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naming and dealing with a dependency issue. ready for first release

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3
.Rbuildignore
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@ -1,9 +1,10 @@
^renv$
^renv\.lock$
^webResearch\.Rproj$
^freesearcheR\.Rproj$
^\.Rproj\.user$
^LICENSE\.md$
^dev$
^\.github$
^inst/shiny-examples/casting/functions\.R$
^functions\.R$
^CODE_OF_CONDUCT\.md$

126
CODE_OF_CONDUCT.md Normal file
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@ -0,0 +1,126 @@
# Contributor Covenant Code of Conduct
## Our Pledge
We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.
## Our Standards
Examples of behavior that contributes to a positive environment for our
community include:
* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community
Examples of unacceptable behavior include:
* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
## Enforcement Responsibilities
Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.
Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.
## Scope
This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at agdamsbo@clin.au.dk.
All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the
reporter of any incident.
## Enforcement Guidelines
Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:
### 1. Correction
**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.
**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.
### 2. Warning
**Community Impact**: A violation through a single incident or series of
actions.
**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.
### 3. Temporary Ban
**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.
**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.
### 4. Permanent Ban
**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.
**Consequence**: A permanent ban from any sort of public interaction within the
community.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
For answers to common questions about this code of conduct, see the FAQ at
<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
[homepage]: https://www.contributor-covenant.org

14
DESCRIPTION
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@ -1,10 +1,10 @@
Package: webResearch
Package: freesearcheR
Title: Browser Based Data Analysis
Version: 24.12.1
Authors@R:
person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7559-1154"))
Description: Browser based basic data analysis and research output.
Description: Free and open source browser based data exploration and analysis with publication ready output.
License: AGPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
@ -17,7 +17,6 @@ Imports:
gtsummary,
haven,
here,
openxlsx2,
quarto,
readODS,
readr,
@ -50,6 +49,9 @@ Imports:
Suggests:
styler,
devtools,
rhub
URL: https://github.com/agdamsbo/webResearch
BugReports: https://github.com/agdamsbo/webResearch/issues
rhub,
usethis,
roxygen2,
pak
URL: https://github.com/agdamsbo/freesearcheR
BugReports: https://github.com/agdamsbo/freesearcheR/issues

10
NAMESPACE
View file

@ -9,12 +9,12 @@ export(cut_variable_ui)
export(default_format_arguments)
export(default_parsing)
export(factorize)
export(file_export)
export(format_writer)
export(getfun)
export(index_embed)
export(is_any_class)
export(is_datetime)
export(m_datafileUI)
export(m_redcap_readServer)
export(m_redcap_readUI)
export(modal_cut_variable)
@ -23,11 +23,17 @@ export(read_input)
export(regression_model)
export(regression_model_uv)
export(regression_table)
export(shiny_webResearch)
export(shiny_freesearcheR)
export(specify_qmd_format)
export(tbl_merge)
export(winbox_cut_variable)
export(write_quarto)
importFrom(REDCapCAST,as_factor)
importFrom(REDCapCAST,numchar2fct)
importFrom(REDCapCAST,parse_data)
importFrom(REDCapCAST,read_redcap_tables)
importFrom(REDCapCAST,redcap_wider)
importFrom(REDCapCAST,suffix2label)
importFrom(classInt,classIntervals)
importFrom(graphics,abline)
importFrom(graphics,axis)

2
R/cut-variable-dates.R
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@ -206,9 +206,11 @@ cut.Date <- function(x,breaks,start.on.monday=TRUE,...){
#' @export
#'
#' @examples
#' \dontrun{
#' vapply(REDCapCAST::redcapcast_data, \(.x){
#' is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt"))
#' }, logical(1))
#' }
is_any_class <- function(data, class.vec) {
any(class(data) %in% class.vec)
}

