From 02dfcf50d669ec36ead980d50485341b97c932ce Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Thu, 23 Jan 2025 08:44:38 +0100
Subject: [PATCH] resolving report creating on server by exporting/importing
 kable/md table. works for now. Not ideal.

---
 DESCRIPTION                                   |  5 +-
 R/helpers.R                                   | 12 ++--
 R/redcap.R                                    |  0
 R/regression_model.R                          |  9 ++-
 R/regression_table.R                          |  5 +-
 inst/apps/data_analysis_modules/app.R         | 50 ++++++++++-----
 .../shinyapps.io/agdamsbo/freesearcheR.dcf    |  2 +-
 inst/apps/data_analysis_modules/server.R      | 15 +++--
 inst/apps/data_analysis_modules/ui.R          |  2 +-
 .../apps/data_analysis_modules/www/report.qmd | 61 +++++++++++--------
 renv.lock                                     | 37 +++++++++++
 11 files changed, 143 insertions(+), 55 deletions(-)
 create mode 100644 R/redcap.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 8d77d15..d7b583d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,7 +54,10 @@ Imports:
     apexcharter,
     teal.modules.general,
     esquisse,
-    janitor
+    janitor,
+    flextable,
+    gt,
+    kableExtra
 Suggests: 
     styler,
     devtools,
diff --git a/R/helpers.R b/R/helpers.R
index 3baed74..5e21b4b 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -29,19 +29,23 @@ getfun <- function(x) {
 #' @return output file name
 #' @export
 #'
-write_quarto <- function(data, ...) {
+write_quarto <- function(data,...) {
   # Exports data to temporary location
   #
   # I assume this is more secure than putting it in the www folder and deleting
   # on session end
-  temp <- tempfile(fileext = ".rds")
-  readr::write_rds(data, file = temp)
+
+  # temp <- base::tempfile(fileext = ".rds")
+  # readr::write_rds(data, file = here)
+
+  readr::write_rds(data, file = "www/web_data.rds")
 
   ## Specifying a output path will make the rendering fail
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   quarto::quarto_render(
-    execute_params = list(data.file = temp),
+    execute_params = list(data.file = "web_data.rds"),
+    # execute_params = list(data.file = temp),
     ...
   )
 }
diff --git a/R/redcap.R b/R/redcap.R
new file mode 100644
index 0000000..e69de29
diff --git a/R/regression_model.R b/R/regression_model.R
index 69de02a..3e89e82 100644
--- a/R/regression_model.R
+++ b/R/regression_model.R
@@ -267,7 +267,8 @@ supported_functions <- function() {
       out.type = "continuous",
       fun = "stats::lm",
       args.list = NULL,
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     ),
     glm = list(
       descr = "Logistic regression model",
@@ -275,7 +276,8 @@ supported_functions <- function() {
       out.type = "dichotomous",
       fun = "stats::glm",
       args.list = list(family = stats::binomial(link = "logit")),
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     ),
     polr = list(
       descr = "Ordinal logistic regression model",
@@ -286,7 +288,8 @@ supported_functions <- function() {
         Hess = TRUE,
         method = "logistic"
       ),
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     )
   )
 }
diff --git a/R/regression_table.R b/R/regression_table.R
index 4a7fce6..2dff279 100644
--- a/R/regression_table.R
+++ b/R/regression_table.R
@@ -11,7 +11,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' gtsummary::trial |>
+#' tbl <- gtsummary::trial |>
 #'   regression_model(
 #'     outcome.str = "stage",
 #'     fun = "MASS::polr"
@@ -140,3 +140,6 @@ tbl_merge <- function(data) {
     data |> gtsummary::tbl_merge(tab_spanner = names(data))
   }
 }
+
+# as_kable(tbl) |> write_lines(file=here::here("inst/apps/data_analysis_modules/www/_table1.md"))
+# as_kable_extra(tbl)|> write_lines(file=here::here("inst/apps/data_analysis_modules/www/table1.md"))
diff --git a/inst/apps/data_analysis_modules/app.R b/inst/apps/data_analysis_modules/app.R
index 6739bf7..54186df 100644
--- a/inst/apps/data_analysis_modules/app.R
+++ b/inst/apps/data_analysis_modules/app.R
@@ -1139,19 +1139,23 @@ getfun <- function(x) {
 #' @return output file name
 #' @export
 #'
-write_quarto <- function(data, ...) {
+write_quarto <- function(data,...) {
   # Exports data to temporary location
   #
   # I assume this is more secure than putting it in the www folder and deleting
   # on session end
-  temp <- tempfile(fileext = ".rds")
-  readr::write_rds(data, file = temp)
+
+  # temp <- base::tempfile(fileext = ".rds")
+  # readr::write_rds(data, file = here)
+
+  readr::write_rds(data, file = "www/web_data.rds")
 
