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Issue361 - adding Clean Window selector to Incidence #362

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merged 2 commits into from
Oct 18, 2024
Merged

Issue361 - adding Clean Window selector to Incidence #362

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4761436
Adding clean window selector to incidence
nhall6 Oct 9, 2024
5b932c5
fixing when target = outcome
nhall6 Oct 9, 2024
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52 changes: 45 additions & 7 deletions R/characterization-incidence.R
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Original file line number Diff line number Diff line change
Expand Up @@ -353,6 +353,23 @@ characterizationIncidenceServer <- function(
)
),

shinyWidgets::pickerInput(
inputId = session$ns('cleanWindows'),
label = 'Select Clean Window',
choices = ciOptions$cleanWindows,
selected = ciOptions$cleanWindows,
multiple = F,
options = shinyWidgets::pickerOptions(
actionsBox = TRUE,
liveSearch = TRUE,
size = 10,
dropupAuto = TRUE,
liveSearchStyle = "contains",
liveSearchPlaceholder = "Type here to search",
virtualScroll = 50
)
),

shinyWidgets::pickerInput(
inputId = session$ns('tars'),
label = 'Select Time at risk (TAR)',
Expand All @@ -370,6 +387,7 @@ characterizationIncidenceServer <- function(
)
),


shiny::actionButton(
inputId = session$ns('generate'),
label = 'Generate',
Expand All @@ -384,12 +402,14 @@ characterizationIncidenceServer <- function(
incidenceRateAgeFilter <- shiny::reactiveVal(NULL)
incidenceRateGenderFilter <- shiny::reactiveVal(NULL)
incidenceRateDbFilter <- shiny::reactiveVal(NULL)
incidenceRateCleanWindowsFilter <- shiny::reactiveVal(NULL)
shiny::observeEvent(input$generate,{
incidenceRateTarFilter(names(ciOptions$tar)[(ciOptions$tar == input$tars)]) # filter needs actual value
incidenceRateCalendarFilter(input$startYears)
incidenceRateAgeFilter(input$ageIds)
incidenceRateGenderFilter(input$sexIds)
incidenceRateDbFilter(input$databaseSelector)
incidenceRateCleanWindowsFilter(input$cleanWindows)
outcomeIds(input$outcomeIds)
})

Expand Down Expand Up @@ -594,11 +614,13 @@ characterizationIncidenceServer <- function(
shiny::validate("Please wait...")
}

else if(targetIds()[1] == outcomeIds()[1] &&
length(targetIds())==1 && length(outcomeIds())==1
){
shiny::validate("Target and outcome cohorts must differ from each other. Make a different selection.")
}
#causing an issue when we want the same target & outcome for recurrent events

# else if(targetIds()[1] == outcomeIds()[1] &&
# length(targetIds())==1 && length(outcomeIds())==1
# ){
# shiny::validate("Target and outcome cohorts must differ from each other. Make a different selection.")
# }

else {
result <- getIncidenceData(targetIds = targetIds(),
Expand All @@ -625,7 +647,8 @@ characterizationIncidenceServer <- function(
.data$genderId %in% !! incidenceRateGenderFilter() &
.data$startYear %in% !! incidenceRateCalendarFilter() &
.data$tar %in% incidenceRateTarFilter() &
.data$cdmSourceAbbreviation %in% !! incidenceRateDbFilter()
.data$cdmSourceAbbreviation %in% !! incidenceRateDbFilter() &
.data$cleanWindow %in% !! incidenceRateCleanWindowsFilter()
) %>%
dplyr::relocate("targetName", .after = "cdmSourceAbbreviation") %>%
dplyr::relocate("outcomeName", .after = "targetName") %>%
Expand Down Expand Up @@ -654,7 +677,7 @@ characterizationIncidenceServer <- function(
id = "incidenceRateTable",
df = filteredData,
selectedCols = c("cdmSourceAbbreviation", "targetName", "targetNameShort", "outcomeName", "outcomeNameShort",
"ageGroupName", "genderName", "startYear", "tar", "outcomes",
"ageGroupName", "genderName", "startYear", "cleanWindow", "tar", "outcomes",
"incidenceProportionP100p", "incidenceRateP100py"),
sortedCols = c("ageGroupName", "genderName", "startYear", "incidenceRateP100py"),
elementId = "incidence-select",
Expand Down Expand Up @@ -1809,6 +1832,20 @@ from @result_schema.@incidence_table_prefixOUTCOME_DEF
outcomes <- outcomeDf$outcomeId
names(outcomes) <- outcomeDf$outcomeName

#getting clean window options
sql <- '
select clean_window
from @result_schema.@incidence_table_prefixOUTCOME_DEF
'
cleanWindowDf <- connectionHandler$queryDb(
sql = sql,
result_schema = resultDatabaseSettings$schema,
incidence_table_prefix = resultDatabaseSettings$incidenceTablePrefix
)
cleanWindows <- cleanWindowDf$cleanWindow
names(cleanWindows) <- cleanWindowDf$cleanWindow


irPlotCategoricalChoices <- list(
"cdmSourceAbbreviation",
"ageGroupName",
Expand Down Expand Up @@ -1867,6 +1904,7 @@ from @result_schema.@incidence_table_prefixOUTCOME_DEF
startYear = startYear,
tar = tar,
outcomes = outcomes,
cleanWindows = cleanWindows,
irPlotNumericChoices = irPlotNumericChoices,
irPlotCategoricalChoices = irPlotCategoricalChoices
)
Expand Down
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