244
R/file-import-module.R
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@ -1,125 +1,125 @@
#' Shiny UI module to load a data file
#' #' Shiny UI module to load a data file
#' #'
#' #' @param id id
#' #'
#' #' @return shiny UI
#' #' @export
#' #'
#' m_datafileUI <- function(id) {
#' ns <- shiny::NS(id)
#' shiny::tagList(
#' shiny::fileInput(
#' inputId = ns("file"),
#' label = "Upload a file",
#' multiple = FALSE,
#' accept = c(
#' ".csv",
#' ".xlsx",
#' ".xls",
#' ".dta",
#' ".ods",
#' ".rds"
#' )
#' ),
#' shiny::h4("Parameter specifications"),
#' shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
#' shiny::uiOutput(ns("include_vars")),
#' DT::DTOutput(ns("data_input")),
#' shiny::actionButton(ns("submit"), "Submit")
#' )
#' }
#'
#' @param id id
#' m_datafileServer <- function(id, output.format = "df") {
#' shiny::moduleServer(id, function(input, output, session, ...) {
#' ns <- shiny::NS(id)
#' ds <- shiny::reactive({
#' REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
#' })
#'
#' @return shiny UI
#' @export
#' output$include_vars <- shiny::renderUI({
#' shiny::req(input$file)
#' shiny::selectizeInput(
#' inputId = ns("include_vars"),
#' selected = NULL,
#' label = "Covariables to include",
#' choices = colnames(ds()),
#' multiple = TRUE
#' )
#' })
#'
m_datafileUI <- function(id) {
ns <- shiny::NS(id)
shiny::tagList(
shiny::fileInput(
inputId = ns("file"),
label = "Upload a file",
multiple = FALSE,
accept = c(
".csv",
".xlsx",
".xls",
".dta",
".ods",
".rds"
)
),
shiny::h4("Parameter specifications"),
shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
shiny::uiOutput(ns("include_vars")),
DT::DTOutput(ns("data_input")),
shiny::actionButton(ns("submit"), "Submit")
)
}
m_datafileServer <- function(id, output.format = "df") {
shiny::moduleServer(id, function(input, output, session, ...) {
ns <- shiny::NS(id)
ds <- shiny::reactive({
REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
})
output$include_vars <- shiny::renderUI({
shiny::req(input$file)
shiny::selectizeInput(
inputId = ns("include_vars"),
selected = NULL,
label = "Covariables to include",
choices = colnames(ds()),
multiple = TRUE
)
})
base_vars <- shiny::reactive({
if (is.null(input$include_vars)) {
out <- colnames(ds())
} else {
out <- input$include_vars
}
out
})
output$data_input <-
DT::renderDT({
shiny::req(input$file)
ds()[base_vars()]
})
shiny::eventReactive(input$submit, {
# shiny::req(input$file)
data <- shiny::isolate({
ds()[base_vars()]
})
file_export(data,
output.format = output.format,
tools::file_path_sans_ext(input$file$name)
)
})
})
}
file_app <- function() {
ui <- shiny::fluidPage(
m_datafileUI("data"),
# DT::DTOutput(outputId = "redcap_prev")
toastui::datagridOutput2(outputId = "redcap_prev")
)
server <- function(input, output, session) {
m_datafileServer("data", output.format = "list")
}
shiny::shinyApp(ui, server)
}
file_app()
tdm_data_upload <- teal::teal_data_module(
ui <- function(id) {
shiny::fluidPage(
m_datafileUI(id)
)
},
server = function(id) {
m_datafileServer(id, output.format = "teal")
}
)
tdm_data_read <- teal::teal_data_module(
ui <- function(id) {
shiny::fluidPage(
m_redcap_readUI(id = "redcap")
)
},
server = function(id) {
moduleServer(
id,
function(input, output, session) {
ns <- session$ns
m_redcap_readServer(id = "redcap", output.format = "teal")
}
)
}
)
#' base_vars <- shiny::reactive({
#' if (is.null(input$include_vars)) {
#' out <- colnames(ds())
#' } else {
#' out <- input$include_vars
#' }
#' out
#' })
#'
#' output$data_input <-
#' DT::renderDT({
#' shiny::req(input$file)
#' ds()[base_vars()]
#' })
#'
#' shiny::eventReactive(input$submit, {
#' # shiny::req(input$file)
#'
#' data <- shiny::isolate({
#' ds()[base_vars()]
#' })
#'
#' file_export(data,
#' output.format = output.format,
#' tools::file_path_sans_ext(input$file$name)
#' )
#' })
#' })
#' }
#'
#'
#'
#'
#'
#' file_app <- function() {
#' ui <- shiny::fluidPage(
#' m_datafileUI("data"),
#' # DT::DTOutput(outputId = "redcap_prev")
#' toastui::datagridOutput2(outputId = "redcap_prev")
#' )
#' server <- function(input, output, session) {
#' m_datafileServer("data", output.format = "list")
#' }
#' shiny::shinyApp(ui, server)
#' }
#'
#' file_app()
#'
#' tdm_data_upload <- teal::teal_data_module(
#' ui <- function(id) {
#' shiny::fluidPage(
#' m_datafileUI(id)
#' )
#' },
#' server = function(id) {
#' m_datafileServer(id, output.format = "teal")
#' }
#' )
#'
#' tdm_data_read <- teal::teal_data_module(
#' ui <- function(id) {
#' shiny::fluidPage(
#' m_redcap_readUI(id = "redcap")
#' )
#' },
#' server = function(id) {
#' moduleServer(
#' id,
#' function(input, output, session) {
#' ns <- session$ns
#'
#' m_redcap_readServer(id = "redcap", output.format = "teal")
#' }
#' )
#' }
#' )

