = "checkbox" }, + { field = "is_patient_admitted_to_icu", ref = "checkbox" }, ] [visit.icu_admission_dates] @@ -266,95 +267,95 @@ [visit.treatment_inotropes_vasopressors] field = "icu_level_care___3" - values = { 1 = true } + ref = "checkbox" [visit.treatment_ecmo] combinedType = "any" fields = [ - { field = "treatment_events___5", values = { 1 = true } }, - { field = "oxygenation_methods_2___6", values = { 1 = true } }, + { field = "treatment_events___5", ref = "checkbox" }, + { field = "oxygenation_methods_2___6", ref = "checkbox" }, ] [visit.treatment_oxygen_therapy] combinedType = "any" excludeWhen = "none" fields = [ - { field = "oxygenation_methods_2___1", values = { 1 = true }, description = "invasive" }, - { field = "oxygenation_methods_2___2", values = { 1 = true }, description = "non-invasive" }, - { field = "oxygenation_methods_2___3", values = { 1 = true }, description = "HFNC" }, - { field = "oxygenation_methods_2___4", values = { 1 = true }, description = "face mask" }, - { field = "oxygenation_methods_2___6", values = { 1 = true }, description = "ecmo" }, - { field = "oxygenation_methods_2___7", values = { 1 = true }, description = "nasal cannula" }, - { field = "icu_level_care___1", values = { 1 = true }, description = "HFNC" }, - { field = "icu_level_care___4", values = { 1 = true }, description = "mechanical ventilation" }, - { field = "icu_level_care___5", values = { 1 = true }, description = "non-invasive +ve pressure ventilation" }, - { field = "icu_level_care___8", values = { 1 = true }, description = "prone ventilation" }, - { field = "treatment_events___1", values = { 1 = true }, description = "prone ventilation" }, - { field = "treatment_events___5", values = { 1 = true }, description = "extracorporeal support (ecmo)" }, + { field = "oxygenation_methods_2___1", ref = "checkbox", description = "invasive" }, + { field = "oxygenation_methods_2___2", ref = "checkbox", description = "non-invasive" }, + { field = "oxygenation_methods_2___3", ref = "checkbox", description = "HFNC" }, + { field = "oxygenation_methods_2___4", ref = "checkbox", description = "face mask" }, + { field = "oxygenation_methods_2___6", ref = "checkbox", description = "ecmo" }, + { field = "oxygenation_methods_2___7", ref = "checkbox", description = "nasal cannula" }, + { field = "icu_level_care___1", ref = "checkbox", description = "HFNC" }, + { field = "icu_level_care___4", ref = "checkbox", description = "mechanical ventilation" }, + { field = "icu_level_care___5", ref = "checkbox", description = "non-invasive +ve pressure ventilation" }, + { field = "icu_level_care___8", ref = "checkbox", description = "prone ventilation" }, + { field = "treatment_events___1", ref = "checkbox", description = "prone ventilation" }, + { field = "treatment_events___5", ref = "checkbox", description = "extracorporeal support (ecmo)" }, ] [visit.treatment_oxygen_mask_prongs] combinedType = "any" fields = [ - { field = "oxygenation_methods_2___4", values = { 1 = true }, description = "face mask" }, - { field = "oxygenation_methods_2___7", values = { 1 = true }, description = "nasal cannula" }, + { field = "oxygenation_methods_2___4", ref = "checkbox", description = "face mask" }, + { field = "oxygenation_methods_2___7", ref = "checkbox", description = "nasal cannula" }, ] [visit.treatment_prone_position] combinedType = "any" fields = [ - { field = "treatment_events___1", values = { 1 = true } }, - { field = "oxygenation_methods_2___5", values = { 1 = true }, description = "proning" }, - { field = "icu_level_care___8", values = { 1 = true }, description = "prone ventilation" }, - { field = "icu_level_care___11", values = { 1 = true }, description = "self-proning not on ventilator" }, + { field = "treatment_events___1", ref = "checkbox" }, + { field = "oxygenation_methods_2___5", ref = "checkbox", description = "proning" }, + { field = "icu_level_care___8", ref = "checkbox", description = "prone ventilation" }, + { field = "icu_level_care___11", ref = "checkbox", description = "self-proning not on ventilator" }, ] [visit.treatment_invasive_ventilation] combinedType = "any" fields = [ - { field = "icu_level_care___4", values = { 1 = true } }, - { field = "oxygenation_methods_2___1", values = { 1 = true } }, + { field = "icu_level_care___4", ref = "checkbox" }, + { field = "oxygenation_methods_2___1", ref = "checkbox" }, ] [visit.treatment_inhaled_nitric_oxide] combinedType = "any" fields = [ - { field = "treatment_events___2", values = { 1 = true } }, - { field = "icu_level_care___9", values = { 1 = true } }, + { field = "treatment_events___2", ref = "checkbox" }, + { field = "icu_level_care___9", ref = "checkbox" }, ] [visit.treatment_noninvasive_ventilation] combinedType = "any" fields = [ - { field = "icu_level_care___5", values = { 1 = true } }, - { field = "oxygenation_methods_2___2", values = { 1 = true } }, + { field = "icu_level_care___5", ref = "checkbox" }, + { field = "oxygenation_methods_2___2", ref = "checkbox" }, ] [visit.treatment_high_flow_nasal_cannula] combinedType = "any" fields = [ - { field = "icu_level_care___1", values = { 1 = true } }, - { field = "oxygenation_methods_2___3", values = { 1 = true } }, + { field = "icu_level_care___1", ref = "checkbox" }, + { field = "oxygenation_methods_2___3", ref = "checkbox" }, ] [visit.treatment_neuromuscular_blocking_agents] combinedType = "any" - fields = [{ field = "icu_level_care___7", values = { 1 = true } }] + fields = [{ field = "icu_level_care___7", ref = "checkbox" }] [visit.treatment_dialysis] combinedType = "any" fields = [ { field = "crrt_duration", apply = { function = "isNotNull" } }, - { field = "icu_level_care___2", values = { 1 = true } }, + { field = "icu_level_care___2", ref = "checkbox" }, ] [visit.treatment_cardiovascular_support] combinedType = "any" fields = [ - { field = "treatment_events___5", values = { 1 = true } }, - { field = "oxygenation_methods_2___6", values = { 1 = true } }, - { field = "icu_level_care___3", values = { 1 = true } }, + { field = "treatment_events___5", ref = "checkbox" }, + { field = "oxygenation_methods_2___6", ref = "checkbox" }, + { field = "icu_level_care___3", ref = "checkbox" }, ] [visit.outcome] @@ -371,31 +372,31 @@ name = "abdominal_pain" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___1", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___1", ref = "checkbox" } [[observation]] name = "confusion" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___8", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___8", ref = "checkbox" } [[observation]] name = "anorexia" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___3", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___3", ref = "checkbox" } [[observation]] name = "chest_pain" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___6", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___6", ref = "checkbox" } [[observation]] name = "conjunctivitis" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___9", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___9", ref = "checkbox" } [[observation]] name = "cough" @@ -405,46 +406,46 @@ [observation.is_present] combinedType = "any" fields = [ - { field = "signs_and_symptoms_at_hosp___10", values = { 1 = true } }, - { field = "signs_and_symptoms_at_hosp___11", values = { 1 = true } }, - { field = "signs_and_symptoms_at_hosp___17", values = { 1 = true } }, + { field = "signs_and_symptoms_at_hosp___10", ref = "checkbox" }, + { field = "signs_and_symptoms_at_hosp___11", ref = "checkbox" }, + { field = "signs_and_symptoms_at_hosp___17", ref = "checkbox" }, ] [[observation]] name = "cough_dry" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___10", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___10", ref = "checkbox" } [[observation]] name = "cough_with_sputum_production" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___11", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___11", ref = "checkbox" } [[observation]] name = "cough_with_haemoptysis" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___17", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___17", ref = "checkbox" } [[observation]] name = "diarrhoea" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___12", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___12", ref = "checkbox" } [[observation]] name = "fatigue_malaise" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___18", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___18", ref = "checkbox" } [[observation]] name = "headache" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___16", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___16", ref = "checkbox" } [[observation]] name = "hepatomegaly" @@ -454,37 +455,37 @@ ] } } duration_type = "event" phase = "study" - is_present = { field = "complications___19", values = { 1 = true } } + is_present = { field = "complications___19", ref = "checkbox" } [[observation]] name = "history_of_fever" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___15", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___15", ref = "checkbox" } [[observation]] name = "joint_pain" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___5", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___5", ref = "checkbox" } [[observation]] name = "musculoskeletal_pain" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___5", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___5", ref = "checkbox" } [[observation]] name = "loss_of_smell" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___4", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___4", ref = "checkbox" } [[observation]] name = "loss_of_taste" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___2", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___2", ref = "checkbox" } [[observation]] name = "loss_of_smell_or_taste" @@ -494,51 +495,51 @@ [observation.is_present] combinedType = "any" fields = [ - { field = "signs_and_symptoms_at_hosp___4", values = { 1 = true } }, - { field = "signs_and_symptoms_at_hosp___2", values = { 1 = true } }, + { field = "signs_and_symptoms_at_hosp___4", ref = "checkbox" }, + { field = "signs_and_symptoms_at_hosp___2", ref = "checkbox" }, ] [[observation]] name = "lymphadenopathy" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___27", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___27", ref = "checkbox" } [[observation]] name = "seizures" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___23", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___23", ref = "checkbox" } [[observation]] name = "shortness_of_breath" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___14", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___14", ref = "checkbox" } [[observation]] name = "skin_rash" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___26", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___26", ref = "checkbox" } [[observation]] name = "sore_throat" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___25", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___25", ref = "checkbox" } [[observation]] name = "vomiting_nausea" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___21", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___21", ref = "checkbox" } [[observation]] name = "runny_nose" date = { field = "ADMIT DATE" } phase = "admission" - is_present = { field = "signs_and_symptoms_at_hosp___20", values = { 1 = true } } + is_present = { field = "signs_and_symptoms_at_hosp___20", ref = "checkbox" } [[observation]] name = "other_symptom" @@ -554,7 +555,7 @@ ] } } duration_type = "event" phase = "study" - is_present = { field = "complications___5", values = { 1 = true } } + is_present = { field = "complications___5", ref = "checkbox" } context = ['bacterial'] [[observation]] @@ -565,5 +566,5 @@ ] } } duration_type = "event" phase = "study" - is_present = { field = "complications___14", values = { 1 = true } } + is_present = { field = "complications___14", ref = "checkbox" } context = ['COP'] diff --git a/isaric/parsers/ncov-france.toml b/isaric/parsers/ncov-france.toml index 1acae08..73cff1a 100644 --- a/isaric/parsers/ncov-france.toml +++ b/isaric/parsers/ncov-france.toml @@ -207,8 +207,8 @@ combinedType = "any" excludeWhen = "none" fields = [ - { field = "ttt_ass_type___1", values = { 1 = true } }, - { field = "ttt_ass_type___2", values = { 1 = true } }, + { field = "ttt_ass_type___1", ref = "checkbox" }, + { field = "ttt_ass_type___2", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] @@ -343,20 +343,20 @@ name = "abdominal_pain" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___2", values = { 1 = true } } + is_present = { field = "signes_clin___2", ref = "checkbox" } context = ["diarrhoea/abdominal pain"] [[observation]] name = "confusion" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___7", values = { 1 = true } } + is_present = { field = "signes_clin___7", ref = "checkbox" } [[observation]] name = "cough" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___1", values = { 1 = true } } + is_present = { field = "signes_clin___1", ref = "checkbox" } [[observation]] name = "diastolic_blood_pressure_mmHg" @@ -368,20 +368,20 @@ name = "diarrhoea" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___2", values = { 1 = true } } + is_present = { field = "signes_clin___2", ref = "checkbox" } context = ["diarrhoea/abdominal pain"] [[observation]] name = "headache" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___4", values = { 1 = true } } + is_present = { field = "signes_clin___4", ref = "checkbox" } [[observation]] name = "history_of_fever" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___5", values = { 1 = true } } + is_present = { field = "signes_clin___5", ref = "checkbox" } [[observation]] name = "glasgow_coma_score" @@ -437,7 +437,7 @@ [observation.is_present] combinedType = "any" fields = [ - { field = "signes_clin___8", values = { 1 = true } }, + { field = "signes_clin___8", ref = "checkbox" }, # { field = "signes_clin___9", values = { 1 = true } }, ] @@ -445,7 +445,7 @@ name = "loss_of_smell" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___8", values = { 1 = true } } + is_present = { field = "signes_clin___8", ref = "checkbox" } [[observation]] name = "mean_arterial_blood_pressure_mmHg" @@ -457,13 +457,13 @@ name = "muscle_aches" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___6", values = { 1 = true } } + is_present = { field = "signes_clin___6", ref = "checkbox" } [[observation]] name = "musculoskeletal_pain" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___6", values = { 1 = true } } + is_present = { field = "signes_clin___6", ref = "checkbox" } [[observation]] name = "oxygen_flow_rate" @@ -554,14 +554,14 @@ start_date = { ref = "admissionDate" } date = { field = "shosp_d", source_date = "%Y-%m-%d" } duration_type = "event" - is_present = { field = "compl_type___1", values = { 1 = true }, description = "VAP" } + is_present = { field = "compl_type___1", ref = "checkbox", description = "VAP" } context = ["Ventilator associated pneumonia"] [[observation]] name = "shortness_of_breath" phase = "admission" date = { ref = "admissionDate" } - is_present = { field = "signes_clin___9", values = { 1 = true } } + is_present = { field = "signes_clin___9", ref = "checkbox" } [[observation]] name = "systolic_blood_pressure_mmHg" diff --git a/isaric/parsers/ncov-malaysia.toml b/isaric/parsers/ncov-malaysia.toml index 182b5a7..970b084 100644 --- a/isaric/parsers/ncov-malaysia.toml +++ b/isaric/parsers/ncov-malaysia.toml @@ -489,10 +489,10 @@ fields = [ { field = "mx_antimalarial", ref = "Y/N" }, { field = "antimalarial_dc", ref = "Y/N" }, - { field = "mx_antimalarial_type___1", values = { 1 = true } }, - { field = "mx_antimalarial_type___2", values = { 1 = true } }, - { field = "type_antimalarial_dc___1", values = { 1 = true } }, - { field = "type_antimalarial_dc___2", values = { 1 = true } }, + { field = "mx_antimalarial_type___1", ref = "checkbox" }, + { field = "mx_antimalarial_type___2", ref = "checkbox" }, + { field = "type_antimalarial_dc___1", ref = "checkbox" }, + { field = "type_antimalarial_dc___2", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] diff --git a/isaric/parsers/western-australia.toml b/isaric/parsers/western-australia.toml index 96574a3..5519cff 100644 --- a/isaric/parsers/western-australia.toml +++ b/isaric/parsers/western-australia.toml @@ -31,14 +31,12 @@ aggregation = "lastNotNull" schema = "../../schemas/dev/observation.schema.json" - [adtl.defs."Y/N/NK".values] + [adtl.defs."Y/N".values] # use in