diff --git a/R/helpers.R b/R/helpers.R index 5e21b4b..aecfce7 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -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 diff --git a/inst/apps/data_analysis_modules/app.R b/inst/apps/data_analysis_modules/app.R index 54186df..ef3bf70 100644 --- a/inst/apps/data_analysis_modules/app.R +++ b/inst/apps/data_analysis_modules/app.R @@ -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 @@ -3874,7 +3895,7 @@ 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") ), ) ) @@ -3916,7 +3937,7 @@ library(gtsummary) # source("functions.R") - +data(mtcars) # light <- custom_theme() # @@ -4559,11 +4580,13 @@ 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$input <- input }, @@ -4579,8 +4602,9 @@ server <- function(input, output, session) { ) output$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}**"))) }) @@ -4659,12 +4683,22 @@ 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$list |> - write_quarto( - output_format = type, - input = file.path(getwd(), "www/report.qmd") + write_rmd( + output_format = format, + input = file.path(getwd(), "www/report.rmd") ) + + # write_quarto( + # output_format = type, + # input = file.path(getwd(), "www/report.qmd") + # ) }) file.rename(paste0("www/report.", type), file) } diff --git a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf index 76b8df5..568771d 100644 --- a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf +++ b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf @@ -5,6 +5,6 @@ account: cognitiveindex server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 13786206 -bundleId: 9687600 +bundleId: 9688503 url: https://cognitiveindex.shinyapps.io/freesearcheR_dev/ version: 1 diff --git a/inst/apps/data_analysis_modules/server.R b/inst/apps/data_analysis_modules/server.R index d0206a7..94c7713 100644 --- a/inst/apps/data_analysis_modules/server.R +++ b/inst/apps/data_analysis_modules/server.R @@ -29,7 +29,7 @@ library(gtsummary) # source("functions.R") - +data(mtcars) # light <- custom_theme() # @@ -672,11 +672,13 @@ server <- function(input, output, session) { }) } - rv$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 }, @@ -692,8 +694,9 @@ 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$descr}**"))) }) @@ -772,12 +775,22 @@ server <- function(input, output, session) { # shiny::req(rv$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) } diff --git a/inst/apps/data_analysis_modules/ui.R b/inst/apps/data_analysis_modules/ui.R index 3c883f9..c6f22cf 100644 --- a/inst/apps/data_analysis_modules/ui.R +++ b/inst/apps/data_analysis_modules/ui.R @@ -510,7 +510,7 @@ 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") ), ) ) diff --git a/inst/apps/data_analysis_modules/www/report.qmd b/inst/apps/data_analysis_modules/www/report.qmd index 188b572..7715c24 100644 --- a/inst/apps/data_analysis_modules/www/report.qmd +++ b/inst/apps/data_analysis_modules/www/report.qmd @@ -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$data.file) -# library(gt) -# library(flextable) -# library(freesearcheR) +library(gtsummary) +library(gt) + +tbl_merge <- function(data) { + if (is.null(names(data))) { + data |> gtsummary::tbl_merge() + } else { + data |> gtsummary::tbl_merge(tab_spanner = names(data)) + } +} ``` ## Introduction @@ -55,13 +38,16 @@ Analyses were conducted in the *freesearcheR* data analysis web-tool based on R Below are the baseline characteristics. -{{< include _table1.md >}} +```{r, results = 'asis'} +tbl <- gtsummary::as_gt(web_data$table1) +knitr::knit_print(tbl) +``` -Below are results from the univariable and multivariable regression analyses. +Below are the results from the - -```{r} -gtsummary::tbl_summary(mtcars,by=cyl) +```{r, results = 'asis'} +reg_tbl <- web_data$regression$tables +knitr::knit_print(tbl_merge(reg_tbl)) ``` ## Discussion diff --git a/inst/apps/data_analysis_modules/www/report.rmd b/inst/apps/data_analysis_modules/www/report.rmd new file mode 100644 index 0000000..5bad138 --- /dev/null +++ b/inst/apps/data_analysis_modules/www/report.rmd @@ -0,0 +1,56 @@ +--- +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)) + } +} +``` + +## 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$table1) +knitr::knit_print(tbl) +``` + +Below are the results from the + +```{r, results = 'asis'} +reg_tbl <- web_data$regression$tables +knitr::knit_print(tbl_merge(reg_tbl)) +``` + +## Discussion + +Good luck on your further work!