mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2026-06-19 04:27:30 +02:00
a bit of trial and error. not completely satisfied with readcap_read-module yet
This commit is contained in:
parent
a5c0a01d8a
commit
00eb49c225
16 changed files with 1186 additions and 383 deletions
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name: webResearch
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title:
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username: agdamsbo
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account: agdamsbo
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server: shinyapps.io
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hostUrl: https://api.shinyapps.io/v1
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appId: 13276335
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bundleId: 9436643
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url: https://agdamsbo.shinyapps.io/webResearch/
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version: 1
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352
inst/apps/data_analysis_modules/server.R
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352
inst/apps/data_analysis_modules/server.R
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# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
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# source(here::here("app/functions.R"))
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# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
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library(readr)
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library(MASS)
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library(stats)
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library(gtsummary)
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library(gt)
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library(openxlsx2)
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library(haven)
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library(readODS)
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library(shiny)
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library(bslib)
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library(assertthat)
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library(dplyr)
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library(quarto)
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library(here)
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library(broom)
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library(broom.helpers)
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library(REDCapCAST)
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library(easystats)
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library(patchwork)
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library(DHARMa)
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# if (!requireNamespace("webResearch")) {
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# devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
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# }
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# library(webResearch)
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if (file.exists(here::here("functions.R"))) {
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source(here::here("functions.R"))
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}
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server <- function(input, output, session) {
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## Listing files in www in session start to keep when ending and removing
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## everything else.
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files.to.keep <- list.files("www/")
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v <- shiny::reactiveValues(
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list = NULL,
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ds = NULL,
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input = exists("webResearch_data"),
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local_temp = NULL,
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quarto = NULL,
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test = "no"
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)
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data_file <- datamods::import_file_server(
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id = "file_import",
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show_data_in = "popup",
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trigger_return = "button",
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return_class = "data.frame",
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read_fns = list(
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ods = function(file) {
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readODS::read_ods(path = file)
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},
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dta = function(file) {
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haven::read_dta(file = file)
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}
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)
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)
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data_redcap <- m_redcap_readServer(
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id = "redcap_import",
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output.format = "list"
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)
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output$redcap_prev <- DT::renderDT(
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{
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DT::datatable(head(purrr::pluck(data_redcap(), 1)(), 5),
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caption = "First 5 observations"
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)
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},
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server = TRUE
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)
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ds <- shiny::reactive({
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# input$file1 will be NULL initially. After the user selects
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# and uploads a file, head of that data file by default,
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# or all rows if selected, will be shown.
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if (v$input) {
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out <- webResearch_data
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} else if (input$source == "file") {
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out <- data_file$data() |>
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REDCapCAST::numchar2fct()
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} else if (input$source == "redcap") {
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out <- purrr::pluck(data_redcap(), 1)() |>
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REDCapCAST::parse_data() |>
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REDCapCAST::as_factor() |>
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REDCapCAST::numchar2fct()
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}
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v$ds <- "loaded"
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# browser()
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# if (input$factorize == "yes") {
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# out <- out |>
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# REDCapCAST::numchar2fct()
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# }
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out
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})
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output$include_vars <- shiny::renderUI({
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selectizeInput(
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inputId = "include_vars",
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selected = NULL,
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label = "Covariables to include",
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choices = colnames(ds()),
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multiple = TRUE
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)
