AE Plugin Definition — pluginAE • gsm.ae

Plugins for gsm.app are defined by a named list with information about the plugin. These can be loaded from a yaml file with gsm.app::plugin_Read(). We provide a ready-to-use plugin definition for this AE plugin.

Usage

pluginAE(
  chrCategoricalFields = c(aeser = "Serious?", mdrpt_nsv = "Preferred Term", mdrsoc_nsv =
    "System Organ Class", aetoxgr = "Toxicity Grade", aeongo = "Ongoing?", aerel =
    "Related?"),
  chrDateFields = c(mincreated_dts = "AE Entry Date", aest_dt = "AE Start Date", aeen_dt
    = "AE End Date"),
  chrMetricID_AE = c(Site = "Analysis_kri0001", Country = "Analysis_cou0001"),
  chrMetricID_SAE = c(Site = "Analysis_kri0002", Country = "Analysis_cou0002")
)

Arguments

chrCategoricalFields: character A named vector of fields in dfAE to treat as categorical, where the names are the column names and the values are what to display to users. Unnamed elements will be used as both the field name and the display name. These fields are currently used in the Prevalence panel.
chrDateFields: character A named vector of fields in dfAE to treat as dates, where the names are the column names and the values are what to display to users. Unnamed elements will be used as both the field name and the display name. These fields are currently used in the Timeline panel.
chrMetricID_AE: character The ID(s) of the adverse events metric(c). The default value is named by GroupLevel, but the names are not currently used. It is advisable to only provide one MetricID per GroupLevel, though.
chrMetricID_SAE: character The ID(s) of the serious adverse events metric(s). The default value is named by GroupLevel, but the names are not currently used. It is advisable to only provide one MetricID per GroupLevel, though.

Value

A plugin definition for use in gsm.app.