   ## Specifying a output path will make the rendering fail
   ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
   ## Outputs to the same as the .qmd file
   quarto::quarto_render(
-    execute_params = list(data.file = temp),
+    execute_params = list(data.file = "web_data.rds"),
+    # execute_params = list(data.file = temp),
     ...
   )
 }
@@ -1711,6 +1715,13 @@ redcap_app <- function() {
 }
 
 
+########
+#### Current file: R//redcap.R 
+########
+
+
+
+
 ########
 #### Current file: R//regression_model.R 
 ########
@@ -1984,7 +1995,8 @@ supported_functions <- function() {
       out.type = "continuous",
       fun = "stats::lm",
       args.list = NULL,
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     ),
     glm = list(
       descr = "Logistic regression model",
@@ -1992,7 +2004,8 @@ supported_functions <- function() {
       out.type = "dichotomous",
       fun = "stats::glm",
       args.list = list(family = stats::binomial(link = "logit")),
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     ),
     polr = list(
       descr = "Ordinal logistic regression model",
@@ -2003,7 +2016,8 @@ supported_functions <- function() {
         Hess = TRUE,
         method = "logistic"
       ),
-      formula.str = "{outcome.str}~{paste(vars,collapse='+')}"
+      formula.str = "{outcome.str}~{paste(vars,collapse='+')}",
+      table.fun = "gtsummary::tbl_regression"
     )
   )
 }
@@ -2332,7 +2346,7 @@ regression_model_uv_list <- function(data,
 #'
 #' @examples
 #' \dontrun{
-#' gtsummary::trial |>
+#' tbl <- gtsummary::trial |>
 #'   regression_model(
 #'     outcome.str = "stage",
 #'     fun = "MASS::polr"
@@ -2462,6 +2476,9 @@ tbl_merge <- function(data) {
   }
 }
 
+# as_kable(tbl) |> write_lines(file=here::here("inst/apps/data_analysis_modules/www/_table1.md"))
+# as_kable_extra(tbl)|> write_lines(file=here::here("inst/apps/data_analysis_modules/www/table1.md"))
+
 
 ########
 #### Current file: R//report.R 
@@ -3736,7 +3753,7 @@ ui_elements <- list(
               label = "Download report",
               icon = shiny::icon("download")
             ),
-            shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
+            # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
             shiny::tags$hr(),
             shiny::h4("Data"),
             shiny::helpText("Choose your favourite output data format to download the modified data."),
@@ -3871,7 +3888,6 @@ ui <- bslib::page_fixed(
 library(readr)
 library(MASS)
 library(stats)
-library(gtsummary)
 library(gt)
 library(openxlsx2)
 library(haven)
@@ -3895,6 +3911,7 @@ library(data.table)
 library(IDEAFilter)
 library(shinyWidgets)
 library(DT)
+library(gtsummary)
 # library(freesearcheR)
 
 # source("functions.R")
@@ -4411,6 +4428,9 @@ server <- function(input, output, session) {
             .x
           }
         })()
+
+      gtsummary::as_kable(rv$list$table1) |>
+        readr::write_lines(file="./www/_table1.md")
     }
   )
 
@@ -4453,7 +4473,7 @@ server <- function(input, output, session) {
 
           # browser()
 
-          rv$list$regression$options <- get_fun_options(input$regression_type) |>
+          rv$list$regression$params <- get_fun_options(input$regression_type) |>
             (\(.x){
               .x[[1]]
             })()
@@ -4542,6 +4562,9 @@ server <- function(input, output, session) {
           rv$list$regression$table <- out |>
             tbl_merge()
 
