implemented checks with 'performance' package

inst/apps/data_analysis/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13276335
-bundleId: 9426438
+bundleId: 9433115
 url: https://agdamsbo.shinyapps.io/webResearch/
 version: 1

inst/apps/data_analysis/server.R

@@ -20,6 +20,8 @@ library(here)
 library(broom)
 library(broom.helpers)
 library(REDCapCAST)
+library(easystats)
+library(patchwork)
 # if (!requireNamespace("webResearch")) {
 #   devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
 # }
@@ -68,7 +70,6 @@ server <- function(input, output, session) {
             REDCapCAST::numchar2fct(.x)
           )
         })()
-
     }
     return(out)
   })
@@ -194,9 +195,20 @@ server <- function(input, output, session) {
           )
         })
 
+      # browser()
+      # check <- performance::check_model(purrr::pluck(models,"Multivariable") |>
+      #                                     (\(x){
+      #                                       class(x) <- class(x)[class(x) != "webresearch_model"]
+      #                                       return(x)
+      #                                     })())
+
+      check <- purrr::pluck(models, "Multivariable") |>
+        performance::check_model()
+
 
       v$list <- list(
         data = data,
+        check = check,
         table1 = data |>
           baseline_table(
             fun.args =
@@ -234,9 +246,27 @@ server <- function(input, output, session) {
         v$list$table2 |>
           gtsummary::as_gt()
       )
+
+      output$check <- shiny::renderPlot({
+        p <- plot(check) +
+          patchwork::plot_annotation(title = "Multivariable regression model checks")
+        p
+        # Generate checks in one column
+        # layout <- sapply(seq_len(length(p)), \(.x){
+        #   patchwork::area(.x, 1)
+        # })
+        #
+        # p + patchwork::plot_layout(design = Reduce(c, layout))
+
+        # patchwork::wrap_plots(ncol=1) +
+        # patchwork::plot_annotation(title = 'Multivariable regression model checks')
+      })
     }
   )
 
+
+
+
   output$uploaded <- shiny::reactive({
     if (is.null(v$ds)) {
       "no"

inst/apps/data_analysis/ui.R

@@ -17,8 +17,12 @@ panels <- list(
     gt::gt_output(outputId = "table1")
   ),
   bslib::nav_panel(
-    title = "Multivariable regression table",
+    title = "Regression table",
     gt::gt_output(outputId = "table2")
+  ),
+  bslib::nav_panel(
+    title = "Regression checks",
+    shiny::plotOutput(outputId = "check")
   )
 )
 
@@ -193,7 +197,8 @@ ui <- bslib::page(
     bslib::nav_spacer(),
     panels[[1]],
     panels[[2]],
-    panels[[3]]
+    panels[[3]],
+    panels[[4]]
 
     # layout_columns(
     #   cards[[1]]

inst/apps/data_analysis/www/report.qmd

@@ -16,7 +16,9 @@ params:
 web_data <- readr::read_rds(file = params$data.file)
 library(gtsummary)
 library(gt)
-library(webResearch)
+library(easystats)
+library(patchwork)
+# library(webResearch)
 ```
 
 ## Introduction
@@ -25,7 +27,7 @@ Research should be free and open with easy access for all. The webResearch tool
 
 ## Methods
 
-Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")` using the web-based data analysis tool 'webResearcher' version `r packageVersion("webResearch")`.
+Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")`.
 
 ## Results
 
@@ -48,3 +50,19 @@ web_data$table2
 ## Discussion
 
 Good luck on your further work!
+
+## Sensitivity
+
+Here are the results from testing the regression model:
+
+
+```{r}
+#| label: tbl-checks
+#| fig-cap: Regression analysis checks
+#| fig-height: 8
+#| fig-width: 6
+#| fig-dpi: 600
+
+plot(web_data$check)
+
+```