33
R/helpers.R
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@ -98,6 +98,7 @@ argsstring2list <- function(string) {
#' @param vars variables to force factorize
#'
#' @return data.frame
#' @importFrom REDCapCAST as_factor
#' @export
factorize <- function(data, vars) {
if (!is.null(vars)) {
@ -105,7 +106,7 @@ factorize <- function(data, vars) {
dplyr::mutate(
dplyr::across(
dplyr::all_of(vars),
REDCapCAST::as_factor
as_factor
)
)
} else {
@ -128,6 +129,17 @@ dummy_Imports <- function() {
}
#' Title
#'
#' @param data data
#' @param output.format output
#' @param filename filename
#' @param ... passed on
#'
#' @returns data
#' @export
#' @importFrom REDCapCAST as_factor parse_data numchar2fct
#'
file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
output.format <- match.arg(output.format)
@ -139,9 +151,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
{
assign(name, value |>
dplyr::bind_cols() |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct())
parse_data() |>
as_factor() |>
numchar2fct())
},
value = data,
name = filename
@ -150,9 +162,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
datanames(out) <- filename
} else if (output.format == "df") {
out <- data|>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct()
parse_data() |>
as_factor() |>
numchar2fct()
} else if (output.format == "list") {
out <- list(
data = data,
@ -172,13 +184,14 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
#'
#' @returns data.frame or tibble
#' @export
#' @importFrom REDCapCAST as_factor parse_data numchar2fct
#'
#' @examples
#' mtcars |> str()
#' mtcars |> default_parsing() |> str()
default_parsing <- function(data){
data |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct()
parse_data() |>
as_factor() |>
numchar2fct()
}

7
R/redcap_read_shiny_module.R
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@ -100,6 +100,7 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
#'
#' @return shiny server module
#' @export
#' @importFrom REDCapCAST read_redcap_tables redcap_wider suffix2label
#'
m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
output.format <- match.arg(output.format)
@ -226,7 +227,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
shiny::req(input$fields)
record_id <- dd()[[1]][1]
redcap_data <- REDCapCAST::read_redcap_tables(
redcap_data <- read_redcap_tables(
uri = input$uri,
token = input$api,
fields = unique(c(record_id, input$fields)),
@ -235,10 +236,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
raw_or_label = "both",
filter_logic = input$filter
) |>
REDCapCAST::redcap_wider() |>
redcap_wider() |>
dplyr::select(-dplyr::ends_with("_complete")) |>
dplyr::select(-dplyr::any_of(record_id)) |>
REDCapCAST::suffix2label()
suffix2label()
out_object <- file_export(redcap_data,
output.format = output.format,

3
R/regression_model.R
View file

@ -10,6 +10,7 @@
#' @param ... ignored for now
#'
#' @importFrom stats as.formula
#' @importFrom REDCapCAST as_factor
#'
#' @return object of standard class for fun
#' @export
@ -66,7 +67,7 @@ regression_model <- function(data,
data <- data |>
purrr::map(\(.x){
if (is.character(.x)) {
suppressWarnings(REDCapCAST::as_factor(.x))
suppressWarnings(as_factor(.x))
} else {
.x
}

4
R/regression_table.R
View file

@ -81,7 +81,7 @@
#' #' @export
#' regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
#' # Stripping custom class
#' class(x) <- class(x)[class(x) != "webresearch_model"]
#' class(x) <- class(x)[class(x) != "freesearcher_model"]
#'
#' if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
#' if (!"exponentiate" %in% names(args.list)) {
@ -110,7 +110,7 @@ regression_table <- function(x, ...) {
regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
# Stripping custom class
class(x) <- class(x)[class(x) != "webresearch_model"]
class(x) <- class(x)[class(x) != "freesearcher_model"]
if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
if (!"exponentiate" %in% names(args.list)) {

25
R/shiny_freesearcheR.R Normal file
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@ -0,0 +1,25 @@
#' Launch the freesearcheR tool locally
#'
#' @description
#' All data.frames in the global environment will be accessible through the app.
#'
#'
#' @param ... arguments passed on to `shiny::runApp()`
#'
#' @return shiny app
#' @export
#'
#' @examples
#' \dontrun{
#' data(mtcars)
#' shiny_freesearcheR(launch.browser = TRUE)
#' }
shiny_freesearcheR <- function(...) {
appDir <- system.file("apps", "data_analysis_modules", package = "freesearcheR")
if (appDir == "") {
stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
}
a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
return(invisible(a))
}

