mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2026-06-19 20:47:29 +02:00
reverting and recovering from renv corruption
This commit is contained in:
parent
99ed934cae
commit
2ad36d6dde
12 changed files with 78 additions and 128 deletions
|
|
@ -1,13 +1,13 @@
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R
|
||||
########
|
||||
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//baseline_table.R
|
||||
#### Current file: R//baseline_table.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -35,7 +35,7 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//cut-variable-dates.R
|
||||
#### Current file: R//cut-variable-dates.R
|
||||
########
|
||||
|
||||
library(datamods)
|
||||
|
|
@ -677,7 +677,7 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//file-import-module.R
|
||||
#### Current file: R//file-import-module.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -808,7 +808,7 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//helpers.R
|
||||
#### Current file: R//helpers.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -912,14 +912,13 @@ argsstring2list <- function(string) {
|
|||
|
||||
|
||||
|
||||
|
||||
factorize <- function(data, vars) {
|
||||
if (!is.null(vars)) {
|
||||
data |>
|
||||
dplyr::mutate(
|
||||
dplyr::across(
|
||||
dplyr::all_of(vars),
|
||||
as_factor
|
||||
REDCapCAST::as_factor
|
||||
)
|
||||
)
|
||||
} else {
|
||||
|
|
@ -952,8 +951,6 @@ dummy_Imports <- function() {
|
|||
|
||||
|
||||
|
||||
|
||||
|
||||
file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
|
||||
output.format <- match.arg(output.format)
|
||||
|
||||
|
|
@ -965,9 +962,7 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
|
|||
{
|
||||
assign(name, value |>
|
||||
dplyr::bind_cols() |>
|
||||
parse_data() |>
|
||||
as_factor() |>
|
||||
numchar2fct())
|
||||
default_parsing())
|
||||
},
|
||||
value = data,
|
||||
name = filename
|
||||
|
|
@ -975,17 +970,15 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
|
|||
|
||||
datanames(out) <- filename
|
||||
} else if (output.format == "df") {
|
||||
out <- data|>
|
||||
parse_data() |>
|
||||
as_factor() |>
|
||||
numchar2fct()
|
||||
out <- data |>
|
||||
default_parsing()
|
||||
} else if (output.format == "list") {
|
||||
out <- list(
|
||||
data = data,
|
||||
name = filename
|
||||
)
|
||||
|
||||
out <- c(out,...)
|
||||
out <- c(out, ...)
|
||||
}
|
||||
|
||||
out
|
||||
|
|
@ -1003,16 +996,17 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
|
|||
|
||||
|
||||
|
||||
default_parsing <- function(data){
|
||||
|
||||
default_parsing <- function(data) {
|
||||
data |>
|
||||
parse_data() |>
|
||||
as_factor() |>
|
||||
numchar2fct()
|
||||
REDCapCAST::parse_data() |>
|
||||
REDCapCAST::as_factor() |>
|
||||
REDCapCAST::numchar2fct()
|
||||
}
|
||||
|
||||
|
||||
########
|
||||
#### Current file: R//redcap_read_shiny_module.R
|
||||
#### Current file: R//redcap_read_shiny_module.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1118,7 +1112,6 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
|
|||
|
||||
|
||||
|
||||
|
||||
m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
|
||||
output.format <- match.arg(output.format)
|
||||
|
||||
|
|
@ -1244,7 +1237,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
|
|||
shiny::req(input$fields)
|
||||
record_id <- dd()[[1]][1]
|
||||
|
||||
redcap_data <- read_redcap_tables(
|
||||
redcap_data <- REDCapCAST::read_redcap_tables(
|
||||
uri = input$uri,
|
||||
token = input$api,
|
||||
fields = unique(c(record_id, input$fields)),
|
||||
|
|
@ -1253,10 +1246,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
|
|||
raw_or_label = "both",
|
||||
filter_logic = input$filter
|
||||
) |>
|
||||
redcap_wider() |>
|
||||
REDCapCAST::redcap_wider() |>
|
||||
dplyr::select(-dplyr::ends_with("_complete")) |>
|
||||
dplyr::select(-dplyr::any_of(record_id)) |>
|
||||
suffix2label()
|
||||
REDCapCAST::suffix2label()
|
||||
|
||||