observations where NK shouldn't be mapped 1 = true 2 = false - 3 = false - [adtl.defs."Y/N".values] # use in observations where NK shouldn't be mapped + [adtl.defs.checkbox.values] 1 = true - 2 = false [adtl.defs.admissionDateHierarchy] combinedType = "firstNonNull" @@ -100,12 +98,12 @@ [subject.works_healthcare] field = "healthwork_erterm" description = "Healthcare Worker?" - ref = "Y/N/NK" + ref = "Y/N" [subject.works_lab] field = "labwork_erterm" description = "Laboratory worker?" - ref = "Y/N/NK" + ref = "Y/N" [subject.pregnancy] field = "pregyn_rptestcd" @@ -119,12 +117,12 @@ [subject.has_asplenia] field = "asplenia_mhyn" description = "Asplenia" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_tuberculosis] field = "tb_mhyn" description = "Tuberculosis" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_hiv] combinedType = "any" @@ -137,12 +135,12 @@ [subject.has_hypertension] field = "hypertension_mhyn" description = "Hypertension" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_malignant_neoplasm] field = "malignantneo_mhyn" description = "Malignant neoplasm" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_smoking] field = "smoking_mhyn" @@ -152,27 +150,27 @@ [subject.has_asthma] field = "asthma_mhyn" description = "Asthma" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_chronic_cardiac_disease] field = "chroniccard_mhyn" description = "Chronic cardiac disease" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_chronic_kidney_disease] field = "renal_mhyn" description = "Chronic kidney disease" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_diabetes] field = "diabetes_mhyn" description = "Diabetes" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_liver_disease] field = "liver_mhyn" description = "Chronic liver disease" - ref = "Y/N/NK" + ref = "Y/N" [subject.has_malnutrition] field = "malnutrition_vsorres" @@ -198,10 +196,10 @@ description = "ICU or High Dependency admission" combinedType = "any" fields = [ - { field = "overall_icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission?" }, + { field = "overall_icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission?" }, { field = "overall_icu_hoyn", values = { 1 = true, 2 = false }, description = "Still in ICU at outcome?" }, - { field = "daily_icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission?" }, - { field = "icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission on the first day of admission?" }, + { field = "daily_icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission?" }, + { field = "icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission on the first day of admission?" }, ] [visit] @@ -235,10 +233,10 @@ description = "ICU or High Dependency admission" combinedType = "any" fields = [ - { field = "overall_icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission?" }, + { field = "overall_icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission?" }, { field = "overall_icu_hoyn", values = { 1 = true, 2 = false }, description = "Still in ICU at outcome?" }, - { field = "daily_icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission?" }, - { field = "icu_hoterm", ref = "Y/N/NK", description = "ICU or High Dependency admission on the first day of admission?" }, + { field = "daily_icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission?" }, + { field = "icu_hoterm", ref = "Y/N", description = "ICU or High Dependency admission on the first day of admission?" }, ] [visit.icu_admission_dates] @@ -252,17 +250,17 @@ description = "Dialysis" combinedType = "any" fields = [ - { field = "overall_rrt_prtrt", ref = "Y/N/NK", description = "Renal replacement therapy (RRT) or dialysis?" }, - { field = "daily_rrt_prtrt", ref = "Y/N/NK", description = "Renal replacement therapy (RRT) or dialysis?" }, + { field = "overall_rrt_prtrt", ref = "Y/N", description = "Renal replacement therapy (RRT) or dialysis?" }, + { field = "daily_rrt_prtrt", ref = "Y/N", description = "Renal replacement therapy (RRT) or dialysis?" }, ] [visit.treatment_inotropes_vasopressors] description = "Inotropes/vasopressors" combinedType = "any" fields = [ - { field = "overall_inotrop_cmtrt", ref = "Y/N/NK", description = "Inotropes/vasopressors?" }, - { field = "daily_inotrop_cmtrt", ref = "Y/N/NK", description = "Inotropes/vasopressors?" }, - { field = "inotrop_cmtrt", ref = "Y/N/NK", description = "Inotropes/vasopressors on the first day of admission?" }, + { field = "overall_inotrop_cmtrt", ref = "Y/N", description = "Inotropes/vasopressors?" }, + { field = "daily_inotrop_cmtrt", ref = "Y/N", description = "Inotropes/vasopressors?" }, + { field = "inotrop_cmtrt", ref = "Y/N", description = "Inotropes/vasopressors on the first day of admission?" }, ] [visit.treatment_ecmo] @@ -271,33 +269,33 @@ [[visit.treatment_ecmo.fields]] field = "overall_extracorp_prtrt" - ref = "Y/N/NK" + ref = "Y/N" description = "Extracorporeal (ECMO) support?" [[visit.treatment_ecmo.fields]] field = "daily_extracorp_prtrt" - ref = "Y/N/NK" + ref = "Y/N" description = "Extracorporeal (ECMO) support?" [[visit.treatment_ecmo.fields]] field = "extracorp_prtrt" - ref = "Y/N/NK" + ref = "Y/N" description = "Extracorporeal (ECMO) support on the first day of admission?" [visit.treatment_cardiovascular_support] combinedType = "any" fields = [ - { fieldPattern = ".*extracorp_prtrt", ref = "Y/N/NK" }, - { fieldPattern = "inotrop_cmtrt", ref = "Y/N/NK" }, + { fieldPattern = ".*extracorp_prtrt", ref = "Y/N" }, + { fieldPattern = "inotrop_cmtrt", ref = "Y/N" }, ] [visit.treatment_corticosteroid] description = "Corticosteroid" combinedType = "any" fields = [ - { field = "overall_corticost_cmyn", ref = "Y/N/NK", description = "Corticosteroid?" }, - { field = "daily_corticost_cmyn", ref = "Y/N/NK", description = "Corticosteroid?" }, - { field = "corticost_cmyn", ref = "Y/N/NK", description = "Corticosteroid on the first day of admission?" }, + { field = "overall_corticost_cmyn", ref = "Y/N", description = "Corticosteroid?" }, + { field = "daily_corticost_cmyn", ref = "Y/N", description = "Corticosteroid?" }, + { field = "corticost_cmyn", ref = "Y/N", description = "Corticosteroid on the first day of admission?" }, ] [visit.treatment_corticosteroid_type] @@ -316,49 +314,49 @@ description = "Oxygen therepy" combinedType = "any" fields = [ - { fieldPattern = ".*oxygen_cmoccur", ref = "Y/N/NK", description = "Oxygen therapy?" }, - { fieldPattern = "overall_oxygen_cmtype.*", values = { 1 = true } }, + { fieldPattern = ".*oxygen_cmoccur", ref = "Y/N", description = "Oxygen therapy?" }, + { fieldPattern = "overall_oxygen_cmtype.*", ref = "checkbox" }, { fieldPattern = ".*oxygen_cmtype", values = { 1 = true, 2 = true, 3 = true, 4 = true, 5 = true } }, - { fieldPattern = ".*invasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, - { fieldPattern = ".*noninvasive_proccur", ref = "Y/N/NK", description = "Non-invasive ventilation?" }, - { fieldPattern = ".*extracorp_prtrt", ref = "Y/N/NK" }, + { fieldPattern = ".*invasive_proccur", ref = "Y/N", description = "Invasive ventilation?" }, + { fieldPattern = ".*noninvasive_proccur", ref = "Y/N", description = "Non-invasive ventilation?" }, + { fieldPattern = ".*extracorp_prtrt", ref = "Y/N" }, ] [visit.treatment_prone_position] description = "Prone Positioning" combinedType = "any" fields = [ - { field = "overall_prone_prtrt", ref = "Y/N/NK", description = "Prone positioning?" }, - { field = "daily_prone_prtrt", ref = "Y/N/NK", description = "Prone positioning?" }, - { field = "prone_prtrt", ref = "Y/N/NK", description = "Prone position on first day of admission?" }, + { field = "overall_prone_prtrt", ref = "Y/N", description = "Prone positioning?" }, + { field = "daily_prone_prtrt", ref = "Y/N", description = "Prone positioning?" }, + { field = "prone_prtrt", ref = "Y/N", description = "Prone position on first day of admission?" }, ] [visit.treatment_invasive_ventilation] description = "Invasive ventilation" combinedType = "any" fields = [ - { field = "overall_invasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, - { field = "daily_invasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, - { field = "invasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation on first day of admission?" }, + { field = "overall_invasive_proccur", ref = "Y/N", description = "Invasive ventilation?" }, + { field = "daily_invasive_proccur", ref = "Y/N", description = "Invasive ventilation?" }, + { field = "invasive_proccur", ref = "Y/N", description = "Invasive ventilation on first day of admission?" }, ] [visit.treatment_antifungal_agent] description = "Antifungal" combinedType = "any" fields = [ - { field = "overall_antifung_cmyn", ref = "Y/N/NK", description = "Antifungal agent?" }, - { field = "daily_antifung_cmyn", ref = "Y/N/NK", description = "Antifungal agent?" }, - { field = "antifung_cmyn", ref = "Y/N/NK", description = "Antifungal agent on the first day of admission?" }, + { field = "overall_antifung_cmyn", ref = "Y/N", description = "Antifungal agent?" }, + { field = "daily_antifung_cmyn", ref = "Y/N", description = "Antifungal agent?" }, + { field = "antifung_cmyn", ref = "Y/N", description = "Antifungal agent on the first day of admission?" }, ] [visit.treatment_antivirals] description = "Antiviral" combinedType = "any" fields = [ - { field = "overall_antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent?" }, - { field = "daily_antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent?" }, - { field = "antiviral_cmyn", ref = "Y/N/NK", description = "Antiviral agent on the first day of admission?" }, - { fieldPattern = ".*exper_cmtype___3", values = { 1 = true } }, + { field = "overall_antiviral_cmyn", ref = "Y/N", description = "Antiviral agent?" }, + { field = "daily_antiviral_cmyn", ref = "Y/N", description = "Antiviral agent?" }, + { field = "antiviral_cmyn", ref = "Y/N", description = "Antiviral agent on the first day of admission?" }, + { fieldPattern = ".*exper_cmtype___3", ref = "checkbox" }, ] @@ -380,9 +378,9 @@ description = "Antibiotics" combinedType = "any" fields = [ - { field = "overall_antibiotic_cmyn", ref = "Y/N/NK", description = "Antibiotic?" }, - { field = "daily_antibiotic_cmyn", ref = "Y/N/NK", description = "Antibiotic?" }, - { field = "antibiotic_cmyn", ref = "Y/N/NK", description = "Antibiotic on the first day of admission?" }, + { field = "overall_antibiotic_cmyn", ref = "Y/N", description = "Antibiotic?" }, + { field = "daily_antibiotic_cmyn", ref = "Y/N", description = "Antibiotic?" }, + { field = "antibiotic_cmyn", ref = "Y/N", description = "Antibiotic on the first day of admission?" }, ] [visit.treatment_other] @@ -408,9 +406,9 @@ description = "Noninvasive ventilation" combinedType = "any" fields = [ - { field = "overall_noninvasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, - { field = "daily_noninvasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation?" }, - { field = "noninvasive_proccur", ref = "Y/N/NK", description = "Invasive ventilation on first day of admission?" }, + { field = "overall_noninvasive_proccur", ref = "Y/N", description = "Invasive ventilation?" }, + { field = "daily_noninvasive_proccur", ref = "Y/N", description = "Invasive ventilation?" }, + { field = "noninvasive_proccur", ref = "Y/N", description = "Invasive ventilation on first day of admission?" }, ] [visit.treatment_ace_inhibitors] @@ -419,12 +417,12 @@ [[visit.treatment_ace_inhibitors.fields]] field = "daily_ace_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Angiotension converting enzyme inhibitors (ACE inhibitors)?" [[visit.treatment_ace_inhibitors.fields]] field = "ace_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Angiotensin converting enzyme inhibitors (ACE) on the first day of admission?" [visit.treatment_arb] @@ -433,12 +431,12 @@ [[visit.treatment_arb.fields]] field = "daily_arb_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Angiotensin II receptor blockers (ARBs)?" [[visit.treatment_arb.fields]] field = "arb_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Angiotensin II receptor blockers (ARBs) on the first day of admission?" @@ -446,17 +444,17 @@ description = "Antimalarial" combinedType = "any" fields = [ - { field = "overall_antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent?" }, - { field = "daily_antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent?" }, - { field = "antimal_cmyn", ref = "Y/N/NK", description = "Antimalarial agent on the first day of admission?" }, - { fieldPattern = ".