27
R/shiny_webResearch.R
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@ -1,27 +0,0 @@
#' Test version of the shiny_cast function to launch the app with a data set in
#' the environment.
#'
#' @param data optional data set to provide for analysis
#' @param ... arguments passed on to `shiny::runApp()`
#'
#' @return shiny app
#' @export
#'
#' @examples
#' \dontrun{
#' mtcars |> shiny_webResearch(launch.browser = TRUE)
#' }
shiny_webResearch <- function(data = NULL, ...) {
appDir <- system.file("apps", "data_analysis_modules", package = "webResearch")
if (appDir == "") {
stop("Could not find the app directory. Try re-installing `webResearch`.", call. = FALSE)
}
G <- .GlobalEnv
if (!is.null(data) && is.data.frame(data)) {
assign("webResearch_data", data, envir = G)
}
a <- shiny::runApp(appDir = appDir, ...)
return(invisible(a))
}

56
README.md
View file

@ -1,20 +1,58 @@
# webResearch
# freesearcheR
<!-- badges: start -->
<!-- badges: end -->
This package is the backbone of the open and freely accessible browser-based data analysis tool with project name "webResearch".
This package is the backbone of the free and open browser based data exploration and analysis tool with publication ready output.
This package and the ***freesearcheR***-tool is part of a large project to democratize health data analysis and removing barriers for clinicians to engage in health research.
As of 2024-12-19 the ***freesearcheR***-tool is online and accessible here: [link to shinyapps.io free hosting](https://agdamsbo.shinyapps.io/freesearcheR/). All feedback is welcome and can be shared as a GitHub issue.
Initiatives for to start funding to continue development of the tool and surrounding initiatives will start soon.
## Roadmap
- A minimally working example
- [ ] Stratified analyses
- Table 1 of baseline characteristics
- Table 2 of main analysis results
- Figure 1 of main results (like forest plot)
- Shiny GUI implementation
- Additional study designs:
- Fundraising for further development
- [x] Cross-sectional data analyses
- Implementation with different focus groups and educational formats.
- [ ] Longitudinal data analyses
- [ ] Survival analysis
- More detailed variable browser
- [ ] Add histograms for data distribution
- [ ] Option to edit labels
- [ ] Plot regression analyses results
- [ ] Export modified data
- [ ] Include reproducible code for all steps
- [x] ~~Modify factor levels~~ Factor level modifications is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12
- [x] More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12
## Install locally
The ***freesearcheR***-tool can also be launched locally. Any data.frame available in the global environment will be accessible from the interface.
```
require("devtools")
devtools::install_github("agdamsbo/freesearcheR")
library(freesearcheR)
```
## Code of Conduct
Please note that the freesearcheR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

0
webResearch.Rproj → freesearcheR.Rproj
View file

19
inst/apps/data_analysis/server.R
View file

@ -1,7 +1,3 @@
# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
# source(here::here("app/functions.R"))
# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
library(readr)
library(MASS)
@ -19,7 +15,7 @@ library(quarto)
library(here)
library(broom)
library(broom.helpers)
library(REDCapCAST)
# library(REDCapCAST)
library(easystats)
library(patchwork)
library(DHARMa)
@ -32,6 +28,17 @@ if (file.exists(here::here("functions.R"))) {
source(here::here("functions.R"))
}
#' freesearcheR server
#'
#' @param input input
#' @param output output
#' @param session session
#'
#' @returns server
#' @export
#' @importFrom REDCapCAST numchar2fct
#'
#' @examples
server <- function(input, output, session) {
## Listing files in www in session start to keep when ending and removing
## everything else.
@ -68,7 +75,7 @@ server <- function(input, output, session) {
out <- out |>
(\(.x){
suppressWarnings(
REDCapCAST::numchar2fct(.x)
numchar2fct(.x)
)
})()
}

