functions to modify qmd for specific exports

.Rbuildignore

@@ -4,3 +4,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^dev$
+.github

DESCRIPTION

@@ -22,9 +22,12 @@ Imports:
     readODS,
     readr,
     shiny,
-    MASS
+    MASS,
+    REDCapCAST,
+    purrr
 Suggests: 
     styler,
-    devtools
+    devtools,
+    rhub
 URL: https://github.com/agdamsbo/webResearch
 BugReports: https://github.com/agdamsbo/webResearch/issues

NAMESPACE

@@ -2,11 +2,17 @@
 
 export(argsstring2list)
 export(baseline_table)
+export(default_format_arguments)
+export(factorize)
+export(format_writer)
 export(getfun)
+export(index_embed)
+export(modify_qmd)
 export(panel_space)
 export(read_input)
 export(regression_model)
 export(regression_table)
 export(shiny_webResearch)
+export(specify_qmd_format)
 export(write_quarto)
 importFrom(stats,as.formula)

R/helpers.R

@@ -24,15 +24,13 @@ getfun <- function(x) {
 #' Wrapper to save data in RDS, load into specified qmd and render
 #'
 #' @param data list to pass to qmd
-#' @param fileformat output format. Ignored if file!=NULL
-#' @param qmd.file qmd file to render. Default is 'here::here("report.qmd")'
 #' @param ... Passed to `quarto::quarto_render()`
 #'
 #' @return output file name
 #' @export
 #'
-write_quarto <- function(data,fileformat=c("html","docx","odt","pdf","all"),qmd.file=here::here("report.qmd"),...){
+write_quarto <- function(data,...){
-  fileformat <- match.arg(fileformat)
+
   # Exports data to temporary location
   #
   # I assume this is more secure than putting it in the www folder and deleting
@@ -43,9 +41,7 @@ write_quarto <- function(data,fileformat=c("html","docx","odt","pdf","all"),qmd.
   ## 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(qmd.file,
+  quarto::quarto_render(execute_params = list(data.file=temp),
-                        output_format = fileformat,
-                        execute_params = list(data.file=temp),
                         ...
   )
 }

R/report.R

@@ -0,0 +1,81 @@
+#' Split vector by an index and embed addition
+#'
+#' @param data vector
+#' @param index split index
+#' @param add addition
+#'
+#' @return vector
+#' @export
+#'
+index_embed <- function(data, index, add = NULL) {
+  start <- seq_len(index)
+  end <- seq_along(data)[-start]
+  c(
+    data[start],
+    add,
+    data[end]
+  )
+}
+
+#' Specify format arguments to include in qmd header/frontmatter
+#'
+#' @param data vector
+#' @param fileformat format to include
+#'
+#' @return vector
+#' @export
+#'
+specify_qmd_format <- function(data, fileformat = c("docx", "odt", "pdf", "all")) {
+  fileformat <- match.arg(fileformat)
+  args_list <- default_format_arguments() |> purrr::imap(format_writer)
+
+  if (fileformat == "all") {
+    out <- data |> index_embed(index = 4, add = Reduce(c, args_list))
+  } else {
+    out <- data |> index_embed(index = 4, add = args_list[[fileformat]])
+  }
+  out
+}
+
+#' Merges list of named arguments for qmd header generation
+#'
+#' @param data vector
+#' @param name name
+#'
+#' @return vector
+#' @export
+#'
+format_writer <- function(data, name) {
+  if (data == "default") {
+    glue::glue("  {name}: {data}")
+  } else {
+    warning("Not implemented")
+  }
+}
+
+#' Defaults qmd formats
+#'
+#' @return list
+#' @export
+#'
+default_format_arguments <- function() {
+  list(
+    docx = list("default"),
+    odt = list("default"),
+    pdf = list("default")
+  )
+}
+
+#' Wrapper to modify quarto file to render specific formats
+#'
+#' @param file filename
+#' @param format desired output
+#'
+#' @return none
+#' @export
+#'
+modify_qmd <- function(file, format) {
+  readLines(file) |>
+    specify_qmd_format(fileformat = "all") |>
+    writeLines(paste0(tools::file_path_sans_ext(file), "_format.", tools::file_ext(file)))
+}

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:
+bundleId: 9402292
 url: https://agdamsbo.shinyapps.io/webResearch/
 version: 1

inst/apps/data_analysis/server.R

@@ -162,9 +162,25 @@ server <- function(input, output, session) {
         v$list$table2 |>
           gtsummary::as_gt()
       )
+
+
+
     }
   )
 