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})
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output$outcome_var <- shiny::renderUI({
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selectInput(
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inputId = "outcome_var",
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selected = NULL,
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label = "Select outcome variable",
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choices = colnames(ds()),
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multiple = FALSE
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)
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})
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output$strat_var <- shiny::renderUI({
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selectInput(
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inputId = "strat_var",
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selected = "none",
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label = "Select variable to stratify baseline",
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choices = c("none", colnames(ds()[base_vars()])),
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multiple = FALSE
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)
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})
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output$factor_vars <- shiny::renderUI({
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selectizeInput(
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inputId = "factor_vars",
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selected = colnames(ds())[sapply(ds(), is.factor)],
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label = "Covariables to format as categorical",
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choices = colnames(ds()),
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multiple = TRUE
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)
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})
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base_vars <- shiny::reactive({
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if (is.null(input$include_vars)) {
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out <- colnames(ds())
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} else {
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out <- unique(c(input$include_vars, input$outcome_var))
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}
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return(out)
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})
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## Have a look at column filters at some point
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## There should be a way to use the filtering the filter data for further analyses
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## Disabled for now, as the JS is apparently not isolated
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output$data_table <-
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DT::renderDT(
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{
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DT::datatable(ds()[base_vars()])
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},
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server = FALSE
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)
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output$data.classes <- gt::render_gt({
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shiny::req(input$file)
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data.frame(matrix(sapply(ds(), \(.x){
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class(.x)[1]
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}), nrow = 1)) |>
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stats::setNames(names(ds())) |>
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gt::gt()
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})
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shiny::observeEvent(input$act_start, {
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bslib::nav_select(id = "main_panel", selected = "Data analysis")
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})
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shiny::observeEvent(
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{
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input$load
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},
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{
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shiny::req(input$outcome_var)
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# Assumes all character variables can be formatted as factors
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data <- ds() |>
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dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor))
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data <- data |> factorize(vars = input$factor_vars)
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# if (is.factor(data[[input$strat_var]])) {
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# by.var <- input$strat_var
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# } else {
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# by.var <- NULL
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# }
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if (input$strat_var == "none") {
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by.var <- NULL
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} else {
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by.var <- input$strat_var
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}
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data <- data[base_vars()]
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# model <- data |>
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# regression_model(
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# outcome.str = input$outcome_var,
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# auto.mode = input$regression_auto == 1,
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# formula.str = input$regression_formula,
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# fun = input$regression_fun,
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# args.list = eval(parse(text = paste0("list(", input$regression_args, ")")))
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# )
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models <- list(
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"Univariable" = regression_model_uv,
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"Multivariable" = regression_model
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) |>
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lapply(\(.fun){
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do.call(
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.fun,
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c(
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list(data = data),
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list(outcome.str = input$outcome_var),
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list(formula.str = input$regression_formula),
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list(fun = input$regression_fun),
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list(args.list = eval(parse(text = paste0("list(", input$regression_args, ")"))))
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)
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)
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})
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# browser()
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# check <- performance::check_model(purrr::pluck(models,"Multivariable") |>
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# (\(x){
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# class(x) <- class(x)[class(x) != "webresearch_model"]
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# return(x)
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# })())
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check <- purrr::pluck(models, "Multivariable") |>
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performance::check_model()
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v$list <- list(
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data = data,
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check = check,
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table1 = data |>
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baseline_table(
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fun.args =
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list(
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by = by.var
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)
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) |>
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(\(.x){
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if (!is.null(by.var)) {
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.x |> gtsummary::add_overall()
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} else {
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.x
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}
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})() |>
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(\(.x){
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if (input$add_p == "yes") {
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.x |>
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gtsummary::add_p() |>
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gtsummary::bold_p()
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} else {
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.x
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}
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})(),
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table2 = models |>
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purrr::map(regression_table) |>
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tbl_merge(),
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input = input
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)
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output$table1 <- gt::render_gt(
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v$list$table1 |>
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gtsummary::as_gt()
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)
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output$table2 <- gt::render_gt(
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v$list$table2 |>
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gtsummary::as_gt()
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)
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output$check <- shiny::renderPlot({
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p <- plot(check) +
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patchwork::plot_annotation(title = "Multivariable regression model checks")
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p
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# Generate checks in one column
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# layout <- sapply(seq_len(length(p)), \(.x){
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# patchwork::area(.x, 1)
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# })
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#
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# p + patchwork::plot_layout(design = Reduce(c, layout))
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# patchwork::wrap_plots(ncol=1) +
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# patchwork::plot_annotation(title = 'Multivariable regression model checks')
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})
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}
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)
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output$uploaded <- shiny::reactive({
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if (is.null(v$ds)) {
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"no"
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} else {
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"yes"
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}
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})
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shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
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output$has_input <- shiny::reactive({
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if (v$input) {
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"yes"
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} else {
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"no"
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}
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})
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shiny::outputOptions(output, "has_input", suspendWhenHidden = FALSE)
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# Could be rendered with other tables or should show progress
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# Investigate quarto render problems
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# On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
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output$report <- downloadHandler(
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filename = shiny::reactive({
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paste0("report.", input$output_type)
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}),
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content = function(file, type = input$output_type) {
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## Notification is not progressing
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## Presumably due to missing
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shiny::withProgress(message = "Generating report. Hold on for a moment..", {
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v$list |>
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write_quarto(
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output_format = type,
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input = file.path(getwd(), "www/report.qmd")
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)
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})
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file.rename(paste0("www/report.", type), file)
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}
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)
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session$onSessionEnded(function() {
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cat("Session Ended\n")
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files <- list.files("www/")
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lapply(files[!files %in% files.to.keep], \(.x){
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unlink(paste0("www/", .x), recursive = FALSE)
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print(paste(.x, "deleted"))
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})
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})
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}
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412
inst/apps/data_analysis_modules/ui.R
Normal file
412
inst/apps/data_analysis_modules/ui.R
Normal file
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library(shiny)
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library(bslib)
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library(datamods)
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library(shinyWidgets)
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library(DT)
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requireNamespace("gt")
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# ns <- NS(id)
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ui_elements <- list(
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# bslib::nav_panel(
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# title = "Data overview",
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# # shiny::uiOutput("data.classes"),
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# # shiny::uiOutput("data.input"),
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# # shiny::p("Classes of uploaded data"),
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# # gt::gt_output("data.classes"),
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# shiny::p("Subset data"),
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# DT::DTOutput(outputId = "data.input")
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# ),
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# bslib::nav_panel(
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# title = "Baseline characteristics",
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# gt::gt_output(outputId = "table1")