+          gtsummary::as_kable(rv$list$regression$table) |>
+            readr::write_lines(file="./www/_regression_table.md")
+
           rv$list$input <- input
         },
         warning = function(warn) {
@@ -4559,7 +4582,7 @@ server <- function(input, output, session) {
     shiny::req(rv$list$regression$table)
     rv$list$regression$table |>
       gtsummary::as_gt() |>
-      gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$options$descr}**")))
+      gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
   })
 
 
@@ -4582,7 +4605,6 @@ server <- function(input, output, session) {
     bslib::nav_select(id = "main_panel", selected = "Data")
   })
 
-
   ##############################################################################
   #########
   #########  Reactivity
@@ -4634,7 +4656,7 @@ server <- function(input, output, session) {
       paste0("report.", input$output_type)
     }),
     content = function(file, type = input$output_type) {
-      shiny::req(rv$list$regression)
+      # shiny::req(rv$list$regression)
       ## Notification is not progressing
       ## Presumably due to missing
       shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
diff --git a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
index 863aec1..d38b3ab 100644
--- a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
+++ b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13611288
-bundleId: 9672500
+bundleId: 9687528
 url: https://agdamsbo.shinyapps.io/freesearcheR/
 version: 1
diff --git a/inst/apps/data_analysis_modules/server.R b/inst/apps/data_analysis_modules/server.R
index 83abc8a..d0206a7 100644
--- a/inst/apps/data_analysis_modules/server.R
+++ b/inst/apps/data_analysis_modules/server.R
@@ -1,7 +1,6 @@
 library(readr)
 library(MASS)
 library(stats)
-library(gtsummary)
 library(gt)
 library(openxlsx2)
 library(haven)
@@ -25,6 +24,7 @@ library(data.table)
 library(IDEAFilter)
 library(shinyWidgets)
 library(DT)
+library(gtsummary)
 # library(freesearcheR)
 
 # source("functions.R")
@@ -541,6 +541,9 @@ server <- function(input, output, session) {
             .x
           }
         })()
+
+      gtsummary::as_kable(rv$list$table1) |>
+        readr::write_lines(file="./www/_table1.md")
     }
   )
 
@@ -583,7 +586,7 @@ server <- function(input, output, session) {
 
           # browser()
 
-          rv$list$regression$options <- get_fun_options(input$regression_type) |>
+          rv$list$regression$params <- get_fun_options(input$regression_type) |>
             (\(.x){
               .x[[1]]
             })()
@@ -672,6 +675,9 @@ server <- function(input, output, session) {
           rv$list$regression$table <- out |>
             tbl_merge()
 
+          gtsummary::as_kable(rv$list$regression$table) |>
+            readr::write_lines(file="./www/_regression_table.md")
+
           rv$list$input <- input
         },
         warning = function(warn) {
@@ -689,7 +695,7 @@ server <- function(input, output, session) {
     shiny::req(rv$list$regression$table)
     rv$list$regression$table |>
       gtsummary::as_gt() |>
-      gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$options$descr}**")))
+      gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
   })
 
 
@@ -712,7 +718,6 @@ server <- function(input, output, session) {
     bslib::nav_select(id = "main_panel", selected = "Data")
   })
 
