From f0c2d14fc076e286c250e7e18aa217020235701a Mon Sep 17 00:00:00 2001 From: jwoolfolk <106008877+jwoolfolk@users.noreply.github.com> Date: Fri, 21 Apr 2023 12:26:27 -0500 Subject: [PATCH 1/3] Addition of nepExplorer yaml draft. --- inst/config/nepExplorer.yaml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 inst/config/nepExplorer.yaml diff --git a/inst/config/nepExplorer.yaml b/inst/config/nepExplorer.yaml new file mode 100644 index 0000000..ac9bd07 --- /dev/null +++ b/inst/config/nepExplorer.yaml @@ -0,0 +1,27 @@ +env: safetyGraphics +label: Nephrotoxicity Explorer +type: htmlwidget +package: safetyCharts +domain: + - labs +dataSpec: + labs: + - id_col + - visit_col + - visitn_col + - studyday_col + - measure_col + - value_col +export: true +workflow: + widget: nepExplorer + ui: nepexplorer_ui + server: nepexplorer_server +links: + Clinical Users Guide (pdf): + Homepage: https://github.com/SafetyGraphics/nep-explorer + Wiki: https://github.com/SafetyGraphics/nep-explorer/wiki + Issues: https://github.com/SafetyGraphics/nep-explorer/issues + Demo: https://safetygraphics.github.io/nep-explorer/test-page/ + safetyCharts: https://github.com/SafetyGraphics/safetycharts + From d8dc0bcbf2c0544c7e05d8e4378b488a596b33d5 Mon Sep 17 00:00:00 2001 From: lgakava Date: Sun, 28 May 2023 21:37:59 +0000 Subject: [PATCH 2/3] draft meta_nepExplorer pending team confirmation. --- data-raw/meta_nepExplorer.csv | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 data-raw/meta_nepExplorer.csv diff --git a/data-raw/meta_nepExplorer.csv b/data-raw/meta_nepExplorer.csv new file mode 100644 index 0000000..1a77439 --- /dev/null +++ b/data-raw/meta_nepExplorer.csv @@ -0,0 +1,11 @@ +text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm +measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (umol/L),Creatinine +measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin +measure_values--BUN,labs,measure_col,BUN,field,Creatinine value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen +measure_values--CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium +measure_values--CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride +measure_values--PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate +measure_values--K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium +measure_values--SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium +measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic Blood Pressure value,Value used for Diastolic Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure +measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic Blood Pressure value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure From bd416b75547afd89dab5a406960606f8be670d61 Mon Sep 17 00:00:00 2001 From: lgakava Date: Sun, 28 May 2023 21:37:59 +0000 Subject: [PATCH 3/3] draft meta_nepExplorer pending team confirmation. --- R/meta.R | 22 +++++++++++++++++++++- data-raw/makeMeta.R | 5 +++++ data-raw/meta_nepExplorer.csv | 11 +++++++++++ 3 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 data-raw/meta_nepExplorer.csv diff --git a/R/meta.R b/R/meta.R index 7177449..5279f37 100644 --- a/R/meta.R +++ b/R/meta.R @@ -179,4 +179,24 @@ #' #' @source Created for this package -"meta_ex" \ No newline at end of file +"meta_ex" + +#' Metadata data frame containing information about the data mapping used to configure safetyGraphics for the nepExplorer Chart. One record per unique data mapping +#' +#' @format A data frame with X rows and 10 columns +#' \describe{ +#' \item{domain}{Data domain} +#' \item{text_key}{Text key indicating the setting name. \code{'--'} delimiter indicates a field level data mapping} +#' \item{col_key}{Key for the column mapping} +#' \item{field_key}{Key for the field mapping (if any)} +#' \item{type}{type of mapping - "field" or "column"} +#' \item{label}{Label} +#' \item{description}{Description} +#' \item{multiple}{Mapping supports multiple columns/fields } +#' \item{standard_adam}{Default values for the ADaM data standard} +#' \item{standard_sdtm}{Default values for the SDTM data standard} +#' } +#' +#' @source Created for this package + +"meta_nepExplorer" \ No newline at end of file diff --git a/data-raw/makeMeta.R b/data-raw/makeMeta.R index fdb2c16..14a67dc 100644 --- a/data-raw/makeMeta.R +++ b/data-raw/makeMeta.R @@ -42,3 +42,8 @@ usethis::use_data(meta_ex, overwrite = TRUE) #hepExplorer meta_hepExplorer<-read_csv("data-raw/meta_hepExplorer.csv")[] usethis::use_data(meta_hepExplorer, overwrite = TRUE) + +#Chart-level metadata +#nepExplorer +meta_nepExplorer<-read_csv("data-raw/meta_nepExplorer.csv")[] +usethis::use_data(meta_nepExplorer, overwrite = TRUE) diff --git a/data-raw/meta_nepExplorer.csv b/data-raw/meta_nepExplorer.csv new file mode 100644 index 0000000..1a77439 --- /dev/null +++ b/data-raw/meta_nepExplorer.csv @@ -0,0 +1,11 @@ +text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm +measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (umol/L),Creatinine +measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin +measure_values--BUN,labs,measure_col,BUN,field,Creatinine value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen +measure_values--CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium +measure_values--CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride +measure_values--PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate +measure_values--K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium +measure_values--SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium +measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic Blood Pressure value,Value used for Diastolic Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure +measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic Blood Pressure value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure