Changes in version 4.10.2 (2026-01-08) - Shiny app ("server.R""): when reading stata files, as_factor is applied to work with codes instead of values. Changes in version 4.10.1 (2025-10-29) - bug fixed in cGroupsWUI() - argument stars also identifies p-values < 0.01 with triple star. Changes in version 4.10.0 (2025-08-19) argument var.equal argument of compareGroups and descrTable functions: - default value has been change to FALSE. - now applies also when comparing two groups and for non-corrected pairwise comparisons. - when var.equal is set to FALSE and there are more than two groups Games-Howell test is applied instead of a Tukey test for normal distributed variables. Changes in version 4.9.3 - table.i: bug fixed when no p-values cannot be computed for categorical variables for survival outcomes (p.ratio) Changes in version 4.9.2 - bug fixed in compareGroups.fit when some variables cannot be described Changes in version 4.9.1 (2024-10-30) - bug fixed in cGroupsWUI() Changes in version 4.9.0 (2024-09-13) - new argument nmax.method to compute the N shown in the header. By default N is computed as the number of rows with at least one valid value in the described variables, but also N can be computed as the total number of rows in the data set or in each group regardless the available data in the described variables. - new argument stars in descrTable and createTable functions to show significance levels asterisks beside p-values. - new argument p.trend.method in compareGroups and descrTable functions to choose between Spearman, Kendall or "Cuzick's trend test for non-normal numerical variables. - WUI: bug fixed when exporting plots Changes in version 4.8.0 (2024-01-29) - URL replaced by - importFrom("stats", "model.frame") included in NAMESPACE - descrTable, createTAble: new argument added "lab.ref" to change label for reference category - createTable, compareGroups functions: isR() removed Changes in version 4.7.2 (2023-10-11) - export2md: table format bug fixed in exporting to HTML when nmax=FALSE Changes in version 4.7.1 (2023-08-22) - version info fixed (DESCRIPTION vs MAN) - missing functions in alias argument from compareGroups-internals.Rd document incorporated Changes in version 4.7.0 (2023-05-24) - WUI: new functionality to convert to factors integer variables. Useful to plot numeric variables with few values as bar plots. - export2md, export2word, export2pdf, export2html: bug fixed in coloring all header lines for stratified tables MINOR - update.formula2 method: new ... argument added. - CITATION file: citEntry() and personList() replaced by bibentry() and c(), respectively. - DESCRIPTION file: Encoding field changed from latin1 to UTF-8 Changes in version 4.6.0 (2022-11-18) - new function padjustCompareGroups to adjust p-values for multiple testing - predimed example data has been removed from the package - export2pdf: new arguments header.background and header.color - z[.compareGroups function: bug fixed when subsetting compareGroups object by variable names Changes in version 4.5.3 - compareGroups: bug fixed in Xext when data contains a single variable Changes in version 4.5.2 - missingTable: bug fixed when applying this function to a descriptive table obtained by descrTable function. - export2latex: it can handle more than one '&' or '%' characters. Changes in version 4.5.1 (2021-03-29) - export2md: add bottom header line when compiling to PDF. Changes in version 4.5.0 - compareGroups, descrTable: new argument 'lab.missing' to specify label for missing category. - export2md.Rd: in the argument 'width' now it is mentioned explicitly that this argument is ignored when exporting the descriptive table to Word. - compareGroups.R: bug fixed when simplify = FALSE and empty categories for groups variables are now kept. - descrTable.Rd, createTable.Rd: bug fixed in the help files for q.type argument. Changes in version 4.4.6 (2020-12-04) - NAMESPACE: functions from importFrom(flextable,...) have been dropped. Changes in version 4.4.5 (2020-09-01) - SNPassoc removed from Suggests - SNPs.rda added to data folder and SNPs.rd help file taken from SNPassoc package and added to compareGroups man files. - Depends on R version >3.5.0 - vignette has been reduced after removing WUI section Changes in version 4.4.4 (2020-08-25) - SNPassoc moved from Depends to Suggests Changes in version 4.4.3 (2020-06-25) - WUI (cGroupsWUI) renewed based on shinydashboardPlus layout