Remove library() calls in shiny app

R/settingsMetadata.R

@@ -12,7 +12,6 @@
 #'    \item{setting_required}{Flag indicating if the setting is required}
 #'    \item{column_mapping}{Flag indicating if the setting corresponds to a column in the associated data}
 #'    \item{column_type}{Expected type for the data column values. Should be "character","logical" or "numeric"}
-#'    \item{column_required}{Flag indicating whether the associated data column should be considered required}
 #'    \item{field_mapping}{Flag indicating whether the setting corresponds to a field-level mapping in the data}
 #'    \item{field_column_key}{Key for the column that provides options for the field-level mapping in the data}
 #'    \item{adam}{Settings values for the ADaM standard}

data-raw/settingsMetadata.csv

@@ -1,26 +1,26 @@
-chart_edish,text_key,label,description,setting_type,setting_required,column_mapping,column_type,column_required,field_mapping,field_column_key,adam,sdtm
-TRUE,id_col,ID column,Unique subject identifier variable name.,character,TRUE,TRUE,character,TRUE,FALSE,,USUBJID,USUBJID
-TRUE,value_col,Value column,Lab result variable name.,character,TRUE,TRUE,numeric,TRUE,FALSE,,AVAL,STRESN
-TRUE,measure_col,Measure column,Lab measure variable name,character,TRUE,TRUE,character,TRUE,FALSE,,PARAM,TEST
-TRUE,normal_col_low,Lower Limit of Normal column,Lower limit of normal variable name,character,TRUE,TRUE,numeric,TRUE,FALSE,,A1LO,STNRLO
-TRUE,normal_col_high,Upper Limit of Normal column,Upper limit of normal variable name,character,TRUE,TRUE,numeric,TRUE,FALSE,,A1HI,STNRHI
-TRUE,studyday_col,Study Day column,Visit day variable name,character,TRUE,TRUE,numeric,TRUE,FALSE,,ADY,DY
-TRUE,visit_col,Visit column,Visit variable name,character,FALSE,TRUE,character,FALSE,FALSE,,VISIT,VISIT
-TRUE,visitn_col,Visit Number column,Visit number variable name,character,FALSE,TRUE,numeric,FALSE,FALSE,,VISITNUM,VISITNUM
-TRUE,filters,Filters columns,"An optional list of specifications for filters. Each filter is a nested, named list (containing the filter value column: 'value_col' and associated label: 'label') within the larger list.",vector,FALSE,TRUE,NA,FALSE,FALSE,,,
-TRUE,group_cols,Group columns,"An optional list of specifications for grouping columns. Each group column is a nested, named list (containing the group variable column: 'value_col' and associated label: 'label') within the larger list. ",vector,FALSE,TRUE,NA,FALSE,FALSE,,,
-TRUE,measure_values--ALT,Alanine Aminotransferase value,Value used for Alanine Aminotransferase in the specified measure column,character,TRUE,FALSE,NA,NA,TRUE,measure_col,Alanine Aminotransferase (U/L),"Aminotransferase, alanine (ALT)"
-TRUE,measure_values--AST,Aspartate Aminotransferase value,Value used for Aspartate Aminotransferase in the specified measure column,character,TRUE,FALSE,NA,NA,TRUE,measure_col,Aspartate Aminotransferase (U/L),"Aminotransferase, aspartate (AST)"
-TRUE,measure_values--TB,Total Bilirubin value,Value used for Total Bilirubin in the specified measure column,character,TRUE,FALSE,NA,NA,TRUE,measure_col,Bilirubin (umol/L),Total Bilirubin
-TRUE,measure_values--ALP,Alkaline Phosphatase value,Value used for Alkaline Phosphatase in the specified measure column,character,TRUE,FALSE,NA,NA,TRUE,measure_col,Alkaline Phosphatase (U/L),Alkaline phosphatase (ALP)
-TRUE,baseline--value_col,Baseline column,An optional list defining which column represent the baseline visit(s) of the study.,character,FALSE,TRUE,NA,FALSE,FALSE,,,