Examples

pluginAE()
#> $meta
#> $meta$Name
#> [1] "Adverse Events"
#> 
#> 
#> $shiny
#> $shiny$UI
#> function (id, chrCategoricalFields = c(aeser = "Serious?", mdrpt_nsv = "Preferred Term", 
#>     mdrsoc_nsv = "System Organ Class", aetoxgr = "Toxicity Grade", 
#>     aeongo = "Ongoing?", aerel = "Related?"), chrDateFields = c(mincreated_dts = "AE Entry Date", 
#>     aest_dt = "AE Start Date", aeen_dt = "AE End Date")) 
#> {
#>     ns <- NS(id)
#>     bslib::page_fillable(mod_AEDashboard_UI(ns("dashboard"), 
#>         chrCategoricalFields = chrCategoricalFields, chrDateFields = chrDateFields))
#> }
#> <bytecode: 0x5651bb162f80>
#> <environment: namespace:gsm.ae>
#> 
#> $shiny$Server
#> function (id, dfAnalyticsInput, dfResults, rctv_dSnapshotDate, 
#>     rctv_dfAE_Study, rctv_strGroupID, rctv_strGroupLevel, rctv_strSubjectID, 
#>     chrCategoricalFields = c(aeser = "Serious?", mdrpt_nsv = "Preferred Term", 
#>         mdrsoc_nsv = "System Organ Class", aetoxgr = "Toxicity Grade", 
#>         aeongo = "Ongoing?", aerel = "Related?"), chrDateFields = c(mincreated_dts = "AE Entry Date", 
#>         aest_dt = "AE Start Date", aeen_dt = "AE End Date"), 
#>     chrMetricID_AE = c(Site = "Analysis_kri0001", Country = "Analysis_cou0001"), 
#>     chrMetricID_SAE = c(Site = "Analysis_kri0002", Country = "Analysis_cou0002")) 
#> {
#>     dfAnalyticsInput <- PrepareGSMData(dfAnalyticsInput, chrMetricID_AE = chrMetricID_AE, 
#>         chrMetricID_SAE = chrMetricID_SAE)
#>     dfResults <- PrepareGSMData(dfResults, chrMetricID_AE = chrMetricID_AE, 
#>         chrMetricID_SAE = chrMetricID_SAE)
#>     moduleServer(id, function(input, output, session) {
#>         rctv_dSnapshotDatePrevious <- reactive({
#>             dSnapshotDates <- as.Date(unique(dfResults$SnapshotDate))
#>             dSnapshotDatesPrevious <- dSnapshotDates[!is.na(dSnapshotDates) & 
#>                 dSnapshotDates < rctv_dSnapshotDate()]
#>             if (length(dSnapshotDatesPrevious)) {
#>                 return(max(dSnapshotDatesPrevious, na.rm = TRUE))
#>             }
#>             return(as.Date(NA, origin = "1970-01-01"))
#>         })
#>         rctv_strGroupID_inferred <- reactive({
#>             strGroupID <- rctv_strGroupID()
#>             strSubjectID <- rctv_strSubjectID()
#>             if (is.null(strGroupID) && length(strSubjectID) == 
#>                 1) {
#>                 test1 <- dfAnalyticsInput$SubjectID == strSubjectID
#>                 test2 <- dfAnalyticsInput$GroupLevel == rctv_strGroupLevel()
#>                 return(dfAnalyticsInput$GroupID[test1 & test2][[1]])
#>             }
#>             return(strGroupID)
#>         }) %>% bindCache(rctv_strSubjectID(), rctv_strGroupID(), 
#>             rctv_strGroupLevel())
#>         mod_AEDashboard_Server("dashboard", dfAnalyticsInput = dfAnalyticsInput, 
#>             rctv_dSnapshotDate = rctv_dSnapshotDate, rctv_dSnapshotDatePrevious = rctv_dSnapshotDatePrevious, 
#>             rctv_dfAE_Study = rctv_dfAE_Study, rctv_strGroupID = rctv_strGroupID_inferred, 
#>             rctv_strGroupLevel = rctv_strGroupLevel, rctv_strSubjectID = rctv_strSubjectID, 
#>             chrCategoricalFields = chrCategoricalFields, chrDateFields = chrDateFields)
#>     })
#> }
#> <bytecode: 0x5651bb165ae0>
#> <environment: namespace:gsm.ae>
#> 
#> 
#> $spec
#> $spec$AE
#> $spec$AE$SubjectID
#> $spec$AE$SubjectID$type
#> [1] "character"
#> 
#> 
#> $spec$AE$GroupID
#> $spec$AE$GroupID$type
#> [1] "character"
#> 
#> 
#> $spec$AE$GroupLevel
#> $spec$AE$GroupLevel$type
#> [1] "character"
#> 
#> 
#> $spec$AE$aeser
#> $spec$AE$aeser$type
#> [1] "character"
#> 
#> 
#> $spec$AE$mdrpt_nsv
#> $spec$AE$mdrpt_nsv$type
#> [1] "character"
#> 
#> 
#> $spec$AE$mdrsoc_nsv
#> $spec$AE$mdrsoc_nsv$type
#> [1] "character"
#> 
#> 
#> $spec$AE$aetoxgr
#> $spec$AE$aetoxgr$type
#> [1] "character"
#> 
#> 
#> $spec$AE$aeongo
#> $spec$AE$aeongo$type
#> [1] "character"
#> 
#> 
#> $spec$AE$aerel
#> $spec$AE$aerel$type
#> [1] "character"
#> 
#> 
#> $spec$AE$mincreated_dts
#> $spec$AE$mincreated_dts$type
#> [1] "Date"
#> 
#> 
#> $spec$AE$aest_dt
#> $spec$AE$aest_dt$type
#> [1] "Date"
#> 
#> 
#> $spec$AE$aeen_dt
#> $spec$AE$aeen_dt$type
#> [1] "Date"
#> 
#> 
#> 
#> $spec$SUBJ
#> $spec$SUBJ$SubjectID
#> $spec$SUBJ$SubjectID$type
#> [1] "character"
#> 
#> 
#> 
#> 
#> $config
#> $config$chrCategoricalFields
#>                aeser            mdrpt_nsv           mdrsoc_nsv 
#>           "Serious?"     "Preferred Term" "System Organ Class" 
#>              aetoxgr               aeongo                aerel 
#>     "Toxicity Grade"           "Ongoing?"           "Related?" 
#> 
#> $config$chrDateFields
#>  mincreated_dts         aest_dt         aeen_dt 
#> "AE Entry Date" "AE Start Date"   "AE End Date" 
#> 
#> $config$chrMetricID_AE
#>               Site            Country 
#> "Analysis_kri0001" "Analysis_cou0001" 
#> 
#> $config$chrMetricID_SAE
#>               Site            Country 
#> "Analysis_kri0002" "Analysis_cou0002" 
#> 
#> 
#> $packages
#> list()
#> 
#> $required_inputs
#> character(0)
#> 
#> $workflows
#> list()
#>