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default filter out empty columns before analyses

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Andreas Gammelgaard Damsbo 2025-01-20 12:00:50 +01:00
parent a6416f27ce
commit 27175d9655
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4 changed files with 28 additions and 7 deletions
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3
DESCRIPTION
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@ -53,7 +53,8 @@ Imports:
data.table, data.table,
apexcharter, apexcharter,
teal.modules.general, teal.modules.general,
esquisse esquisse,
janitor
Suggests: Suggests:
styler, styler,
devtools, devtools,

16
inst/apps/data_analysis_modules/app.R
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@ -3620,6 +3620,13 @@ ui_elements <- list(
# bslib::layout_sidebar( # bslib::layout_sidebar(
# fillable = TRUE, # fillable = TRUE,
sidebar = bslib::sidebar( sidebar = bslib::sidebar(
shiny::sliderInput(inputId = "complete_cutoff",
label = "Cut-off for column completeness",
min = 0,
max = 1,
step = 0.1,
value = 0.5),
shiny::helpText("To improve speed, columns are removed before analysing data"),
shiny::radioButtons( shiny::radioButtons(
inputId = "all", inputId = "all",
label = "Specify covariables", label = "Specify covariables",
@ -4134,7 +4141,8 @@ server <- function(input, output, session) {
shiny::reactive(rv$data), shiny::reactive(rv$data),
shiny::reactive(rv$data_original), shiny::reactive(rv$data_original),
data_filter(), data_filter(),
base_vars() base_vars(),
input$complete_cutoff
), ),
{ {
rv$data_filtered <- data_filter() rv$data_filtered <- data_filter()
@ -4143,7 +4151,8 @@ server <- function(input, output, session) {
REDCapCAST::fct_drop.data.frame() |> REDCapCAST::fct_drop.data.frame() |>
(\(.x){ (\(.x){
.x[base_vars()] .x[base_vars()]
})() })() |>
janitor::remove_empty(which = "cols",cutoff = input$complete_cutoff)
} }
) )
@ -4344,7 +4353,8 @@ server <- function(input, output, session) {
data_filter(), data_filter(),
input$strat_var, input$strat_var,
input$include_vars, input$include_vars,
input$add_p input$add_p,
input$complete_cutoff
), ),
{ {
shiny::req(input$strat_var) shiny::req(input$strat_var)

9
inst/apps/data_analysis_modules/server.R
View file

@ -277,7 +277,8 @@ server <- function(input, output, session) {
shiny::reactive(rv$data), shiny::reactive(rv$data),
shiny::reactive(rv$data_original), shiny::reactive(rv$data_original),
data_filter(), data_filter(),
base_vars() base_vars(),
input$complete_cutoff
), ),
{ {
rv$data_filtered <- data_filter() rv$data_filtered <- data_filter()
@ -286,7 +287,8 @@ server <- function(input, output, session) {
REDCapCAST::fct_drop.data.frame() |> REDCapCAST::fct_drop.data.frame() |>
(\(.x){ (\(.x){
.x[base_vars()] .x[base_vars()]
})() })() |>
janitor::remove_empty(which = "cols",cutoff = input$complete_cutoff)
} }
) )
@ -487,7 +489,8 @@ server <- function(input, output, session) {
data_filter(), data_filter(),
input$strat_var, input$strat_var,
input$include_vars, input$include_vars,
input$add_p input$add_p,
input$complete_cutoff
), ),
{ {
shiny::req(input$strat_var) shiny::req(input$strat_var)

7
inst/apps/data_analysis_modules/ui.R
View file

@ -278,6 +278,13 @@ ui_elements <- list(
# bslib::layout_sidebar( # bslib::layout_sidebar(
# fillable = TRUE, # fillable = TRUE,
sidebar = bslib::sidebar( sidebar = bslib::sidebar(
shiny::sliderInput(inputId = "complete_cutoff",
label = "Cut-off for column completeness",
min = 0,
max = 1,
step = 0.1,
value = 0.5),
shiny::helpText("To improve speed, columns are removed before analysing data"),
shiny::radioButtons( shiny::radioButtons(
inputId = "all", inputId = "all",
label = "Specify covariables", label = "Specify covariables",