and more options. - wrong description of file argument from export2xls function fixed. - bug fixed in getResults(, "ratio") when only one variable is described. - bug fixed in xlab and ylab in box.plot internal function. - new component in 'extra.labels' argument from 'createTable' function to append label for surv variables. - internal function snpQC syntax code: replace mclapply for lapply - shinydashboardPlus package added to suggested - compareSNPs: bug fixed when only one SNP is described Changes in version 4.4.2 - bug fixed when exporting tables to PDF in cGroupsWUI() Changes in version 4.4.1 (2020-03-19) - bug fixed in internal function compare.i when computing binom.test with zero freqs. - confinterval function to compute confidence interval of means and medians return NA and not error when it cannot compute IC for medians. - conf.level (confidence level) argument in compareGroups and descrTable function also applies to hazard, odds and risk ratios. - epitools package removed from importFrom (NAMESPACE) - functions qnorm, rbinom and uniroot functions from stats package added in importFrom Changes in version 4.4.0 - compareGroups, descrTable: new argument 'compute.prop' added (to compute proportions instead of percentages for categorical row-variables). - createTable, descrTable: new argument 'all.last' added (to place descriptives of the whole sample after descriptives by groups). Changes in version 4.3.1 - compareGroups.Rd: p.trend for categorical variables modified. - export2word: new arguments added (same as export2md). - export2md: longtable fixed. - bug fixed in internal table.i function when identifying reference category when NA. - bug fixed in cGroupsGUI: updated to new updates of compareGroups.fit function. - export2pdf: new arguments incorportated and makes use of export2md function. Changes in version 4.3.0 - export2word supports stratified tables - Risk Ratios are now computed. See riskratio argument from compareGroups function. Changes in version 4.2.0 (2019-09-19) - flextable package dependency - export2md supports tables to export to word in nicer format using flextable - export2md supports stratified tables when exporting to word (new export2mdwordcbind internal function) - new argument perc in report function (same as plot) - export2word bug fixed Changes in version 4.1.1 - bug fixed in export2md when exportd in a Rmd notebook. - norm.plot: par(mfrow=c(1,1)) added at the end, to restore mutiplots device. - export2md: more understandable warning message when used outside the Rmarkdown chunk. Changes in version 4.1.0 (2019-05-27) - new argument show.ci and conf.level in createTable and compareGroups, respectively, to compute confidence intervals of means, medians, proportions and incidences. - new argument "position" to export2md function, to place tables justified to the left, centerd or to the right (only when compiling to HTML or PDF) - no longer Hmisc, xtable, gdata package dependies. Imports write_xlsx from writexl and suggests readxl packages. - xlsx removed from suggested packages. - export2xls uses write_xlsx function from writexl pacakge. - cGroupsWUI improved and updated. - shinythemes package suggested. This saves a lot of space in app folder. - shinyWidgets package suggested (for awasome dropdownbuttons and colour picker in the shiny app) - export2md, export2mdcbind: bug fixed when drawing header line and no Nmax is reported. - labelled class from "predimed", "regicor" variables removed. - byrow add a choice to compute proportions by combinations of rows and columns (i.e. to sum up 100%). MINOR - bug fixed in compareGroups.R when using "select" argument. - compare.i function: bug fixed when "include.miss". - bug fixed when variable names contains spaces. - "..." argument removed from export2word. - internal function simplify.formula removed. Changes in version 4.0.0 (2018-11-02) - new argument var.equal to compareGroups and descrTable. - update.compareGroups: changed. - dates variables supported - compareGroups.default and compareGroups.formula unified in a single compareGroups function. - new strataTable function: to create stratified tables without having to use cbind. Also incorporates an update method. - package vignette improved. - new descrTable created. This function builds a descriptive table in one step. - Imports: kableExtra and chron added, - Suggested: car removed - export2md: new arguments added (format, width, strip, first.strip, background, size and landscape) - compareGroups: new arguments added (chisq.test.B and chisq.test.seed) - table.i, createTable: checking OS to print +/- sign removed from table.i and passed to createTable. This speeds up the bivariate construction a lot. - compareGroups.default: '...' argument removed. Changes in version 3.4.0 (2018-05-18) - compareGroups now handles tibble objects Changes in version 3.3.4 (2018-04-22) - bug fixed when checking vignette v3.3.3 - bug fixed for Hmisc::label in examples and vignette Changes in version 3.3.2 - createTable: bug fixed related to hide.no v3.3.1 - createTable: bug fixed related to extra.labels argument v3.3 - createTable: new "extra.labels" argument indicating the key to normal, non-normal or categorical variables. - compareGroups: new "byrow" argument to report percentages by rows or by columns. v3.2.5 - export2md, export2html: Var removed from descriptive table header. v3.2.4 - compareGroups.default: new argument chisq.test.perm to perform simulation chisq test instead of fisher test v3.2.3 - export2word: changed working directory v3.2.2 - plot do not open new windows when file argument is NULL. - new argument "verbose" set to FALSE by default in "compareSNPs" - new component in header.labels argument to modify OR/HR bivariate table column label. - bug fixed in getResults function when exctracting proportions. v3.2.1 - package vignette updated. - new argument "oddsratio.method" in "compareGroups.default" function to compute odds ratio under different methods. - XLConnect and shinythemes removed from suggested packages. v3.2 - cGroupsWUI: improved. - Internal function descripSurv has been modified fixing a bug when computing K-M probabilities. - xlsx not imported but suggested. Only required when calling export2xls function. Changes in version 3.1 (2015-09-07) - cGroupsWUI: improved shiny app interface. - export2word: new function to export tables to Word. - export2md: new function to export tables to Markdown. - export2html: file argument can be left missing to return HTML code, similar to export2latex. Changes in version 3.0.1 (2015-05-13) - cGroupsWUI: udpates and improvements in the aspect of the GUI web based application. Changes in version 3.0 (2015-01-23) 2015-01-14 - new argument header.labels incorporated to functions to print and export the bivariate table. This offers the possibility to change some 'key' labels such as p.overall or p.trend. - new function getResults to retrieve results from compareGroups or createTable object as vectors and matrices. - new argument 'margin' implemented in 'export2pdf' function. MAJOR CHANGES: - new function cGroupsWUI has been implemented which opens a web browser with a Web User Interface using Shiny functions. - new vignette compareGroupsWUI_vignette.pdf created to illustrate how WUI works. MINOR CHANGES: - 'file' argument from export2csv, export2latex, export2html, export2pdf and report functions must specify the extension. This has been changed from previous versions where no extension (.pdf, .tex, .html or .pdf) was required. - fixed: 'hide' argument from createTable does not produce an error but a warning when a non-existing variable is specified. - fixed: indentation when exporting a rbind.createTable object to HTML - SNPs data removed. Changes in version 2.0.5 (2014-08-28) 2014-8-25 - Bug fixed regarding number of decimals when applying subsetting '[' method to createTable, rbind.createTable and cbind.createTable class objects. Changes in version 2.0.4 (2014-05-02) 2014-05-02 - JSS paper citation included, in compareGroups.Rd and in createTable.Rd help files. Changes in version 2.0.3 (2014-04-29) 2014-04-29 - high line and +/- symbol when printint table on R console replaced by standard C-locale if necessary. Changes in version 2.0.2 (2014-03-26) 2014-03-26 - fixed: +/- symbol Changes in version 2.0.1 (2014-03-17) 2014-03-17 - check package: Sweave.sty removed from vignette folder. - integerToAscii replaced by intToUtf8 function. - internal functions 'snp.R', 'SNPHWE.R', 'sortSNPs.R', etc. removed since SNPassoc package has been incorporated in depends list. Changes in version 2.0 (2013-08-02) 2013-08-02 - new argument 'type' in 'plot.compareGroups' method to save plots in different formats. - new argument 'include.miss' in compareGroups function. This treats NA values as a new category for categorical row-variables. - new function 'radiograph' that reports raw data in the data set. - new function 'missTable' has been created, to report missingness tables. - new function 'compareSNPs' has been created, with its own 'print' method. - new functions 'report' and 'export2pdf' have been created to generate PDF files with tables and/or plots. - new argumen 'landscape' has been incorporated to 'export2latex' function. - new package dependencies required: SNPassoc and HardyWeinberg MINOR CHANGES: - when computing p-values to compare groups for a categorical row-variables, if only one row or one column has some non-zero count, p-value is '.'