andreas/FreesearchR
1
0
Fork 0
mirror of https://github.com/agdamsbo/FreesearchR.git synced 2025-12-15 00:52:09 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

Updated for new version

Browse source
This commit is contained in:
Andreas Gammelgaard Damsbo 2025-09-23 12:23:51 +02:00
parent 123f11c760
commit 61538a8dd5
No known key found for this signature in database
13 changed files with 92 additions and 25 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
.gitignore vendored
View file

@ -12,6 +12,7 @@ docs
inst/doc
app_dev
app_stable
app_test
app
page
demo

13
CITATION.cff
View file

@ -7,17 +7,16 @@ cff-version: 1.2.0
message: 'To cite package "FreesearchR" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
with publication ready output'
version: 25.8.3
title: 'FreesearchR: Easy data analysis for clinicians'
version: 25.9.1
doi: 10.5281/zenodo.14527429
identifiers:
- type: url
value: https://app.FreesearchR.org/
abstract: Easily evaluate and analysis clinical health data in your browser on a server
or on your own device. Import data from multiple sources, summarise, modify and
visualise data and export key metrics and regression analysis results in a publication
ready format.
abstract: Easily evaluate and analyse clinical health data in your browser, either
based on a hosted version or run on your own device. Import data from multiple sources,
summarise, modify and visualise data and create regression models. Export key metrics
and regression analysis results in a publication ready document format.
authors:
- family-names: Damsbo
given-names: Andreas Gammelgaard

3
NAMESPACE
View file

@ -19,6 +19,8 @@ export(clean_sep)
export(columnSelectInput)
export(compare_missings)
export(contrast_text)
export(corr_pairs_validate)
export(correlation_pairs)
export(create_baseline)
export(create_column_server)
export(create_column_ui)
@ -80,6 +82,7 @@ export(m_redcap_readServer)
export(m_redcap_readUI)
export(make_validation)
export(make_validation_alerts)
export(mcar_validate)
export(merge_expression)
export(merge_long)
export(missing_fraction)

4
NEWS.md
View file

@ -1,8 +1,8 @@
# FreesearchR 25.8.3 - DEV
# FreesearchR 25.9.1
*NEW* Language has been revised to make the app more accessible and easier to understand.
*NEW* Initial and very rudimentary translation for Danish and Swahili is introduced. Other languages can be added as well.
*NEW* Foundations for introducing an internationalised UI has been introduced. Initial and very rudimentary translation for Danish and Swahili is included. Other languages can be added as well.
*NEW* Alerts as to guide on select important steps and aspects are introduced. This is expected to expand.

2
R/app_version.R
View file

@ -1 +1 @@
app_version <- function()'25.8.3'
app_version <- function()'25.9.1'

2
R/hosted_version.R
View file

@ -1 +1 @@
hosted_version <- function()'v25.8.3-250911'
hosted_version <- function()'v25.9.1-250923'

BIN
R/sysdata.rda
View file

Binary file not shown.

