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abandoned quarto to render report using rmarkdown instead. works smoothly!

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Andreas Gammelgaard Damsbo 2025-01-23 13:21:41 +01:00
commit d51fd27996
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7 changed files with 165 additions and 55 deletions
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56
inst/apps/data_analysis_modules/app.R
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@ -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)
}