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 cc26b34..2651506 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 @@ -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$list |> - write_quarto( - output_format = type, - input = file.path(getwd(), "www/report.qmd") + write_rmd( + output_format = format, + input = file.path(getwd(), "www/report.rmd") ) + + # write_quarto( + # output_format = type, + # input = file.path(getwd(), "www/report.qmd") + # ) }) file.rename(paste0("www/report.", type), file) } diff --git a/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf new file mode 100644 index 0000000..ab5be8e --- /dev/null +++ b/inst/apps/data_analysis_modules/rsconnect/shinyapps.io/cognitiveindex/freesearcheR_dev.dcf @@ -0,0 +1,10 @@ +name: freesearcheR_dev +title: +username: cognitiveindex +account: cognitiveindex +server: shinyapps.io +hostUrl: https://api.shinyapps.io/v1 +appId: 13786206 +bundleId: 9688582 +url: https://cognitiveindex.shinyapps.io/freesearcheR_dev/ +version: 1 diff --git a/inst/apps/data_analysis_modules/server.R b/inst/apps/data_analysis_modules/server.R index 223f20f..623e64f 100644 --- a/inst/apps/data_analysis_modules/server.R +++ b/inst/apps/data_analysis_modules/server.R @@ -29,7 +29,7 @@ library(gtsummary) # source("functions.R") - +data(mtcars) # light <- custom_theme() # @@ -673,11 +673,13 @@ server <- function(input, output, session) { }) } - rv$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) } diff --git a/inst/apps/data_analysis_modules/ui.R b/inst/apps/data_analysis_modules/ui.R index 7cc12e8..04fffdd 100644 --- a/inst/apps/data_analysis_modules/ui.R +++ b/inst/apps/data_analysis_modules/ui.R @@ -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") ), ) ) diff --git a/inst/apps/data_analysis_modules/www/report.qmd b/inst/apps/data_analysis_modules/www/report.qmd index d70b84d..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$data.file) -# library(gt) -# library(flextable) -# library(freesearcheR) +library(gtsummary) +library(gt) + +tbl_merge <- function(data) { + if (is.null(names(data))) { + data |> gtsummary::tbl_merge() + } else { + data |> gtsummary::tbl_merge(tab_spanner = names(data)) + } +} ``` ## Introduction @@ -55,11 +38,17 @@ Analyses were conducted in the *freesearcheR* data analysis web-tool based on R Below are the baseline characteristics. -{{< include _table1.md >}} +```{r, results = 'asis'} +tbl <- gtsummary::as_gt(web_data$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 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..f314587 --- /dev/null +++ b/inst/apps/data_analysis_modules/www/report.rmd @@ -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!