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# ),
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# bslib::nav_panel(
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# title = "Regression table",
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# gt::gt_output(outputId = "table2")
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# ),
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# bslib::nav_panel(
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# title = "Regression checks",
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# shiny::plotOutput(outputId = "check")
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# ),
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##############################################################################
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#########
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######### Import panel
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#########
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##############################################################################
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"import" = bslib::nav_panel(
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title = "Data import",
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shiny::h4("Upload your dataset"),
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shiny::conditionalPanel(
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condition = "output.has_input=='yes'",
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# Input: Select a file ----
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shiny::helpText("Analyses are performed on provided data")
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),
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shiny::conditionalPanel(
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condition = "output.has_input=='no'",
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# Input: Select a file ----
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shiny::radioButtons(
|
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inputId = "source",
|
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label = "Upload file or export from REDCap?",
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selected = "file",
|
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inline = TRUE,
|
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choices = list(
|
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"File" = "file",
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"REDCap" = "redcap"
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)
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),
|
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shiny::conditionalPanel(
|
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condition = "input.source=='file'",
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datamods::import_file_ui("file_import",
|
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title = "Choose a datafile to upload",
|
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file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
|
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)
|
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),
|
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shiny::conditionalPanel(
|
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condition = "input.source=='redcap'",
|
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m_redcap_readUI("redcap_import"),
|
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DT::DTOutput(outputId = "redcap_prev")
|
||||
)
|
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),
|
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shiny::br(),
|
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shiny::actionButton(inputId = "act_start",label = "Start")
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),
|
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##############################################################################
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#########
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######### Data analyses panel
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#########
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##############################################################################
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"analyze" = bslib::nav_panel(
|
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title = "Data analysis",
|
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bslib::page_navbar(
|
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title = "",
|
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# bslib::layout_sidebar(
|
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# fillable = TRUE,
|
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sidebar = bslib::sidebar(
|
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shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
|
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shiny::uiOutput("outcome_var"),
|
||||
shiny::uiOutput("strat_var"),
|
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shiny::conditionalPanel(
|
||||
condition = "input.strat_var!='none'",
|
||||
shiny::radioButtons(
|
||||
inputId = "add_p",
|
||||
label = "Compare strata?",
|
||||
selected = "no",
|
||||
inline = TRUE,
|
||||
choices = list(
|
||||
"No" = "no",
|
||||
"Yes" = "yes"
|
||||
)
|
||||
),
|
||||
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
|
||||
),
|
||||
shiny::radioButtons(
|
||||
inputId = "all",
|
||||
label = "Specify covariables",
|
||||
inline = TRUE, selected = 2,
|
||||
choiceNames = c(
|
||||
"Yes",
|
||||
"No"
|
||||
),
|
||||
choiceValues = c(1, 2)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.all==1",
|
||||
shiny::uiOutput("include_vars")
|
||||
),
|
||||
shiny::radioButtons(
|
||||
inputId = "specify_factors",
|
||||
label = "Specify categorical variables?",
|
||||
selected = "no",
|
||||
inline = TRUE,
|
||||
choices = list(
|
||||
"Yes" = "yes",
|
||||
"No" = "no"
|
||||
)
|
||||
),
|
||||
shiny::conditionalPanel(
|
||||
condition = "input.specify_factors=='yes'",
|
||||
shiny::uiOutput("factor_vars")
|
||||
),
|
||||
bslib::input_task_button(
|
||||
id = "load",
|
||||
label = "Analyse",
|
||||
icon = shiny::icon("pencil", lib = "glyphicon"),
|
||||
label_busy = "Working...",
|
||||
icon_busy = fontawesome::fa_i("arrows-rotate",
|
||||
class = "fa-spin",
|
||||
"aria-hidden" = "true"
|
||||
),
|
||||
type = "primary",
|
||||
auto_reset = TRUE
|
||||
),
|
||||
shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables")
|
||||
# )
|
||||
),
|
||||
bslib::nav_spacer(),
|
||||
bslib::nav_panel(
|
||||
title = "Data overview",
|
||||
DT::DTOutput(outputId = "data_table")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Baseline characteristics",
|
||||
gt::gt_output(outputId = "table1")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression table",
|
||||
gt::gt_output(outputId = "table2")
|
||||
),
|
||||
bslib::nav_panel(
|
||||
title = "Regression checks",
|
||||
shiny::plotOutput(outputId = "check")
|
||||
)
|
||||
)
|
||||
),
|
||||
##############################################################################
|
||||
#########
|
||||
######### Documentation panel
|
||||
#########
|
||||
##############################################################################
|
||||
"docs" = bslib::nav_panel(
|
||||
title = "Intro",
|
||||
shiny::markdown(readLines("www/intro.md")),
|
||||
shiny::br()
|
||||
)
|
||||
)
|
||||
|
||||
# cards <- list(
|
||||
# "overview"=bslib::card(
|
||||
# title = "Data overview",
|
||||
# # shiny::uiOutput("data.classes"),
|
||||
# # shiny::uiOutput("data.input"),
|
||||
# # shiny::p("Classes of uploaded data"),
|
||||
# # gt::gt_output("data.classes"),
|
||||
# shiny::p("Subset data"),
|
||||
# DT::DTOutput(outputId = "data_table")
|
||||
# ),
|
||||
# "baseline"=bslib::card(
|
||||
# title = "Baseline characteristics",
|
||||
# gt::gt_output(outputId = "table1")
|
||||
# ),
|
||||
# "regression"= bslib::card(
|
||||
# title = "Regression table",
|
||||
# gt::gt_output(outputId = "table2")
|
||||
# ),
|
||||
# "checks" =bslib::card(
|
||||
# title = "Regression checks",
|
||||
# shiny::plotOutput(outputId = "check")
|
||||
# )
|
||||
# )
|
||||
|
||||
ui <- bslib::page(
|
||||
title = "freesearcheR",
|
||||
theme = bslib::bs_theme(
|
||||
primary = "#1E4A8F",
|
||||
secondary = "#FF6F61",
|
||||
bootswatch = "minty",
|
||||
base_font = bslib::font_google("Montserrat"),
|
||||
code_font = bslib::font_google("Open Sans")