*exper_cmtype___1", values = { 1 = true } }, - { fieldPattern = ".*exper_cmtype___2", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___1", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___2", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___3", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___4", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___5", values = { 1 = true } }, - { fieldPattern = ".*antimal_cmtype___6", values = { 1 = true } }, + { field = "overall_antimal_cmyn", ref = "Y/N", description = "Antimalarial agent?" }, + { field = "daily_antimal_cmyn", ref = "Y/N", description = "Antimalarial agent?" }, + { field = "antimal_cmyn", ref = "Y/N", description = "Antimalarial agent on the first day of admission?" }, + { fieldPattern = ".*exper_cmtype___1", ref = "checkbox" }, + { fieldPattern = ".*exper_cmtype___2", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___1", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___2", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___3", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___4", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___5", ref = "checkbox" }, + { fieldPattern = ".*antimal_cmtype___6", ref = "checkbox" }, ] [visit.treatment_antimalarial_type] @@ -478,9 +476,9 @@ combinedType = "any" fields = [ { fieldPattern = ".*oxygen_cmtype", values = { 1 = true, 2 = false, 3 = true, 4 = true, 5 = false } }, - { field = "overall_oxygen_cmtype___1", values = { 1 = true } }, - { field = "overall_oxygen_cmtype___3", values = { 1 = true } }, - { field = "overall_oxygen_cmtype___4", values = { 1 = true } }, + { field = "overall_oxygen_cmtype___1", ref = "checkbox" }, + { field = "overall_oxygen_cmtype___3", ref = "checkbox" }, + { field = "overall_oxygen_cmtype___4", ref = "checkbox" }, ] [visit.treatment_high_flow_nasal_cannula] @@ -489,7 +487,7 @@ [[visit.treatment_high_flow_nasal_cannula.fields]] field = "overall_oxygen_cmtype___2" - values = { 1 = true } + ref = "checkbox" [[visit.treatment_high_flow_nasal_cannula.fields]] field = "daily_oxygen_cmtype" @@ -505,26 +503,26 @@ [[visit.treatment_nsaid.fields]] field = "overall_nsaid_cmyn" - ref = "Y/N/NK" + ref = "Y/N" description = "Non-steroidal anti-inflammatory (NSAID)?" [[visit.treatment_nsaid.fields]] field = "daily_nsaid_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Non-steroidal anti-inflammatory (NSAID)?" [[visit.treatment_nsaid.fields]] field = "nsaid_cmoccur" - ref = "Y/N/NK" + ref = "Y/N" description = "Non-steroidal anti-inflammatory (NSAID) on first day of admission?" [visit.treatment_intravenous_fluids] description = "IV fluids" combinedType = "any" fields = [ - { field = "overall_iv_fluids_cmyn", ref = "Y/N/NK", description = "Intraveonous fluids?" }, - { field = "daily_iv_fluids_cmyn", ref = "Y/N/NK", description = "Intraveonous fluids?" }, - { field = "iv_fluids_cmyn", ref = "Y/N/NK", description = "Intraveonous fluids on the first day of admission?" }, + { field = "overall_iv_fluids_cmyn", ref = "Y/N", description = "Intraveonous fluids?" }, + { field = "daily_iv_fluids_cmyn", ref = "Y/N", description = "Intraveonous fluids?" }, + { field = "iv_fluids_cmyn", ref = "Y/N", description = "Intraveonous fluids on the first day of admission?" }, ] [visit.outcome] @@ -559,7 +557,7 @@ name = "bleeding_haemorrhage" date = { ref = "admissionDateHierarchy" } phase = "admission" - is_present = { field = "bleed_ceoccur_v2", ref = "Y/N/NK" } + is_present = { field = "bleed_ceoccur_v2", ref = "Y/N" } [[observation]] name = "cough" @@ -568,7 +566,7 @@ [observation.is_present] combinedType = "any" fields = [ - { field = "cough_ceoccur_v2", ref = "Y/N/NK" }, + { field = "cough_ceoccur_v2", ref = "Y/N" }, { field = "coughsput_ceoccur_v2", ref = "Y/N" }, { field = "coughhb_ceoccur_v2", ref = "Y/N" }, ] @@ -577,7 +575,7 @@ name = "cough_dry" date = { ref = "admissionDateHierarchy" } phase = "admission" - is_present = { field = "cough_ceoccur_v2", ref = "Y/N/NK" } + is_present = { field = "cough_ceoccur_v2", ref = "Y/N" } [[observation]] name = "cough_with_sputum_production"