diff --git a/.gitignore b/.gitignore index f01e8231..39765ab7 100644 --- a/.gitignore +++ b/.gitignore @@ -12,6 +12,7 @@ docs inst/doc app_dev app_stable +app_test app page demo diff --git a/CITATION.cff b/CITATION.cff index 1866a54a..2fdc6bec 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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 diff --git a/NAMESPACE b/NAMESPACE index ebd9e891..867a9020 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -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) diff --git a/NEWS.md b/NEWS.md index da0d8185..7aaf5f98 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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. diff --git a/R/app_version.R b/R/app_version.R index 5498842b..c806ac1b 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'25.8.3' +app_version <- function()'25.9.1' diff --git a/R/hosted_version.R b/R/hosted_version.R index d8b66a95..8b8a2896 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v25.8.3-250911' +hosted_version <- function()'v25.9.1-250923' diff --git a/R/sysdata.rda b/R/sysdata.rda index 041f8a67..c01e454e 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/SESSION.md b/SESSION.md index 64ac7904..51e20b56 100644 --- a/SESSION.md +++ b/SESSION.md @@ -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) | diff --git a/man/corr_pairs_validate.Rd b/man/corr_pairs_validate.Rd new file mode 100644 index 00000000..d085f36b --- /dev/null +++ b/man/corr_pairs_validate.Rd @@ -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() +} diff --git a/man/correlation_pairs.Rd b/man/correlation_pairs.Rd new file mode 100644 index 00000000..fe9d90ef --- /dev/null +++ b/man/correlation_pairs.Rd @@ -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),]) +} diff --git a/man/make_validation.Rd b/man/make_validation.Rd index a60f1365..80799d32 100644 --- a/man/make_validation.Rd +++ b/man/make_validation.Rd @@ -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() diff --git a/man/mcar_validate.Rd b/man/mcar_validate.Rd new file mode 100644 index 00000000..395ba416 --- /dev/null +++ b/man/mcar_validate.Rd @@ -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 +} diff --git a/man/missings_validate.Rd b/man/missings_validate.Rd index 16383831..b71fb77e 100644 --- a/man/missings_validate.Rd +++ b/man/missings_validate.Rd @@ -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) }