-TRUE,baseline--values,Baseline values,An optional list defining which values (one or more) represent the baseline visit(s) of the study.,vector,FALSE,FALSE,NA,NA,TRUE,baseline--value_col,,
-TRUE,analysisFlag--value_col,Analysis Flag column,An optional list defining which column should be used in eDish and mDish analyses.,character,FALSE,TRUE,NA,FALSE,FALSE,,,
-TRUE,analysisFlag--values,Analysis Flag values,An optional list defining which values should be used in eDish and mDish analyses.,vector,FALSE,FALSE,NA,NA,TRUE,analysisFlag--value_col,,
-TRUE,x_options,X axis options,"Specifies variable options for the x-axis using the key values from measure_values (e.g. 'ALT'). When multiple options are specified, a control allowing the user to interactively change the x variable is shown. ",vector,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,y_options,Y axis options,"Specifies variable options for the y-axis using the key values from measure_values (e.g. 'TB'). When multiple options are specified, a control allowing the user to interactively change the y variable is shown. ",vector,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,visit_window,Default Visit Window in Days ,Default visit window used to highlight eDish points where x and y measures occurred within the specified number of days. Editable by user after render. ,numeric,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,r_ratio_filter,Show R Ratio Filter?,Specifies whether the R Ratio filter should be shown. R ratio is defined as: (ALT value/ULN for ALT) / (ALP value/ULN for ALP).,logical,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,r_ratio_cut,Default R Ratio Cut,Default cut point for R Ratio filter. Ignored when r_ratio_filter = FALSE. User can update this setting via the UI when r_ratio_filter = TRUE. ,numeric,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,showTitle,Show Chart Title? ,Specifies whether the title should be drawn above the controls.,logical,FALSE,FALSE,NA,NA,FALSE,,,
-TRUE,warningText,Warning text,"Informational text to be displayed near the top of the controls (beneath the title, if any). No warning is displayed if warningText = ''. ",Character,FALSE,FALSE,NA,NA,FALSE,,,
+chart_edish,text_key,label,description,setting_type,setting_required,column_mapping,column_type,field_mapping,field_column_key,adam,sdtm
+TRUE,id_col,ID column,Unique subject identifier variable name.,character,TRUE,TRUE,character,FALSE,,USUBJID,USUBJID
+TRUE,value_col,Value column,Lab result variable name.,character,TRUE,TRUE,numeric,FALSE,,AVAL,STRESN
+TRUE,measure_col,Measure column,Lab measure variable name,character,TRUE,TRUE,character,FALSE,,PARAM,TEST
+TRUE,normal_col_low,Lower Limit of Normal column,Lower limit of normal variable name,character,TRUE,TRUE,numeric,FALSE,,A1LO,STNRLO
+TRUE,normal_col_high,Upper Limit of Normal column,Upper limit of normal variable name,character,TRUE,TRUE,numeric,FALSE,,A1HI,STNRHI
+TRUE,studyday_col,Study Day column,Visit day variable name,character,TRUE,TRUE,numeric,FALSE,,ADY,DY
+TRUE,visit_col,Visit column,Visit variable name,character,FALSE,TRUE,character,FALSE,,VISIT,VISIT
+TRUE,visitn_col,Visit Number column,Visit number variable name,character,FALSE,TRUE,numeric,FALSE,,VISITNUM,VISITNUM
+TRUE,filters,Filters columns,"An optional list of specifications for filters. Each filter is a nested, named list (containing the filter value column: 'value_col' and associated label: 'label') within the larger list.",vector,FALSE,TRUE,NA,FALSE,,,
+TRUE,group_cols,Group columns,"An optional list of specifications for grouping columns. Each group column is a nested, named list (containing the group variable column: 'value_col' and associated label: 'label') within the larger list. ",vector,FALSE,TRUE,NA,FALSE,,,
+TRUE,measure_values--ALT,Alanine Aminotransferase value,Value used for Alanine Aminotransferase in the specified measure column,character,TRUE,FALSE,NA,TRUE,measure_col,Alanine Aminotransferase (U/L),"Aminotransferase, alanine (ALT)"
+TRUE,measure_values--AST,Aspartate Aminotransferase value,Value used for Aspartate Aminotransferase in the specified measure column,character,TRUE,FALSE,NA,TRUE,measure_col,Aspartate Aminotransferase (U/L),"Aminotransferase, aspartate (AST)"
+TRUE,measure_values--TB,Total Bilirubin value,Value used for Total Bilirubin in the specified measure column,character,TRUE,FALSE,NA,TRUE,measure_col,Bilirubin (umol/L),Total Bilirubin
+TRUE,measure_values--ALP,Alkaline Phosphatase value,Value used for Alkaline Phosphatase in the specified measure column,character,TRUE,FALSE,NA,TRUE,measure_col,Alkaline Phosphatase (U/L),Alkaline phosphatase (ALP)
+TRUE,baseline--value_col,Baseline column,An optional list defining which column represent the baseline visit(s) of the study.,character,FALSE,TRUE,NA,FALSE,,,
+TRUE,baseline--values,Baseline values,An optional list defining which values (one or more) represent the baseline visit(s) of the study.,vector,FALSE,FALSE,NA,TRUE,baseline--value_col,,
+TRUE,analysisFlag--value_col,Analysis Flag column,An optional list defining which column should be used in eDish and mDish analyses.,character,FALSE,TRUE,NA,FALSE,,,
+TRUE,analysisFlag--values,Analysis Flag values,An optional list defining which values should be used in eDish and mDish analyses.,vector,FALSE,FALSE,NA,TRUE,analysisFlag--value_col,,
+TRUE,x_options,X axis options,"Specifies variable options for the x-axis using the key values from measure_values (e.g. 'ALT'). When multiple options are specified, a control allowing the user to interactively change the x variable is shown. ",vector,FALSE,FALSE,NA,FALSE,,,
+TRUE,y_options,Y axis options,"Specifies variable options for the y-axis using the key values from measure_values (e.g. 'TB'). When multiple options are specified, a control allowing the user to interactively change the y variable is shown. ",vector,FALSE,FALSE,NA,FALSE,,,
+TRUE,visit_window,Default Visit Window in Days ,Default visit window used to highlight eDish points where x and y measures occurred within the specified number of days. Editable by user after render. ,numeric,FALSE,FALSE,NA,FALSE,,,
+TRUE,r_ratio_filter,Show R Ratio Filter?,Specifies whether the R Ratio filter should be shown. R ratio is defined as: (ALT value/ULN for ALT) / (ALP value/ULN for ALP).,logical,FALSE,FALSE,NA,FALSE,,,
+TRUE,r_ratio_cut,Default R Ratio Cut,Default cut point for R Ratio filter. Ignored when r_ratio_filter = FALSE. User can update this setting via the UI when r_ratio_filter = TRUE. ,numeric,FALSE,FALSE,NA,FALSE,,,
+TRUE,showTitle,Show Chart Title? ,Specifies whether the title should be drawn above the controls.,logical,FALSE,FALSE,NA,FALSE,,,
+TRUE,warningText,Warning text,"Informational text to be displayed near the top of the controls (beneath the title, if any). No warning is displayed if warningText = ''. ",Character,FALSE,FALSE,NA,FALSE,,,