|
||||
),
|
||||
bslib::page_navbar(
|
||||
id = "main_panel",
|
||||
ui_elements$import,
|
||||
ui_elements$analyze,
|
||||
ui_elements$docs
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# ui <- bslib::page(
|
||||
# theme = bslib::bs_theme(
|
||||
# bootswatch = "minty",
|
||||
# base_font = font_google("Inter"),
|
||||
# code_font = font_google("JetBrains Mono")
|
||||
# ),
|
||||
# title = "fresearcheR - free, web-based research analyses",
|
||||
# bslib::page_navbar(
|
||||
# title = "fresearcheR - free, web-based research analyses",
|
||||
# header = h6("Welcome to the fresearcheR tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."),
|
||||
# sidebar = bslib::sidebar(
|
||||
# width = 300,
|
||||
# open = "open",
|
||||
# shiny::h4("Upload your dataset"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.has_input=='yes'",
|
||||
# # Input: Select a file ----
|
||||
# shiny::helpText("Analyses are performed on provided data")
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.has_input=='no'",
|
||||
# # Input: Select a file ----
|
||||
# shiny::radioButtons(
|
||||
# inputId = "source",
|
||||
# label = "Upload file or export from REDCap?",
|
||||
# selected = "file",
|
||||
# inline = TRUE,
|
||||
# choices = list(
|
||||
# "File" = "file",
|
||||
# "REDCap" = "redcap"
|
||||
# )
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.source=='file'",
|
||||
# datamods::import_file_ui("file_import",
|
||||
# file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav",".ods",".dta"))
|
||||
# )
|
||||
# ,
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.source=='redcap'",
|
||||
# m_redcap_readUI("redcap_import")
|
||||
# ),
|
||||
# # Does not work??
|
||||
# # shiny::actionButton(inputId = "test_data",
|
||||
# # label = "Load test data", class = "btn-primary")
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "output.uploaded=='yes'",
|
||||
# shiny::h4("Parameter specifications"),
|
||||
# shiny::radioButtons(
|
||||
# inputId = "factorize",
|
||||
# label = "Factorize variables with few levels?",
|
||||
# selected = "yes",
|
||||
# inline = TRUE,
|
||||
# choices = list(
|
||||
# "Yes" = "yes",
|
||||
# "No" = "no"
|
||||
# )
|
||||
# ),
|
||||
# shiny::radioButtons(
|
||||
# inputId = "regression_auto",
|
||||
# label = "Automatically choose function",
|
||||
# inline = TRUE,
|
||||
# choiceNames = c(
|
||||
# "Yes",
|
||||
# "No"
|
||||
# ),
|
||||
# choiceValues = c(1, 2)
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.regression_auto==2",
|
||||
# shiny::textInput(
|
||||
# inputId = "regression_formula",
|
||||
# label = "Formula string to render with 'glue::glue'",
|
||||
# value = NULL
|
||||
# ),
|
||||
# shiny::textInput(
|
||||
# inputId = "regression_fun",
|
||||
# label = "Function to use for analysis (needs pasckage and name)",
|
||||
# value = "stats::lm"
|
||||
# ),
|
||||
# shiny::textInput(
|
||||
# inputId = "regression_args",
|
||||
# label = "Arguments to pass to the function (provided as a string)",
|
||||
# value = ""
|
||||
# )
|
||||
# ),
|
||||
# shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
|
||||
# shiny::uiOutput("outcome_var"),
|
||||
# shiny::uiOutput("strat_var"),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.strat_var!='none'",
|
||||
# shiny::radioButtons(
|
||||
# inputId = "add_p",
|
||||
# label = "Compare strata?",
|
||||
# selected = "no",
|
||||
# inline = TRUE,
|
||||
# choices = list(
|
||||
# "No" = "no",
|
||||
# "Yes" = "yes"
|
||||
# )
|
||||
# ),
|
||||
# shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
|
||||
# ),
|
||||
# shiny::radioButtons(
|
||||
# inputId = "all",
|
||||
# label = "Specify covariables",
|
||||
# inline = TRUE, selected = 2,
|
||||
# choiceNames = c(
|
||||
# "Yes",
|
||||
# "No"
|
||||
# ),
|
||||
# choiceValues = c(1, 2)
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.all==1",
|
||||
# shiny::uiOutput("include_vars")
|
||||
# ),
|
||||
# shiny::radioButtons(
|
||||
