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Merge pull request #1 from agdamsbo/report

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Report export solved
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Andreas Gammelgaard Damsbo 2025-01-23 14:26:06 +01:00 • committed by GitHub
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7 changed files with 187 additions and 52 deletions
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21
R/helpers.R
View file

@ -50,6 +50,27 @@ write_quarto <- function(data,...) {
)
}
write_rmd <- 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 <- 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
rmarkdown::render(
params = list(data.file = "web_data.rds"),
# execute_params = list(data.file = temp),
...
)
}
#' Flexible file import based on extension
#'
#' @param file file name

56
inst/apps/data_analysis_modules/app.R
View file

@ -1160,6 +1160,27 @@ write_quarto <- function(data,...) {
)
}
write_rmd <- 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 <- 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
rmarkdown::render(
params = list(data.file = "web_data.rds"),
# execute_params = list(data.file = temp),
...
)
}
#' Flexible file import based on extension
#'
#' @param file file name
@ -3882,7 +3903,7 @@ ui <- bslib::page_fixed(
),
shiny::p(
style = "margin: 1; color: #888;",
"AG Damsbo | v", format(Sys.Date(),format = '%y%m%d')," | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
"AG Damsbo | v", format(Sys.time(),format = '%y%m%d_%H%M')," | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
),
)
)
@ -3924,7 +3945,7 @@ library(gtsummary)
# source("functions.R")
data(mtcars)
# light <- custom_theme()
#
@ -4568,11 +4589,13 @@ server <- function(input, output, session) {
})
}
rv$list$regression$table <- out |>
tbl_merge()
rv$list$regression$tables <- out
gtsummary::as_kable(rv$list$regression$table) |>
readr::write_lines(file="./www/_regression_table.md")
# rv$list$regression$table <- out |>
# tbl_merge()
# gtsummary::as_kable(rv$list$regression$table) |>
# readr::write_lines(file="./www/_regression_table.md")
rv$list$input <- input
},
@ -4588,8 +4611,9 @@ server <- function(input, output, session) {
)
output$table2 <- gt::render_gt({
shiny::req(rv$list$regression$table)
rv$list$regression$table |>
shiny::req(rv$list$regression$tables)
rv$list$regression$tables |>
tbl_merge() |>
gtsummary::as_gt() |>
gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
})
@ -4668,12 +4692,22 @@ server <- function(input, output, session) {
# shiny::req(rv$list$regression)
## Notification is not progressing
## Presumably due to missing
#Simplified for .rmd output attempt
format <- ifelse(type=="docx","word_document","odt_document")
shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
rv$list |>
write_quarto(
output_format = type,
input = file.path(getwd(), "www/report.qmd")
write_rmd(
output_format = format,
input = file.path(getwd(), "www/report.rmd")
)
# write_quarto(
# output_format = type,
# input = file.path(getwd(), "www/report.qmd")
# )
})
file.rename(paste0("www/report.", type), file)
}

10
inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf Normal file
View file

@ -0,0 +1,10 @@
name: freesearcheR_dev
title:
username: cognitiveindex
account: cognitiveindex
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 13786206
bundleId: 9688582
url: https://cognitiveindex.shinyapps.io/freesearcheR_dev/
version: 1

33
inst/apps/data_analysis_modules/server.R
View file

@ -29,7 +29,7 @@ library(gtsummary)
# source("functions.R")
data(mtcars)
# light <- custom_theme()
#
@ -673,11 +673,13 @@ server <- function(input, output, session) {
})
}
rv$list$regression$table <- out |>
tbl_merge()
rv$list$regression$tables <- out
gtsummary::as_kable(rv$list$regression$table) |>
readr::write_lines(file="./www/_regression_table.md")
# rv$list$regression$table <- out |>
# tbl_merge()
# gtsummary::as_kable(rv$list$regression$table) |>
# readr::write_lines(file="./www/_regression_table.md")
rv$list$input <- input
},
@ -693,8 +695,9 @@ server <- function(input, output, session) {
)
output$table2 <- gt::render_gt({
shiny::req(rv$list$regression$table)
rv$list$regression$table |>
shiny::req(rv$list$regression$tables)
rv$list$regression$tables |>
tbl_merge() |>
gtsummary::as_gt() |>
gt::tab_header(gt::md(glue::glue("**Table 2: {rv$list$regression$params$descr}**")))
})
@ -773,12 +776,22 @@ server <- function(input, output, session) {
# shiny::req(rv$list$regression)
## Notification is not progressing
## Presumably due to missing
#Simplified for .rmd output attempt
format <- ifelse(type=="docx","word_document","odt_document")
shiny::withProgress(message = "Generating the report. Hold on for a moment..", {
rv$list |>
write_quarto(
output_format = type,
input = file.path(getwd(), "www/report.qmd")
write_rmd(
output_format = format,
input = file.path(getwd(), "www/report.rmd")
)
# write_quarto(
# output_format = type,
# input = file.path(getwd(), "www/report.qmd")
# )
})
file.rename(paste0("www/report.", type), file)
}

2
inst/apps/data_analysis_modules/ui.R
View file

@ -518,7 +518,7 @@ ui <- bslib::page_fixed(
),
shiny::p(
style = "margin: 1; color: #888;",
"AG Damsbo | v", format(Sys.Date(),format = '%y%m%d')," | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
"AG Damsbo | v", format(Sys.time(),format = '%y%m%d_%H%M')," | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target = "_blank", rel = "noopener noreferrer")
),
)
)

49
inst/apps/data_analysis_modules/www/report.qmd
View file

@ -13,34 +13,17 @@ params:
```{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$data.file)
# library(gt)
# library(flextable)
# library(freesearcheR)
library(gtsummary)
library(gt)
tbl_merge <- function(data) {
if (is.null(names(data))) {
data |> gtsummary::tbl_merge()
} else {
data |> gtsummary::tbl_merge(tab_spanner = names(data))
}
}
```
## Introduction
@ -55,11 +38,17 @@ Analyses were conducted in the *freesearcheR* data analysis web-tool based on R
Below are the baseline characteristics.
{{< include _table1.md >}}
```{r, results = 'asis'}
tbl <- gtsummary::as_gt(web_data$table1)
knitr::knit_print(tbl)
```
Below are results from the univariable and multivariable regression analyses.
Below are the results from the
{{< include _regression_table.md >}}
```{r, results = 'asis'}
reg_tbl <- web_data$regression$tables
knitr::knit_print(tbl_merge(reg_tbl))
```
## Discussion

68
inst/apps/data_analysis_modules/www/report.rmd Normal file
View file

@ -0,0 +1,68 @@
---
title: "freesearcheR analysis results"
date: today
format: docx
author: freesearcheR Tool
toc: false
params:
data.file: NA
---
```{r setup, echo = FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
```
```{r}
web_data <- readr::read_rds(file = params$data.file)
library(gtsummary)
library(gt)
tbl_merge <- function(data) {
if (is.null(names(data))) {
data |> gtsummary::tbl_merge()
} else {
data |> gtsummary::tbl_merge(tab_spanner = names(data))
}
}
vec2sentence <- function(data, sep.word = "and") {
sep.word <- paste0(" ", gsub(" ", "", sep.word), " ")
if (length(data) < 2) {
out <- data
} else if (length(data) == 2) {
out <- paste(data, collapse = sep.word)
} else {
out <- paste(paste(data[-length(data)], collapse = ","), data[length(data)], sep = sep.word)
}
return(out)
}
```
## Introduction
Research should be free and open with easy access for all. The freesearcheR tool attempts to help lower the bar to participate in contributing to science by making guided data analysis easily accessible in the web-browser.
## Methods
Analyses were conducted in the *freesearcheR* data analysis web-tool based on R version 4.4.1.
## Results
Below are the baseline characteristics.
```{r, results = 'asis'}
tbl <- gtsummary::as_gt(web_data$table1)
knitr::knit_print(tbl)
```
Below are the results from the `r tolower(vec2sentence(names(web_data$regression$tables)))` `r web_data$regression$params$descr`.
```{r, results = 'asis'}
reg_tbl <- web_data$regression$tables
knitr::knit_print(tbl_merge(reg_tbl))
```
## Discussion
Good luck on your further work!