inst/eDISH_app/global.R

@@ -1,4 +1,3 @@
-# temporarily load deps
 library(safetyGraphics)
 library(shiny)
 library(shinyjs)

inst/eDISH_app/modules/renderChart/eDishReport/eDishReport.Rmd

@@ -12,14 +12,10 @@ params:
 
 ## Customized Interactive Safety Graphic {.tabset .tabset-fade} 
 
-```{r, echo = FALSE}
-library(safetyGraphics)
-library(knitr)
-```
-
 ### Chart
 
 ```{r, fig.width=12, fig.height=15, echo = FALSE}
+library(safetyGraphics)
 
 eDISH(data = params$data,
       settings = params$settings)

inst/eDISH_app/ui.R

@@ -1,6 +1,3 @@
-library(shiny)
-library(shinyjs)
-
 tagList(
   useShinyjs(),
   tags$style(HTML("

tests/testthat/test_getRequiredSettings.R

@@ -17,16 +17,15 @@ defaultRequiredSettings <- list(
 
 
 customMetadata<- data.frame(
-  chart_linechart = c(TRUE, FALSE), 
-  chart_barchart = c(FALSE,TRUE), 
+  chart_linechart = c(TRUE, FALSE),
+  chart_barchart = c(FALSE,TRUE),
   text_key = c("line_col","value_col--label"),
   label=c("label1","label2"),
   description=c("desc1","desc2"),
   setting_type="character",
   setting_required=TRUE,
   column_mapping=TRUE,
   column_type="character",
-  column_required=TRUE,
   field_mapping=FALSE
 )
 
@@ -51,4 +50,4 @@ test_that("nested keys are supported",{
 
 test_that("invalid options return null",{
   expect_null(safetyGraphics::getRequiredSettings(chart="notachart"))
-})
+})

tests/testthat/test_getSettingsMetadata.R

@@ -7,20 +7,19 @@ library(magrittr)
 rawMetadata <- safetyGraphics::settingsMetadata
 
 customMetadata<- data.frame(
-  chart_linechart = c(TRUE, FALSE), 
-  chart_barchart = c(FALSE,TRUE), 
+  chart_linechart = c(TRUE, FALSE),
+  chart_barchart = c(FALSE,TRUE),
   text_key = c("line_col","value_col"),
   label=c("label1","label2"),
   description=c("desc1","desc2"),
   setting_type="character",
   column_mapping=TRUE,
   column_type="character",
-  column_required=TRUE,
   field_mapping=FALSE
 )
 
 mergedMetadata = suppressWarnings(bind_rows(
-  rawMetadata%>%mutate(chart_linechart= FALSE)%>%mutate(chart_barchart= FALSE), 
+  rawMetadata%>%mutate(chart_linechart= FALSE)%>%mutate(chart_barchart= FALSE),
   customMetadata%>%mutate(chart_edish= FALSE)
 ))
 
@@ -34,71 +33,71 @@ test_that("Pulling from a custom metadata file works as expected",{
   custom<-safetyGraphics:::getSettingsMetadata(metadata=customMetadata)
   expect_is(custom,"data.frame")
   expect_equal(dim(custom), dim(customMetadata))
-  
+
   merged<-safetyGraphics:::getSettingsMetadata(metadata=customMetadata)
   expect_is(custom,"data.frame")
   expect_equal(dim(custom), dim(customMetadata))
 })
 
 test_that("charts parameter works as expected",{
-  
+
   #return a dataframe for valid input
   expect_is(safetyGraphics:::getSettingsMetadata(charts=c("edish")),"data.frame")
   expect_is(safetyGraphics:::getSettingsMetadata(charts="edish"),"data.frame")
-  
+
   #error if charts isn't a character
   expect_error(safetyGraphics:::getSettingsMetadata(charts=123))
   expect_error(safetyGraphics:::getSettingsMetadata(charts=list("edish")))
-  
+
   #return null if no valid charts are passed
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts=c(""))))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts="abc")))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts=c("notachart"))))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts=c("notachart","stillnotachart"))))
-  
+
   #no partial matches supported
-  expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts=c("edi")))) 
-  
+  expect_true(is.null(safetyGraphics:::getSettingsMetadata(charts=c("edi"))))
+
   #return a dataframe if at least one valid chart type is passed
   expect_is(safetyGraphics:::getSettingsMetadata(charts=c("notachart","edish")),"data.frame")
-  
+
   #capitalization doesn't matter
   expect_is(safetyGraphics:::getSettingsMetadata(charts=c("EdIsH")),"data.frame")
-  
+