# inputId = "specify_factors",
|
||||
# label = "Specify categorical variables?",
|
||||
# selected = "no",
|
||||
# inline = TRUE,
|
||||
# choices = list(
|
||||
# "Yes" = "yes",
|
||||
# "No" = "no"
|
||||
# )
|
||||
# ),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.specify_factors=='yes'",
|
||||
# shiny::uiOutput("factor_vars")
|
||||
# ),
|
||||
# bslib::input_task_button(
|
||||
# id = "load",
|
||||
# label = "Analyse",
|
||||
# icon = shiny::icon("pencil", lib = "glyphicon"),
|
||||
# label_busy = "Working...",
|
||||
# icon_busy = fontawesome::fa_i("arrows-rotate",
|
||||
# class = "fa-spin",
|
||||
# "aria-hidden" = "true"
|
||||
# ),
|
||||
# type = "primary",
|
||||
# auto_reset = TRUE
|
||||
# ),
|
||||
# shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables"),
|
||||
# # shiny::actionButton("load", "Analyse", class = "btn-primary"),
|
||||
# #
|
||||
# # # Horizontal line ----
|
||||
# tags$hr(),
|
||||
# shiny::conditionalPanel(
|
||||
# condition = "input.load",
|
||||
# h4("Download results"),
|
||||
# shiny::helpText("Choose your favourite output file format for further work."),
|
||||
# shiny::selectInput(
|
||||
# inputId = "output_type",
|
||||
# label = "Choose your desired output format",
|
||||
# selected = NULL,
|
||||
# choices = list(
|
||||
# "Word" = "docx",
|
||||
# "LibreOffice" = "odt"
|
||||
# # ,
|
||||
# # "PDF" = "pdf",
|
||||
# # "All the above" = "all"
|
||||
# )
|
||||
# ),
|
||||
#
|
||||
# # Button
|
||||
# downloadButton(
|
||||
# outputId = "report",
|
||||
# label = "Download",
|
||||
# icon = shiny::icon("download")
|
||||
# )
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
# bslib::nav_spacer(),
|
||||
# panels[[1]],
|
||||
# panels[[2]],
|
||||
# panels[[3]],
|
||||
# panels[[4]]
|
||||
#
|
||||
# # layout_columns(
|
||||
# # cards[[1]]
|
||||
# # ),
|
||||
# # layout_columns(
|
||||
# # cards[[2]], cards[[3]]
|
||||
# # )
|
||||
# )
|
||||
# )
|
||||
3
inst/apps/data_analysis_modules/www/intro.md
Normal file
3
inst/apps/data_analysis_modules/www/intro.md
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
# Intro to webResearch/freesearcheR/VOICE
|
||||
|
||||
This is just placeholder text.
|
||||
68
inst/apps/data_analysis_modules/www/report.qmd
Normal file
68
inst/apps/data_analysis_modules/www/report.qmd
Normal file
|
|
@ -0,0 +1,68 @@
|
|||
---
|
||||
format:
|
||||
html:
|
||||
embed-resources: true
|
||||
title: "webResearch analysis results"
|
||||
date: today
|
||||
author: webResearch Tool
|
||||
toc: true
|
||||
execute:
|
||||
echo: false
|
||||
params:
|
||||
data.file: NA
|
||||
---
|
||||
|
||||
```{r setup}
|
||||
web_data <- readr::read_rds(file = params$data.file)
|
||||
library(gtsummary)
|
||||
library(gt)
|
||||
library(easystats)
|
||||
library(patchwork)
|
||||
# library(webResearch)
|
||||
```
|
||||
|
||||
## Introduction
|
||||
|
||||
Research should be free and open with easy access for all. The webResearch tool attempts to help lower the bar to participate in contributing to science.
|
||||
|
||||
## Methods
|
||||
|
||||
Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")`.
|
||||
|
||||
## Results
|
||||
|
||||
Below is the baseline characteristics plotted.
|
||||
|
||||
```{r}
|
||||
#| label: tbl-baseline
|
||||
#| tbl-cap: Baseline characteristics of included data
|
||||
web_data$table1
|
||||
```
|
||||
|
||||
Here are the regression results.
|
||||
|
||||
```{r}
|
||||
#| label: tbl-regression
|
||||
#| tbl-cap: Regression analysis results
|
||||
web_data$table2
|
||||
```
|
||||
|
||||
## Discussion
|
||||
|
||||
Good luck on your further work!
|
||||
|
||||
## Sensitivity
|
||||
|
||||
Here are the results from testing the regression model:
|
||||
|
||||
|
||||
```{r}
|
||||
#| label: tbl-checks
|
||||
#| fig-cap: Regression analysis checks
|
||||
#| fig-height: 8
|
||||
#| fig-width: 6
|
||||
#| fig-dpi: 600
|
||||
|
||||
plot(web_data$check)
|
||||
|
||||
```
|
||||
Loading…
Add table
Add a link
Reference in a new issue