+  # renderUI({
+  #   tags$iframe(seamless="seamless",
+  #               src= "Hub_Infographic.html",
+  #               width=800,
+  #               height=800)
+  # })
+  #
+  #
+  # getPage<-shiny::reactive({
+  #   shiny::req(file.exists(file.path(getwd(), "www/report_format.html")))
+  #   return(shiny::includeHTML(file.path(getwd(), "www/report_format.html")))
+  # })
+
   output$uploaded <- shiny::reactive({
     if (is.null(v$ds)) {
       "no"
@@ -195,8 +211,8 @@ server <- function(input, output, session) {
     content = function(file, type = input$output_type) {
       v$list |>
         write_quarto(
-          fileformat = type,
+          output_format = type,
-          qmd.file = file.path(getwd(), "www/report.qmd")
+          input = file.path(getwd(), "www/report.qmd")
         )
       file.rename(paste0("www/report.", type), file)
     }
@@ -210,5 +226,5 @@ server <- function(input, output, session) {
       print(paste(.x, "deleted"))
     })
   })
-  #
+
 }

inst/apps/data_analysis/ui.R

@@ -47,7 +47,19 @@ panels <- list(
 
 
 ui <- bslib::page(
-  theme = bslib::bs_theme(bootswatch = "minty"),
+  theme = bslib::bs_theme(bootswatch = "minty",
+                            base_font = font_google("Inter"),
+                            code_font = font_google("JetBrains Mono")
+                          ),
+  # theme = bslib::bs_theme(
+    # bg = "#101010",
+    # fg = "#FFF",
+  #   primary = "#E69F00",
+  #   secondary = "#0072B2",
+  #   success = "#009E73",
+  #   base_font = font_google("Inter"),
+  #   code_font = font_google("JetBrains Mono")
+  # ),
   title = "webResearcher for easy data analysis",
   bslib::page_navbar(
     title = "webResearcher",
@@ -159,7 +171,8 @@ ui <- bslib::page(
             choices = list(
               "Word" = "docx",
               "LibreOffice" = "odt",
-              "PDF" = "pdf"
+              "PDF" = "pdf",
+              "All the above" = "all"
             )
           ),
 

inst/apps/data_analysis/www/report.qmd

@@ -1,16 +1,13 @@
 ---
+format: 
+  html:
+    embed-resources: true
 title: "webResearch analysis results"
 date: today
 author: webResearch Tool
 toc: true
 execute: 
   echo: false
-format: 
-  html:
-    embed-resources: true
-  docx: default
-  odt: default
-  pdf: default
 params:
   data.file: NA
 ---

man/default_format_arguments.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{default_format_arguments}
+\alias{default_format_arguments}
+\title{Defaults qmd formats}
+\usage{
+default_format_arguments()
+}
+\value{
+list
+}
+\description{
+Defaults qmd formats
+}

man/factorize.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpers.R
+\name{factorize}
+\alias{factorize}
+\title{Factorize variables in data.frame}
+\usage{
+factorize(data, vars)
+}
+\arguments{
+\item{data}{data.frame}
+
+\item{vars}{variables to force factorize}
+}
+\value{
+data.frame
+}
+\description{
+Factorize variables in data.frame
+}

man/format_writer.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{format_writer}
+\alias{format_writer}
+\title{Merges list of named arguments for qmd header generation}
+\usage{
+format_writer(data, name)
+}
+\arguments{
+\item{data}{vector}
+
+\item{name}{name}
+}
+\value{
+vector
+}
+\description{
+Merges list of named arguments for qmd header generation
+}

man/index_embed.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{index_embed}
+\alias{index_embed}
+\title{Split vector by an index and embed addition}
+\usage{
+index_embed(data, index, add = NULL)
+}
+\arguments{
+\item{data}{vector}
+
+\item{index}{split index}
+
+\item{add}{addition}
+}
+\value{
+vector
+}
+\description{
+Split vector by an index and embed addition
+}

man/modify_qmd.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{modify_qmd}
+\alias{modify_qmd}
+\title{Wrapper to modify quarto file to render specific formats}
+\usage{
+modify_qmd(file, format)
+}
+\arguments{
+\item{file}{filename}
+
+\item{format}{desired output}
+}
+\value{
+none
+}
+\description{
+Wrapper to modify quarto file to render specific formats
+}

man/specify_qmd_format.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{specify_qmd_format}
+\alias{specify_qmd_format}
+\title{Specify format arguments to include in qmd header/frontmatter}
+\usage{
+specify_qmd_format(data, fileformat = c("docx", "odt", "pdf", "all"))
+}
+\arguments{
+\item{data}{vector}
+
+\item{fileformat}{format to include}
+}
+\value{
+vector
+}
+\description{
+Specify format arguments to include in qmd header/frontmatter
+}

man/write_quarto.Rd

@@ -4,18 +4,11 @@
 \alias{write_quarto}
 \title{Wrapper to save data in RDS, load into specified qmd and render}
 \usage{
-write_quarto(
+write_quarto(data, qmd.file = here::here("report.qmd"), ...)
-  data,
-  fileformat = c("html", "docx", "odt", "pdf", "all"),
-  qmd.file = here::here("report.qmd"),
-  ...
-)
 }
 \arguments{
 \item{data}{list to pass to qmd}
 
-\item{fileformat}{output format. Ignored if file!=NULL}
-
 \item{qmd.file}{qmd file to render. Default is 'here::here("report.qmd")'}
 
 \item{...}{Passed to \code{quarto::quarto_render()}}