   #get the right number of records with various combinations
   lineonly <- safetyGraphics:::getSettingsMetadata(charts=c("linechart"),metadata=mergedMetadata)
   expect_equal(dim(lineonly)[1],1)
-  
+
   linesandbars <- safetyGraphics:::getSettingsMetadata(charts=c("linechart","barchart"),metadata=mergedMetadata)
   expect_equal(dim(linesandbars)[1],2)
-  
+
   allcharts <- safetyGraphics:::getSettingsMetadata(charts=c("linechart","barchart","edish"),metadata=mergedMetadata)
   expect_equal(dim(allcharts)[1],dim(mergedMetadata)[1])
 })
 
 test_that("text_keys parameter works as expected",{
   #return a dataframe for valid input
   expect_is(safetyGraphics:::getSettingsMetadata(text_keys=c("id_col")),"data.frame")
-  
+
   #error if text_keys isn't a character
   expect_error(safetyGraphics:::getSettingsMetadata(text_keys=123))
   expect_error(safetyGraphics:::getSettingsMetadata(text_keys=list("id_col")))
-  
+
   #return null if no valid text_keys are passed
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys=c(""))))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys="abc")))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys=c("notakey"))))
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys=c("notakey","stillnotakey"))))
-  
+
   #no partial matches supported
-  expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys=c("id_")))) 
-  
+  expect_true(is.null(safetyGraphics:::getSettingsMetadata(text_keys=c("id_"))))
+
   #return a dataframe if at least one valid chart type is passed
   expect_is(safetyGraphics:::getSettingsMetadata(text_keys=c("notachart","id_col")),"data.frame")
-  
+
   #capitalization doesn't matter
   expect_is(safetyGraphics:::getSettingsMetadata(text_keys=c("Id_COl")),"data.frame")
-  
+
   #get the right number of records with various combinations
   expect_equal(dim(safetyGraphics:::getSettingsMetadata(text_keys=c("id_col"),metadata=mergedMetadata))[1],1)
   expect_equal(dim(safetyGraphics:::getSettingsMetadata(text_keys=c("value_col"),metadata=mergedMetadata))[1],2)
@@ -107,33 +106,33 @@ test_that("text_keys parameter works as expected",{
 })
 
 test_that("cols parameter works as expected",{
-  
+
   #returns a data frame if multiple columns are requested
   expect_is(safetyGraphics:::getSettingsMetadata(cols=c("label","text_key")),"data.frame")
-  
+
   #returns a vector if a single column is specified
   one_col <- safetyGraphics:::getSettingsMetadata(cols=c("label"))
   expect_is(one_col,"character")
   expect_equal(length(one_col),dim(rawMetadata)[1])
-  
+
   #returns an atomic value if a single value is specified
   one_val <- safetyGraphics:::getSettingsMetadata(cols=c("label"), text_keys="line_col", metadata= mergedMetadata)
   expect_is(one_val,"character")
   expect_equal(length(one_val),1)
   expect_equal(one_val,"label1")
   expect_true(safetyGraphics:::getSettingsMetadata(cols=c("column_mapping"), text_keys="line_col", metadata= mergedMetadata))
   expect_false(safetyGraphics:::getSettingsMetadata(cols=c("field_mapping"), text_keys="line_col", metadata= mergedMetadata))
-  
+
   #returns null if no valid columns are requested
   expect_true(is.null(safetyGraphics:::getSettingsMetadata(cols=c("asda123"))))
 })
 
 test_that("filter_expr parameters works as expected",{
   expect_equal(
-    safetyGraphics:::getSettingsMetadata(filter_expr=text_key=="id_col"), 
+    safetyGraphics:::getSettingsMetadata(filter_expr=text_key=="id_col"),
     safetyGraphics:::getSettingsMetadata(text_key="id_col")
   )
   expect_equal(safetyGraphics:::getSettingsMetadata(filter_expr=text_key=="id_col",cols="description"),"Unique subject identifier variable name.")
   expect_length(safetyGraphics:::getSettingsMetadata(filter_expr=column_type=="numeric",cols="text_key",chart="edish"),5)
   expect_length(safetyGraphics:::getSettingsMetadata(filter_expr=setting_required,cols="text_key",chart="edish"),10)
-  })
+  })