348
inst/apps/data_analysis_modules/app.R
View file

@ -1,7 +1,7 @@
########
#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/functions.R
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/functions.R
########
@ -249,6 +249,8 @@ cut.Date <- function(x,breaks,start.on.monday=TRUE,...){
is_any_class <- function(data, class.vec) {
any(class(data) %in% class.vec)
}
@ -685,124 +687,124 @@ plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112
m_datafileUI <- function(id) {
ns <- shiny::NS(id)
shiny::tagList(
shiny::fileInput(
inputId = ns("file"),
label = "Upload a file",
multiple = FALSE,
accept = c(
".csv",
".xlsx",
".xls",
".dta",
".ods",
".rds"
)
),
shiny::h4("Parameter specifications"),
shiny::helpText(shiny::em("Select the desired variables and press 'Submit'")),
shiny::uiOutput(ns("include_vars")),
DT::DTOutput(ns("data_input")),
shiny::actionButton(ns("submit"), "Submit")
)
}
m_datafileServer <- function(id, output.format = "df") {
shiny::moduleServer(id, function(input, output, session, ...) {
ns <- shiny::NS(id)
ds <- shiny::reactive({
REDCapCAST::read_input(input$file$datapath) |> REDCapCAST::parse_data()
})
output$include_vars <- shiny::renderUI({
shiny::req(input$file)
shiny::selectizeInput(
inputId = ns("include_vars"),
selected = NULL,
label = "Covariables to include",
choices = colnames(ds()),
multiple = TRUE
)
})
base_vars <- shiny::reactive({
if (is.null(input$include_vars)) {
out <- colnames(ds())
} else {
out <- input$include_vars
}
out
})
output$data_input <-
DT::renderDT({
shiny::req(input$file)
ds()[base_vars()]
})
shiny::eventReactive(input$submit, {
# shiny::req(input$file)
data <- shiny::isolate({
ds()[base_vars()]
})
file_export(data,
output.format = output.format,
tools::file_path_sans_ext(input$file$name)
)
})
})
}
file_app <- function() {
ui <- shiny::fluidPage(
m_datafileUI("data"),
# DT::DTOutput(outputId = "redcap_prev")
toastui::datagridOutput2(outputId = "redcap_prev")
)
server <- function(input, output, session) {
m_datafileServer("data", output.format = "list")
}
shiny::shinyApp(ui, server)
}
file_app()
tdm_data_upload <- teal::teal_data_module(
ui <- function(id) {
shiny::fluidPage(
m_datafileUI(id)
)
},
server = function(id) {
m_datafileServer(id, output.format = "teal")
}
)
tdm_data_read <- teal::teal_data_module(
ui <- function(id) {
shiny::fluidPage(
m_redcap_readUI(id = "redcap")
)
},
server = function(id) {
moduleServer(
id,
function(input, output, session) {
ns <- session$ns
m_redcap_readServer(id = "redcap", output.format = "teal")
}
)
}
)
########
@ -910,13 +912,14 @@ argsstring2list <- function(string) {
factorize <- function(data, vars) {
if (!is.null(vars)) {
data |>
dplyr::mutate(
dplyr::across(
dplyr::all_of(vars),
REDCapCAST::as_factor
as_factor
)
)
} else {
@ -939,6 +942,18 @@ dummy_Imports <- function() {
}
file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
output.format <- match.arg(output.format)
@ -950,9 +965,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
{
assign(name, value |>
dplyr::bind_cols() |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct())
parse_data() |>
as_factor() |>
numchar2fct())
},
value = data,
name = filename
@ -961,9 +976,9 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
datanames(out) <- filename
} else if (output.format == "df") {
out <- data|>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct()
parse_data() |>
as_factor() |>
numchar2fct()
} else if (output.format == "list") {
out <- list(
data = data,
@ -987,11 +1002,12 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
default_parsing <- function(data){
data |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
REDCapCAST::numchar2fct()
parse_data() |>
as_factor() |>
numchar2fct()
}
@ -1102,6 +1118,7 @@ m_redcap_readUI <- function(id, include_title = TRUE) {
m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
output.format <- match.arg(output.format)
@ -1227,7 +1244,7 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
shiny::req(input$fields)
record_id <- dd()[[1]][1]
redcap_data <- REDCapCAST::read_redcap_tables(
redcap_data <- read_redcap_tables(
uri = input$uri,
token = input$api,
fields = unique(c(record_id, input$fields)),
@ -1236,10 +1253,10 @@ m_redcap_readServer <- function(id, output.format = c("df", "teal", "list")) {
raw_or_label = "both",
filter_logic = input$filter
) |>
REDCapCAST::redcap_wider() |>
redcap_wider() |>
dplyr::select(-dplyr::ends_with("_complete")) |>
dplyr::select(-dplyr::any_of(record_id)) |>
REDCapCAST::suffix2label()
suffix2label()
out_object <- file_export(redcap_data,
output.format = output.format,
@ -1400,6 +1417,7 @@ redcap_app <- function() {
regression_model <- function(data,
@ -1437,7 +1455,7 @@ regression_model <- function(data,
data <- data |>
purrr::map(\(.x){
if (is.character(.x)) {
suppressWarnings(REDCapCAST::as_factor(.x))
suppressWarnings(as_factor(.x))
} else {
.x
}
@ -1691,7 +1709,7 @@ regression_table <- function(x, ...) {
regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
# Stripping custom class
class(x) <- class(x)[class(x) != "webresearch_model"]
class(x) <- class(x)[class(x) != "freesearcher_model"]
if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
if (!"exponentiate" %in% names(args.list)) {
@ -1811,7 +1829,7 @@ modify_qmd <- function(file, format) {
########
#### Current file: R//shiny_webResearch.R
#### Current file: R//shiny_freesearcheR.R
########
@ -1827,18 +1845,16 @@ modify_qmd <- function(file, format) {
shiny_webResearch <- function(data = NULL, ...) {
appDir <- system.file("apps", "data_analysis_modules", package = "webResearch")
shiny_freesearcheR <- function(...) {
appDir <- system.file("apps", "data_analysis_modules", package = "freesearcheR")
if (appDir == "") {
stop("Could not find the app directory. Try re-installing `webResearch`.", call. = FALSE)
stop("Could not find the app directory. Try re-installing `freesearcheR`.", call. = FALSE)
}
G <- .GlobalEnv
if (!is.null(data) && is.data.frame(data)) {
assign("webResearch_data", data, envir = G)
}
a <- shiny::runApp(appDir = appDir, ...)
a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...)
return(invisible(a))
}
@ -1885,7 +1901,7 @@ custom_theme <- function(...,
########
#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/ui.R
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/ui.R
########
# ns <- NS(id)
@ -2214,7 +2230,7 @@ ui <- bslib::page_fluid(
"Data is only stored for analyses and deleted immediately afterwards."),
shiny::p(
style = "margin: 1; color: #888;",
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/webResearch/", target="_blank", rel="noopener noreferrer")
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target="_blank", rel="noopener noreferrer")
),
)
)
@ -2222,14 +2238,9 @@ ui <- bslib::page_fluid(
########
#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/server.R
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/server.R
########
# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
# source(here::here("app/functions.R"))
# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
library(readr)
library(MASS)
library(stats)
@ -2246,7 +2257,7 @@ library(quarto)
library(here)
library(broom)
library(broom.helpers)
library(REDCapCAST)
# library(REDCapCAST)
library(easystats)
library(patchwork)
library(DHARMa)
@ -2255,10 +2266,7 @@ library(toastui)
library(IDEAFilter)
library(shinyWidgets)
library(DT)
# if (!requireNamespace("webResearch")) {
# devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
# }
# library(webResearch)
# library(freesearcheR)
# source("functions.R")
@ -2269,7 +2277,17 @@ 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.
@ -2308,7 +2326,6 @@ server <- function(input, output, session) {
rv <- shiny::reactiveValues(
list = list(),
ds = NULL,
input = exists("webResearch_data"),
local_temp = NULL,
ready = NULL,
test = "no",
@ -2373,33 +2390,6 @@ server <- function(input, output, session) {
rv$data_original <- from_env$data()
})
# ds <-
# shiny::reactive({
# # input$file1 will be NULL initially. After the user selects
# # and uploads a file, head of that data file by default,
# # or all rows if selected, will be shown.
# # if (v$input) {
# # out <- webResearch_data
# # } else if (input$source == "file") {
# # req(data_file$data())
# # out <- data_file$data()
# # } else if (input$source == "redcap") {
# # req(purrr::pluck(data_redcap(), "data")())
# # out <- purrr::pluck(data_redcap(), "data")()
# # }
#
# req(rv$data_original)
#
# rv$ds <- "loaded"
#
# rv$data <- rv$data_original
#
#
# # rv$data <- rv$data_original
#
# # rv$data_original
# })
##############################################################################
#########
######### Data modification section
@ -2589,7 +2579,7 @@ server <- function(input, output, session) {
{
data <- data_filter() |>
dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
REDCapCAST::fct_drop.data.frame() |>
fct_drop.data.frame() |>
factorize(vars = input$factor_vars)
if (input$strat_var == "none") {
@ -2809,7 +2799,7 @@ server <- function(input, output, session) {
########
#### Current file: /Users/au301842/webResearch/inst/apps/data_analysis_modules/launch.R
#### Current file: /Users/au301842/freesearcheR/inst/apps/data_analysis_modules/launch.R
########
shinyApp(ui, server)