out_object <- file_export(redcap_data,
|
||||
output.format = output.format,
|
||||
|
|
@ -1383,7 +1376,7 @@ redcap_app <- function() {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//regression_model.R
|
||||
#### Current file: R//regression_model.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1417,7 +1410,6 @@ redcap_app <- function() {
|
|||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
regression_model <- function(data,
|
||||
|
|
@ -1455,7 +1447,7 @@ regression_model <- function(data,
|
|||
data <- data |>
|
||||
purrr::map(\(.x){
|
||||
if (is.character(.x)) {
|
||||
suppressWarnings(as_factor(.x))
|
||||
suppressWarnings(REDCapCAST::as_factor(.x))
|
||||
} else {
|
||||
.x
|
||||
}
|
||||
|
|
@ -1594,7 +1586,7 @@ regression_model_uv <- function(data,
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//regression_table.R
|
||||
#### Current file: R//regression_table.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1742,7 +1734,7 @@ tbl_merge <- function(data) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//report.R
|
||||
#### Current file: R//report.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1829,7 +1821,7 @@ modify_qmd <- function(file, format) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//shiny_freesearcheR.R
|
||||
#### Current file: R//shiny_freesearcheR.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1860,7 +1852,7 @@ shiny_freesearcheR <- function(...) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: R//theme.R
|
||||
#### Current file: R//theme.R
|
||||
########
|
||||
|
||||
|
||||
|
|
@ -1901,7 +1893,7 @@ custom_theme <- function(...,
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R
|
||||
########
|
||||
|
||||
# ns <- NS(id)
|
||||
|
|
@ -2213,7 +2205,7 @@ ui <- bslib::page_fluid(
|
|||
title = "freesearcheR",
|
||||
theme = light,
|
||||
shiny::useBusyIndicators(),
|
||||
bslib::page_navbar(
|
||||
bslib::page_navbar(title = "freesearcheR",
|
||||
id = "main_panel",
|
||||
# header = shiny::tags$header(shiny::p("Data is only stored temporarily for analysis and deleted immediately afterwards.")),
|
||||
ui_elements$import,
|
||||
|
|
@ -2221,7 +2213,7 @@ ui <- bslib::page_fluid(
|
|||
ui_elements$analyze,
|
||||
ui_elements$docs,
|
||||
# bslib::nav_spacer(),
|
||||
# bslib::nav_item(shinyWidgets::materialSwitch(inputId = "mode", label = icon("moon"), right=TRUE,status = "success")),
|
||||
# bslib::nav_item(shinyWidgets::circleButton(inputId = "mode", icon = icon("moon"),status = "primary")),
|
||||
fillable = TRUE,
|
||||
footer = shiny::tags$footer(
|
||||
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
|
||||
|
|
@ -2238,7 +2230,7 @@ ui <- bslib::page_fluid(
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R
|
||||
########
|
||||
|
||||
library(readr)
|
||||
|
|
@ -2277,17 +2269,6 @@ library(DT)
|
|||
# dark <- custom_theme(bg = "#000",fg="#fff")
|
||||
|
||||
|
||||
#' freesearcheR server
|
||||
#'
|
||||
#' @param input input
|
||||
#' @param output output
|
||||
#' @param session session
|
||||
#'
|
||||
#' @returns server
|
||||
#' @export
|
||||
#' @importFrom REDCapCAST fct_drop.data.frame
|
||||
#'
|
||||
#' @examples
|
||||
server <- function(input, output, session) {
|
||||
## Listing files in www in session start to keep when ending and removing
|
||||
## everything else.
|
||||
|
|
@ -2579,7 +2560,7 @@ server <- function(input, output, session) {
|
|||
{
|
||||
data <- data_filter() |>
|
||||
dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
|
||||
fct_drop.data.frame() |>
|
||||
REDCapCAST::fct_drop.data.frame() |>
|
||||
factorize(vars = input$factor_vars)
|
||||
|
||||
if (input$strat_var == "none") {
|
||||
|
|
@ -2799,7 +2780,7 @@ server <- function(input, output, session) {
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R
|
||||
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R
|
||||
########
|
||||
|
||||
shinyApp(ui, server)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue