
FreesearchR
- Source:vignettes/FreesearchR.Rmd
+ Source: vignettes/FreesearchR.Rmd
FreesearchR.Rmd

Data types
- Source:vignettes/data-types.Rmd
+ Source: vignettes/data-types.Rmd
data-types.Rmd

Missingness in data
- Source:vignettes/missingness.Rmd
+ Source: vignettes/missingness.Rmd
missingness.Rmd

Session info
- Source:vignettes/session.Rmd
+ Source: vignettes/session.Rmd
session.Rmd

On visuals
- Source:vignettes/visuals.Rmd
+ Source: vignettes/visuals.Rmd
visuals.Rmd
Citation
-Source: DESCRIPTION
Source: DESCRIPTION
Damsbo A (2025). FreesearchR: A free and open-source browser based data analysis tool for researchers with publication ready output. diff --git a/news/index.html b/news/index.html index f6975d1..ce5a34d 100644 --- a/news/index.html +++ b/news/index.html @@ -38,13 +38,14 @@
FreesearchR 25.8.2 - DEV
-- -NEW preparing to automatically only show relevant tabs to simplify interface. NOT IMPLEMENTED YET +
NEW Including the NHANES dataset for experimentation.
+BUG Improved JS to correctly handle menu drop downs on mobile devices
+DOCS Updated “Prepare > Overview” to “Prepare > Overview and filter” to better reflect options.
FreesearchR 25.8.2
+FreesearchR 25.8.1
diff --git a/pkgdown.yml b/pkgdown.yml index 5c35491..76d6eef 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,7 +7,7 @@ articles: missingness: missingness.html session: session.html visuals: visuals.html -last_built: 2025-08-08T12:44Z +last_built: 2025-08-27T10:52Z urls: reference: https://agdamsbo.github.io/FreesearchR/reference article: https://agdamsbo.github.io/FreesearchR/articles diff --git a/reference/FreesearchR_palette.html b/reference/FreesearchR_palette.html index 0192ceb..871bb34 100644 --- a/reference/FreesearchR_palette.html +++ b/reference/FreesearchR_palette.html @@ -38,7 +38,7 @@
Convert class grid column to icon
- Source:R/data-summary.R
+ Source: R/data-summary.R
add_class_icon.Rd

Convert string of arguments to list of arguments
- Source:R/helpers.R
+ Source: R/helpers.R
argsstring2list.Rd

Print a flexible baseline characteristics table
- Source:R/baseline_table.R
+ Source: R/baseline_table.R
baseline_table.Rd

Extract and clean axis ranges
- Source:R/data_plots.R
+ Source: R/data_plots.R
clean_common_axis.Rd

Attempts at applying uniform date format
- Source:R/update-variables-ext.R
+ Source: R/update-variables-ext.R
clean_date.Rd

gsub wrapper for piping with default values for separator substituting
- Source:R/update-variables-ext.R
+ Source: R/update-variables-ext.R
clean_sep.Rd

A selectizeInput customized for data frames with column labels
- Source:R/custom_SelectInput.R
+ Source: R/custom_SelectInput.R
columnSelectInput.Rd

Pairwise comparison of missings across covariables
- Source:R/missings-module.R
+ Source: R/missings-module.R
compare_missings.Rd

Create a baseline table
- Source:R/baseline_table.R
+ Source: R/baseline_table.R
create_baseline.Rd

Create summetric log ticks
- Source:R/regression_plot.R
+ Source: R/regression_plot.R
create_log_tics.Rd

Create a data overview datagrid
- Source:R/data-summary.R
+ Source: R/data-summary.R
create_overview_datagrid.Rd

Module to Convert Numeric to Factor
- Source:R/cut-variable-dates.R
+ Source: R/cut-variable-dates.R
cut-variable.Rd

Extended cutting function with fall-back to the native base::cut
- Source:R/cut-variable-dates.R
+ Source: R/cut-variable-dates.R
cut_var.Rd

Data correlations evaluation module
- Source:R/correlations-module.R
+ Source: R/correlations-module.R
data-correlations.Rd

Test app for the data-import module
- Source:R/data-import.R
+ Source: R/data-import.R
data-import.Rd

Data correlations evaluation module
- Source:R/missings-module.R
, R/visual_summary.R
+ Source: R/missings-module.R
, R/visual_summary.R
data-missings.Rd

Data correlations evaluation module
- Source:R/data_plots.R
, R/plot_box.R
, R/plot_hbar.R
, and 4 more
+ Source: R/data_plots.R
, R/plot_box.R
, R/plot_hbar.R
, and 4 more
data-plots.Rd

Data summary for printing visual summary
- Source:R/visual_summary.R
+ Source: R/visual_summary.R
data_summary_gather.Rd

Filter function to filter data set by variable type
- Source:R/helpers.R
+ Source: R/helpers.R
data_type_filter.Rd

Recognised data types from data_type
- Source:R/regression_model.R
+ Source: R/regression_model.R
data_types.Rd

Drop empty events from REDCap export
- Source:R/redcap_read_shiny_module.R
+ Source: R/redcap_read_shiny_module.R
drop_empty_event.Rd

Deparses expression as string, substitutes native pipe and adds assign
- Source:R/helpers.R
+ Source: R/helpers.R
expression_string.Rd

Merges list of named arguments for qmd header generation
- Source:R/report.R
+ Source: R/report.R
format_writer.Rd

Get the function options based on the selected function description
- Source:R/regression_model.R
+ Source: R/regression_model.R
get_fun_options.Rd

Print label, and if missing print variable name
- Source:R/data_plots.R
+ Source: R/data_plots.R
get_label.Rd

Get the function options based on the selected function description
- Source:R/data_plots.R
+ Source: R/data_plots.R
get_plot_options.Rd

Easily get variable icon based on data type or class
- Source:R/data-summary.R
+ Source: R/data-summary.R
get_var_icon.Rd

Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'
- Source:R/helpers.R
+ Source: R/helpers.R
getfun.Rd

GGplot default theme for plotting export objects
- Source:R/theme.R
+ Source: R/theme.R
gg_theme_export.Rd

GGplot default theme for plotting in Shiny
- Source:R/theme.R
+ Source: R/theme.R
gg_theme_shiny.Rd

Matches pattern to vector based on match type
- Source:R/wide2long.R
+ Source: R/wide2long.R
grepl_fix.Rd

Wrapper to ease data file import
- Source:R/import-file-ext.R
+ Source: R/import-file-ext.R
import-file-type.Rd

Test app for the import_file module
- Source:R/import-file-ext.R
+ Source: R/import-file-ext.R
import-file_module.Rd

Split vector by an index and embed addition
- Source:R/report.R
+ Source: R/report.R
index_embed.Rd

Checks if elements in vector are equally spaced as indication of ID
- Source:R/data-summary.R
+ Source: R/data-summary.R
is_consecutive.Rd

Test is date/datetime/time
- Source:R/cut-variable-dates.R
+ Source: R/cut-variable-dates.R
is_datetime.Rd

Test if element is identical to the previous
- Source:R/helpers.R
+ Source: R/helpers.R
is_identical_to_previous.Rd

Test if url is valid format for REDCap API
- Source:R/redcap_read_shiny_module.R
+ Source: R/redcap_read_shiny_module.R
is_valid_redcap_url.Rd

Validate REDCap token
- Source:R/redcap_read_shiny_module.R
+ Source: R/redcap_read_shiny_module.R
is_valid_token.Rd

Easily launch the FreesearchR app
- Source:R/launch_FreesearchR.R
+ Source: R/launch_FreesearchR.R
launch_FreesearchR.Rd

Easily round log scale limits for nice plots
- Source:R/regression_plot.R
+ Source: R/regression_plot.R
limit_log.Rd

Line breaking at given number of characters for nicely plotting labels
- Source:R/data_plots.R
+ Source: R/data_plots.R
line_break.Rd

Wrapper to pivot gtsummary table data to long for plotting
- Source:R/regression_plot.R
+ Source: R/regression_plot.R
merge_long.Rd

Plot missings and class with apexcharter
- Source:R/visual_summary.R
+ Source: R/visual_summary.R
missings_apex_plot.Rd

Wrapper to modify quarto file to render specific formats
- Source:R/report.R
+ Source: R/report.R
modify_qmd.Rd

Create a data overview data.frame ready for sparklines
- Source:R/data-summary.R
+ Source: R/data-summary.R
overview_vars.Rd

Reduce character vector with the native pipe operator or character string
- Source:R/helpers.R
+ Source: R/helpers.R
pipe_string.Rd

Regression coef plot from gtsummary. Slightly modified to pass on arguments
- Source:R/regression_plot.R
+ Source: R/regression_plot.R
plot.tbl_regression.Rd

Easily plot single euler diagrams
- Source:R/plot_euler.R
+ Source: R/plot_euler.R
plot_euler_single.Rd

Get possible regression models
- Source:R/regression_model.R
+ Source: R/regression_model.R
possible_functions.Rd

Shiny module to browser and export REDCap data
- Source:R/redcap_read_shiny_module.R
+ Source: R/redcap_read_shiny_module.R
redcap_read_shiny_module.Rd

Create a regression model programatically
- Source:R/regression_model.R
+ Source: R/regression_model.R
regression_model.Rd

Create table of regression model
- Source:R/regression_table.R
+ Source: R/regression_table.R
regression_table.Rd

Create regression summary table
- Source:R/regression_table.R
+ Source: R/regression_table.R
regression_table_create.Rd

Removes columns with completenes below cutoff
- Source:R/helpers.R
+ Source: R/helpers.R
remove_empty_cols.Rd

Very simple function to remove nested lists, like when uploading .rds
- Source:R/helpers.R
+ Source: R/helpers.R
remove_nested_list.Rd

Get names of repeated instruments
- Source:R/redcap_read_shiny_module.R
+ Source: R/redcap_read_shiny_module.R
repeated_instruments.Rd

Create a select input control with icon(s)
- Source:R/import-file-ext.R
+ Source: R/import-file-ext.R
selectInputIcon.Rd

Display a table in a window
- Source:R/datagrid-infos-mod.R
+ Source: R/datagrid-infos-mod.R
show_data.Rd

Simplified version of the snakecase packages to_snake_case
- Source:R/helpers.R
+ Source: R/helpers.R
simple_snake.Rd

Drop-in replacement for the base::sort_by with option to remove NAs
- Source:R/helpers.R
+ Source: R/helpers.R
sort_by.Rd

Specify format arguments to include in qmd header/frontmatter
- Source:R/report.R
+ Source: R/report.R
specify_qmd_format.Rd

Easily subset by data type function
- Source:R/data_plots.R
+ Source: R/data_plots.R
subset_types.Rd

Implemented functions
- Source:R/regression_model.R
+ Source: R/regression_model.R
supported_functions.Rd

Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
- Source:R/regression_plot.R
+ Source: R/regression_plot.R
symmetrical_scale_x_log10.Rd

A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names.
- Source:R/regression_table.R
+ Source: R/regression_table.R
tbl_merge.Rd

Create unique short names of character vector items based on index
- Source:R/visual_summary.R
+ Source: R/visual_summary.R
unique_short.Rd

Module to Reorder the Levels of a Factor Variable
- Source:R/update-factor-ext.R
+ Source: R/update-factor-ext.R
update-factor.Rd

Select, rename and convert variables
- Source:R/update-variables-ext.R
+ Source: R/update-variables-ext.R
update-variables.Rd

Modified from the datamods pacakge
- Source:R/update-variables-ext.R
+ Source: R/update-variables-ext.R
update_variables_datagrid.Rd

A selectizeInput customized for named vectors
- Source:R/custom_SelectInput.R
+ Source: R/custom_SelectInput.R
vectorSelectInput.Rd

Vertical stacked bar plot wrapper
- Source:R/plot_hbar.R
+ Source: R/plot_hbar.R
vertical_stacked_bars.Rd

Ggplot2 data summary visualisation based on visdat::vis_dat.
- Source:R/visual_summary.R
+ Source: R/visual_summary.R
visual_summary.Rd

Alternative pivoting method for easily pivoting based on name pattern
- Source:R/wide2long.R
+ Source: R/wide2long.R
wide2long.Rd

Wrapper to save data in RDS, load into specified qmd and render
- Source:R/helpers.R
+ Source: R/helpers.R
write_quarto.Rd