16
SESSION.md
View file

@ -11,11 +11,11 @@
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2025-09-10 |
|date |2025-09-23 |
|rstudio |2025.05.0+496 Mariposa Orchid (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.7.30 @ /usr/local/bin/quarto |
|FreesearchR |25.8.3.250910 |
|FreesearchR |25.9.1.250923 |
--------------------------------------------------------------------------------
@ -43,7 +43,6 @@
|cardx |0.2.5 |2025-07-03 |CRAN (R 4.4.1) |
|caTools |1.18.3 |2024-09-04 |CRAN (R 4.4.1) |
|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.4.0) |
|cffr |1.2.0 |2025-01-25 |CRAN (R 4.4.1) |
|checkmate |2.3.2 |2024-07-29 |CRAN (R 4.4.0) |
|class |7.3-23 |2025-01-01 |CRAN (R 4.4.1) |
|classInt |0.4-11 |2025-01-08 |CRAN (R 4.4.1) |
@ -53,7 +52,6 @@
|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.4.1) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|curl |6.4.0 |2025-06-22 |CRAN (R 4.4.1) |
|data.table |1.17.8 |2025-07-10 |CRAN (R 4.4.1) |
|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
|datawizard |1.2.0 |2025-07-17 |CRAN (R 4.4.1) |
@ -84,7 +82,7 @@
|foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) |
|foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) |
|Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) |
|FreesearchR |25.8.3 |NA |NA |
|FreesearchR |25.9.1 |NA |NA |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|gdtools |0.4.2 |2025-03-27 |CRAN (R 4.4.1) |
|generics |0.1.4 |2025-05-09 |CRAN (R 4.4.1) |
@ -112,16 +110,18 @@
|iterators |1.0.14 |2022-02-05 |CRAN (R 4.4.1) |
|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) |
|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) |
|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.4.1) |
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
|keyring |1.4.1 |2025-06-15 |CRAN (R 4.4.1) |
|knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) |
|labeling |0.4.3 |2023-08-29 |CRAN (R 4.4.1) |
|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) |
|lattice |0.22-7 |2025-04-02 |CRAN (R 4.4.1) |
|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
|litedown |0.7 |2025-04-08 |CRAN (R 4.4.1) |
|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|lubridate |1.9.4 |2024-12-08 |CRAN (R 4.4.1) |
|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|markdown |2.0 |2025-03-23 |CRAN (R 4.4.1) |
|MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) |
|Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) |
|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) |
@ -165,7 +165,6 @@
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.4.0) |
|rappdirs |0.3.3 |2021-01-31 |CRAN (R 4.4.1) |
|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) |
|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) |
|Rcpp |1.1.0 |2025-07-02 |CRAN (R 4.4.1) |
@ -220,8 +219,9 @@
|usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) |
|utf8 |1.2.6 |2025-06-08 |CRAN (R 4.4.1) |
|uuid |1.2-1 |2024-07-29 |CRAN (R 4.4.1) |
|V8 |6.0.6 |2025-08-18 |CRAN (R 4.4.1) |
|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) |
|viridis |0.6.5 |2024-01-29 |CRAN (R 4.4.0) |
|viridisLite |0.4.2 |2023-05-02 |CRAN (R 4.4.1) |
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
|writexl |1.5.4 |2025-04-15 |CRAN (R 4.4.1) |

20
man/corr_pairs_validate.Rd Normal file
View file

@ -0,0 +1,20 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/validation.R
\name{corr_pairs_validate}
\alias{corr_pairs_validate}
\title{Correlation pairs validation}
\usage{
corr_pairs_validate(data)
}
\arguments{
\item{data}{data.frame}
}
\value{
data.frame
}
\description{
Correlation pairs validation
}
\examples{
# correlation_pairs(mtcars) |> corr_pairs_validate()
}

24
man/correlation_pairs.Rd Normal file
View file

@ -0,0 +1,24 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/correlations-module.R
\name{correlation_pairs}
\alias{correlation_pairs}
\title{Determine significant correlations in the data set}
\usage{
correlation_pairs(data, threshold = 0.8)
}
\arguments{
\item{data}{data.frame}
\item{threshold}{correlation threshold}
}
\value{
data.frame
}
\description{
Determine significant correlations in the data set
}
\examples{
correlation_pairs(mtcars)
correlation_pairs(mtcars,.9)
correlation_pairs(mtcars[c(1:4),])
}

11
man/make_validation.Rd
View file

@ -21,15 +21,16 @@ Create validation data.frame
i18n <- shiny.i18n::Translator$new(translation_csvs_path = here::here("inst/translations"))
i18n$set_translation_language("en")
df_original <- mtcars
df_original[1,2:4] <- NA
df_obs <- df_original |> dplyr::filter(carb==4)
df_original[1, 2:4] <- NA
df_obs <- df_original |> dplyr::filter(carb == 4)
df_vars <- df_original[1:7]
val <- purrr::map2(
.x = validation_lib(),
.y = list(
list(x = df_original, y = df_obs),
list(x = df_original, y = df_vars),
list(x=df_original)),
list(x = df_original, y = df_obs),
list(x = df_original, y = df_vars),
list(x = df_original)
),
make_validation
)
val |> make_validation_alerts()

19
man/mcar_validate.Rd Normal file
View file

@ -0,0 +1,19 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/validation.R
\name{mcar_validate}
\alias{mcar_validate}
\title{MCAR validation based on a gtsummary table bady}
\usage{
mcar_validate(data, outcome = NULL)
}
\arguments{
\item{data}{data}
\item{outcome}{outcome variable}
}
\value{
data.frame
}
\description{
MCAR validation based on a gtsummary table bady
}

2
man/missings_validate.Rd
View file

@ -17,6 +17,6 @@ Validate function of missingness in data
}
\examples{
df <- mtcars
df[1,2:4] <- NA
df[1, 2:4] <- NA
missings_validate(df)
}