54
inst/apps/data_analysis_modules/server.R
View file

@ -1,8 +1,3 @@
# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
# source(here::here("app/functions.R"))
# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
library(readr)
library(MASS)
library(stats)
@ -19,7 +14,7 @@ library(quarto)
library(here)
library(broom)
library(broom.helpers)
library(REDCapCAST)
# library(REDCapCAST)
library(easystats)
library(patchwork)
library(DHARMa)
@ -28,10 +23,7 @@ library(toastui)
library(IDEAFilter)
library(shinyWidgets)
library(DT)
# if (!requireNamespace("webResearch")) {
# devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
# }
# library(webResearch)
# library(freesearcheR)
# source("functions.R")
@ -42,7 +34,17 @@ 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.
@ -81,7 +83,6 @@ server <- function(input, output, session) {
rv <- shiny::reactiveValues(
list = list(),
ds = NULL,
input = exists("webResearch_data"),
local_temp = NULL,
ready = NULL,
test = "no",
@ -146,33 +147,6 @@ server <- function(input, output, session) {
rv$data_original <- from_env$data()
})
# ds <-
# shiny::reactive({
# # input$file1 will be NULL initially. After the user selects
# # and uploads a file, head of that data file by default,
# # or all rows if selected, will be shown.
# # if (v$input) {
# # out <- webResearch_data
# # } else if (input$source == "file") {
# # req(data_file$data())
# # out <- data_file$data()
# # } else if (input$source == "redcap") {
# # req(purrr::pluck(data_redcap(), "data")())
# # out <- purrr::pluck(data_redcap(), "data")()
# # }
#
# req(rv$data_original)
#
# rv$ds <- "loaded"
#
# rv$data <- rv$data_original
#
#
# # rv$data <- rv$data_original
#
# # rv$data_original
# })
##############################################################################
#########
######### Data modification section
@ -362,7 +336,7 @@ server <- function(input, output, session) {
{
data <- data_filter() |>
dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) |>
REDCapCAST::fct_drop.data.frame() |>
fct_drop.data.frame() |>
factorize(vars = input$factor_vars)
if (input$strat_var == "none") {

