moving towards first working state

.gitignore

@@ -5,3 +5,4 @@ dev/
 .httr-oauth
 .DS_Store
 .quarto
+app/rsconnect

DESCRIPTION

@@ -11,6 +11,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports: 
     assertthat,
+    bslib,
     dplyr,
     glue,
     gt,
@@ -20,7 +21,8 @@ Imports:
     openxlsx2,
     quarto,
     readODS,
-    readr
+    readr,
+    shiny
 Suggests: 
     MASS,
     styler

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(argsstring2list)
 export(baseline_table)
 export(file_extension)
 export(getfun)

app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13276335
-bundleId: 9334284
+bundleId: 9334579
 url: https://agdamsbo.shinyapps.io/webResearch/
 version: 1

app/server.R

@@ -1,5 +1,23 @@
 # project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
-source(here::here("app/functions.R"))
+# source(here::here("functions.R"))
+
+source("https://raw.githubusercongittent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
+
+library(readr)
+library(MASS)
+library(stats)
+library(gt)
+library(gtsummary)
+library(openxlsx2)
+library(haven)
+library(readODS)
+library(shiny)
+library(bslib)
+library(assertthat)
+library(dplyr)
+library(quarto)
+library(here)
+
 
 server <- function(input, output, session) {
   v <- shiny::reactiveValues(
@@ -108,7 +126,7 @@ server <- function(input, output, session) {
   output$report <- downloadHandler(
     filename = "analyses.html",
     content = function(file) {
-      v$list |> write_quarto(file = file)
+      v$list |> write_quarto(file = file,qmd.file = "www/analyses.qmd")
     }
   )
 

app/ui.R

@@ -104,16 +104,16 @@ ui <- bslib::page_sidebar(
       ),
       actionButton("load", "Analyse", class = "btn-primary")
     )
-    # ,
+     ,
 
-    # Horizontal line ----
+     # Horizontal line ----
-    # tags$hr(),
+     tags$hr(),
-    # h4("Download results"),
+     h4("Download results"),
-    #
+
-    # # Button
+     # Button
-    # downloadButton(outputId="report",
+     downloadButton(outputId="report",
-    #                label= "Download",
+                    label= "Download",
-    #                icon = shiny::icon("download"))
+                    icon = shiny::icon("download"))
   ),
   layout_columns(
     cards[[1]]

app/www/analyses.qmd

@@ -7,22 +7,8 @@ params:
   data.file: NA
 ---
 
-<!-- ## Abstract -->
-
-<!-- ### Background -->
-
-<!-- ### Methods -->
-
-<!-- ### Results -->
-
-<!-- ### Conclusion -->
-
-
 ```{r setup}
 web_data <- readRDS(file = params$data.file)
-# readr::read_rds(file = here::here("data.Rds"))
-library(gtsummary)
-library(gt)
 ```
 
 ## Introduction

man/argsstring2list.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{argsstring2list}
+\alias{argsstring2list}
+\title{Convert string of arguments to list of arguments}
+\usage{
+argsstring2list(string)
+}
+\arguments{
+\item{string}{string to convert to list to use with do.call}
+}
+\value{
+list
+}
+\description{
+Idea from the answer: https://stackoverflow.com/a/62979238
+}

man/regression_model.Rd

@@ -6,11 +6,11 @@
 \usage{
 regression_model(
   data,
-  outcome.str = "gear",
+  outcome.str,
-  outcome.factor = TRUE,
+  auto.mode = TRUE,
   formula.str = NULL,
-  args.list = list(Hess = TRUE, method = "logistic"),
+  args.list = NULL,
-  fun = "MASS::polr",
+  fun = NULL,
   vars = NULL
 )
 }
@@ -19,7 +19,7 @@ regression_model(
 
 \item{outcome.str}{Name of outcome variable. Character vector.}
 
-\item{outcome.factor}{Factorize outcome variable. Logical.}
+\item{auto.mode}{Make assumptions on function dependent on outcome data format.}
 
 \item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.}
 
@@ -37,11 +37,10 @@ Print a flexible baseline characteristics table
 }
 \examples{
 gtsummary::trial |>
-  regression_model(outcome.str = "stage", fun = "MASS::polr")
+  regression_model(outcome.str = "age")
 gtsummary::trial |>
   regression_model(
     outcome.str = "age",
-    outcome.factor = FALSE,
     fun = "stats::lm",
     formula.str = "{outcome.str}~.",
     args.list = NULL

man/regression_table.Rd

@@ -29,7 +29,6 @@ gtsummary::trial |>
 gtsummary::trial |>
   regression_model(
     outcome.str = "age",
-    outcome.factor = FALSE,
     fun = "stats::lm",
     formula.str = "{outcome.str}~.",
     args.list = NULL
@@ -41,5 +40,5 @@ gtsummary::trial |>
     fun = "stats::glm",
     args.list = list(family = binomial(link = "logit"))
   ) |>
-  regression_table(args.list = list(exponentiate = TRUE))
+  regression_table()
 }

publish_shiny.R

@@ -7,7 +7,7 @@ project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here(
 shiny::runApp(appDir = here::here("app/"), launch.browser = TRUE)
 
 project.aid::deploy_shiny(
-  files = c("server.R", "ui.R"),
+  path="app/",
   account.name = "agdamsbo",
   name.app = "webResearch",
   name.token = "rsconnect_agdamsbo_token",

renv.lock

@@ -9,6 +9,21 @@
     ]
   },
   "Packages": {
+    "MASS": {
+      "Package": "MASS",
+      "Version": "7.3-61",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
+    },
     "PKI": {
       "Package": "PKI",
       "Version": "0.1-14",