-
   ##############################################################################
   #########
   #########  Reactivity
@@ -764,7 +769,7 @@ server <- function(input, output, session) {
       paste0("report.", input$output_type)
     }),
     content = function(file, type = input$output_type) {
-      shiny::req(rv$list$regression)
+      # shiny::req(rv$list$regression)
       ## Notification is not progressing
       ## Presumably due to missing
       shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
diff --git a/inst/apps/data_analysis_modules/ui.R b/inst/apps/data_analysis_modules/ui.R
index a22021f..3c883f9 100644
--- a/inst/apps/data_analysis_modules/ui.R
+++ b/inst/apps/data_analysis_modules/ui.R
@@ -389,7 +389,7 @@ ui_elements <- list(
               label = "Download report",
               icon = shiny::icon("download")
             ),
-            shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
+            # shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
             shiny::tags$hr(),
             shiny::h4("Data"),
             shiny::helpText("Choose your favourite output data format to download the modified data."),
diff --git a/inst/apps/data_analysis_modules/www/report.qmd b/inst/apps/data_analysis_modules/www/report.qmd
index 9ddee9e..d70b84d 100644
--- a/inst/apps/data_analysis_modules/www/report.qmd
+++ b/inst/apps/data_analysis_modules/www/report.qmd
@@ -1,22 +1,45 @@
 ---
-format: 
-  html:
-    embed-resources: true
 title: "freesearcheR analysis results"
 date: today
+format: docx
 author: freesearcheR Tool
-toc: true
+toc: false
 execute: 
   echo: false
 params:
   data.file: NA
 ---
 
-```{r setup}
+```{r}
+#| message: false
+#| warning: false
+# if (!requireNamespace("gtsummary")){
+#   install.packages("gtsummary")
+#   } else {
+#   library(gtsummary)
+#   }
+# 
+# if (!requireNamespace("gt")){
+#   install.packages("gt")
+#   } else {
+#   library(gt)
+#   }
+# 
+# if (!requireNamespace("readr")){
+#   install.packages("readr")
+#   } else {
+#   library(readr)
+#   }
+# requireNamespace("gtsummary")
+# requireNamespace("gt")
+# require(gt)
+# require(flextable)
+# if (!requireNamespace("readr")){
+#   install.packages("readr")
+# }
 web_data <- readr::read_rds(file = params$data.file)
-library(gtsummary)
-library(gt)
-library(flextable)
+# library(gt)
+# library(flextable)
 # library(freesearcheR)
 ```
 
@@ -26,29 +49,17 @@ Research should be free and open with easy access for all. The freesearcheR tool
 
 ## Methods
 
-Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")`.
+Analyses were conducted in the *freesearcheR* data analysis web-tool based on R version 4.4.1.
 
 ## Results
 
-Below is the baseline characteristics plotted.
+Below are the baseline characteristics.
 
-```{r}
-#| label: tbl-baseline
-#| tbl-cap: Baseline characteristics of included data
-web_data$table1 |> 
-  gtsummary::as_flex_table() |> 
-  flextable::set_table_properties(width = 1, layout = "autofit")
-```
+{{< include _table1.md >}}
 
-Here are the results from the `r web_data$regression$options$descr`.
+Below are results from the univariable and multivariable regression analyses.
 
-```{r}
-#| label: tbl-regression
-#| tbl-cap: Regression analysis results
-web_data$regression$table|> 
-  gtsummary::as_flex_table() |> 
-  flextable::set_table_properties(width = 1, layout = "autofit")
-```
+{{< include _regression_table.md >}}
 
 ## Discussion
 
diff --git a/renv.lock b/renv.lock
index 52263e5..309f851 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1742,6 +1742,31 @@
       ],
       "Hash": "3bcd11943da509341838da9399e18bce"
     },
+    "kableExtra": {
+      "Package": "kableExtra",
+      "Version": "1.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "digest",
+        "grDevices",
+        "graphics",
+        "htmltools",
+        "knitr",
+        "magrittr",
+        "rmarkdown",
+        "rstudioapi",
+        "scales",
+        "stats",
+        "stringr",
+        "svglite",
+        "tools",
+        "viridisLite",
+        "xml2"
+      ],
+      "Hash": "532d16304274c23c8563f94b79351c86"
+    },
     "keyring": {
       "Package": "keyring",
       "Version": "1.3.2",
@@ -3104,6 +3129,18 @@
       ],
       "Hash": "fe42836742a4f065b3f3f5de81fccab9"
     },
+    "svglite": {
+      "Package": "svglite",
+      "Version": "2.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cpp11",
+        "systemfonts"
+      ],
+      "Hash": "124a41fdfa23e8691cb744c762f10516"
+    },
     "sys": {
       "Package": "sys",
       "Version": "3.4.3",