2
inst/apps/data_analysis_modules/ui.R
View file

@ -324,7 +324,7 @@ ui <- bslib::page_fluid(
"Data is only stored for analyses and deleted immediately afterwards."),
shiny::p(
style = "margin: 1; color: #888;",
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/webResearch/", target="_blank", rel="noopener noreferrer")
"Andreas G Damsbo | AGPLv3 license | ", shiny::tags$a("Source on Github", href = "https://github.com/agdamsbo/freesearcheR/", target="_blank", rel="noopener noreferrer")
),
)
)

6
inst/apps/data_analysis_modules/www/docs.html
View file

@ -40,7 +40,7 @@ margin: 0 0.8em 0.2em -1em; vertical-align: middle;
<p>So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.</p>
<p>Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.</p>
<h2 id="contribute">Contribute</h2>
<p>Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please <a href="https://github.com/agdamsbo/webResearch/issues">share and report on the project page on GitHub</a>.</p>
<p>Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please <a href="https://github.com/agdamsbo/freesearcheR/issues">share and report on the project page on GitHub</a>.</p>
<h2 id="roadmap">Roadmap</h2>
<ul>
<li><p><label><input type="checkbox">Stratified analyses</label></p></li>
@ -58,8 +58,8 @@ margin: 0 0.8em 0.2em -1em; vertical-align: middle;
<li><p><label><input type="checkbox">Plot regression analyses results</label></p></li>
<li><p><label><input type="checkbox">Export modified data</label></p></li>
<li><p><label><input type="checkbox">Include reproducible code for all steps</label></p></li>
<li><p><label><input type="checkbox">Modify factor levels (including naming, order, collapsing, removing)</label></p></li>
<li><p><label><input type="checkbox">More options for date/datetime/time grouping/factoring</label></p></li>
<li><p><label><input type="checkbox" checked><del>Modify factor levels</del> Factor level modification is possible through converting factors to numeric &gt; cutting numeric with desired fixed values. 2024-12-12</label></p></li>
<li><p><label><input type="checkbox" checked>More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12</label></p></li>
</ul>

34
inst/apps/data_analysis_modules/www/docs.md
View file

@ -1,34 +0,0 @@
# Documentation on the freesearcheR platform
Welcome! So glad to see you here! Welcome to test this early concept of a platform to easily explore, manipulate and analyse clinical data.
Below will be a more detailed description of the included features and possibilities, as well as the planned and possible feature additions.
## Roadmap
- [ ] Stratified analyses
- Additional study designs:
- [x] Cross-sectional data analyses
- [ ] Longitudinal data analyses
- [ ] Survival analysis
- More detailed variable browser
- [ ] Add histograms for datadistribution
- [ ] Option to edit labels
- [ ] Plot regression analyses results
- [ ] Export modified data
- [ ] Include reproducible code for all steps
- [ ] Modify factor levels
- [ ] More options for date/datetime/time grouping/factoring

6
inst/apps/data_analysis_modules/www/docs.qmd
View file

@ -14,7 +14,7 @@ Below will be a more detailed description of the included features and possibili
## Contribute
Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please [share and report on the project page on GitHub](https://github.com/agdamsbo/webResearch/issues).
Contributions are very welcome. If you find anything odd, or you think of features to add or remove, please [share and report on the project page on GitHub](https://github.com/agdamsbo/freesearcheR/issues).
## Roadmap
@ -40,6 +40,6 @@ Contributions are very welcome. If you find anything odd, or you think of featur
- [ ] Include reproducible code for all steps
- [ ] Modify factor levels (including naming, order, collapsing, removing)
- [x] ~~Modify factor levels~~ Factor level modification is possible through converting factors to numeric > cutting numeric with desired fixed values. 2024-12-12
- [ ] More options for date/datetime/time grouping/factoring
- [x] More options for date/datetime/time grouping/factoring. Included weekday and month-only options. 2024-12-12

4
inst/apps/teal_test/app.R
View file

@ -56,8 +56,8 @@ tm_variable_browser_module <- tm_variable_browser(
filters <- teal::teal_slices()
app_source <- "https://github.com/agdamsbo/webresearch"
gh_issues_page <- "https://github.com/agdamsbo/webresearch/issues"
app_source <- "https://github.com/agdamsbo/freesearcheR"
gh_issues_page <- "https://github.com/agdamsbo/freesearcheR/issues"
header <- tags$span(
style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",

23
man/file_export.Rd Normal file
View file

@ -0,0 +1,23 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/helpers.R
\name{file_export}
\alias{file_export}
\title{Title}
\usage{
file_export(data, output.format = c("df", "teal", "list"), filename, ...)
}
\arguments{
\item{data}{data}
\item{output.format}{output}
\item{filename}{filename}
\item{...}{passed on}
}
\value{
data
}
\description{
Title
}

2
man/is_any_class.Rd
View file

@ -18,7 +18,9 @@ factor
Test class
}
\examples{
\dontrun{
vapply(REDCapCAST::redcapcast_data, \(.x){
is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt"))
}, logical(1))
}
}

17
man/m_datafileUI.Rd
View file

@ -1,17 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/file-import-module.R
\name{m_datafileUI}
\alias{m_datafileUI}
\title{Shiny UI module to load a data file}
\usage{
m_datafileUI(id)
}
\arguments{
\item{id}{id}
}
\value{
shiny UI
}
\description{
Shiny UI module to load a data file
}

2
man/regression_table.Rd
View file

@ -93,7 +93,7 @@ regression_table.list <- function(x, ...) {
#' @export
regression_table.default <- function(x, ..., args.list = NULL, fun = "gtsummary::tbl_regression") {
# Stripping custom class
class(x) <- class(x)[class(x) != "webresearch_model"]
class(x) <- class(x)[class(x) != "freesearcher_model"]
if (any(c(length(class(x)) != 1, class(x) != "lm"))) {
if (!"exponentiate" \%in\% names(args.list)) {

23
man/shiny_freesearcheR.Rd Normal file
View file

@ -0,0 +1,23 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/shiny_freesearcheR.R
\name{shiny_freesearcheR}
\alias{shiny_freesearcheR}
\title{Launch the freesearcheR tool locally}
\usage{
shiny_freesearcheR(...)
}
\arguments{
\item{...}{arguments passed on to \code{shiny::runApp()}}
}
\value{
shiny app
}
\description{
All data.frames in the global environment will be accessible through the app.
}
\examples{
\dontrun{
data(mtcars)
shiny_freesearcheR(launch.browser = TRUE)
}
}

26
man/shiny_webResearch.Rd
View file

@ -1,26 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/shiny_webResearch.R
\name{shiny_webResearch}
\alias{shiny_webResearch}
\title{Test version of the shiny_cast function to launch the app with a data set in
the environment.}
\usage{
shiny_webResearch(data = NULL, ...)
}
\arguments{
\item{data}{optional data set to provide for analysis}
\item{...}{arguments passed on to \code{shiny::runApp()}}
}
\value{
shiny app
}
\description{
Test version of the shiny_cast function to launch the app with a data set in
the environment.
}
\examples{
\dontrun{
mtcars |> shiny_webResearch(launch.browser = TRUE)
}
}

557
renv.lock
View file

@ -57,27 +57,6 @@
],
"Hash": "64ff3427f559ce3f2597a4fe13255cb6"
},
"Deriv": {
"Package": "Deriv",
"Version": "4.1.6",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"methods"
],
"Hash": "cd52c065c9e687c60c56b51f10f7bcd3"
},
"Formula": {
"Package": "Formula",
"Version": "1.2-5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"stats"
],
"Hash": "7a29697b75e027767a53fde6c903eca7"
},
"IDEAFilter": {
"Package": "IDEAFilter",
"Version": "0.2.0",
@ -138,30 +117,6 @@
],
"Hash": "5122bb14d8736372411f955e1b16bc8a"
},
"MatrixModels": {
"Package": "MatrixModels",
"Version": "0.5-3",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"Matrix",
"R",
"methods",
"stats"
],
"Hash": "0776bf7526869e0286b0463cb72fb211"
},
"PKI": {
"Package": "PKI",
"Version": "0.1-14",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"base64enc"
],
"Hash": "f5b9c6b2f62f1fa3dd53fd1ddccbb241"
},
"R.cache": {
"Package": "R.cache",
"Version": "0.16.0",
@ -238,9 +193,13 @@
},
"REDCapCAST": {
"Package": "REDCapCAST",
"Version": "24.12.1",
"Source": "Repository",
"Repository": "CRAN",
"Version": "24.11.3",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
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19
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