. - cGroupsGUI no longer saves objects in .GlobalEnv but uses .compareGroupsEnv environment. - cGroupsGUI input cannot be left missing. - bug fixed in cGroupsGUI function when exporting to html format. - internal function prepare has been modified in order to fit the bivariate table columns to their width. - internal function descripSurv has been modified to accomodate group codes containing regular expression symbols (such as +, -, etc.). - bug fixed in export2html function when exporting a table with one row. - bug fixed in 'ref.no' argument of compareGroups function. Changes in version 1.4 (2012-11-07) 2012-11-06 - an internal bug fixed when specifying selec for a particular row-varible in building Xlong attribute for compareGroups object. - cGroupsGUI: improved, more compact. Changes in version 1.3 (2012-09-10) 2012-07-19 - createTable objects can be plotted and it is also possible to apply varinfo function on them. - cGroupsGUI: new smaller frame. - createTable: new argument q.type, to specify how the quartiles (percentiles) are displayed for a non-normal distributed row-variable. - createTable: new argument sd.type, to allow the user change the format in displaying SD; 1-inside brackets (default), 2- mean +/- SD. - createTable: new argument digits.p added, to allow the user specify the number of decimals for all p-values displayed on the bivariate table. - createTable: new argument p.ratio has been added. This computes de p-value corresponding to each OR/HR individually. - Nmax reported changed: now it represents the number of patients with at least one valid value across all analized variables. - a bug fixed in compareGroup: when some row-variable could not be performed 'varnames.orig' attribute was bad built. This affected other functions such as createTable. - a bug fixed in [.createTable: an error ocurred when a literal category specified to be hiden when subsetting a createTable object. - MINOR CHANGE: 1.95 replaced by 1.96 in 'compareGroups.Rd' file. Changes in version 1.2 (2012-07-11) 2012-07-10 - export2html: a bug fixed in N. - repeated row-variables are kept after applying the generic function 'update'. This was not possible in the previous version 1.1. - new internal function 'simplify.formula' added. Changes in version 1.1 (2012-05-13) 2012-05-13 - [.compareGroups: a bug fixed when a row-variable present multiple times. - compareGroups: new argument 'compute.ratio'. - compareGroups: default value for argument 'simplify' changed to TRUE. - load tcltk only when cGroupsGUI is called. - bug fixed in export2latex.cbind.createTable when drawing hlines. - export2latex: apostrophes have been changed from '' to `' in writing default table caption. Changes in version 1.0 (2012-02-03) 2011-11-29 MAIN CHANGES - new method '[' implemented for createTable objects. - new method rbind implemented for compareGroups and createGroups objects. - new method cbind implemented for createTable objects. - new method summary implemented for createTable objects. - createTable: new value for type (3) displays only absolute frequencies for categorical variables. - export2latex.createTable, export2latex.cbind.createTable: new argument 'label' implemented to put a label for each table to be cited in the main LaTeX document. - chisq.test2: computes simulated p-values for the chi-squared test when it is not possible to compute assymptotic nor exact fisher test. - compareGroups: new argument 'p.mult.corrected' added that gives the option of computing multiple comparison corrected p-values or non-corrected p-values. - regicor: some variables names have been changed (gender to sex, histbp to histhtn). - example data sets: 'myData' example data set has been removed and 'regicor' data set is used in the examples instead. Changes in version 0.1-6 2010-03-25 MAIN CHANGES - compareGroups: can deal with Surv objects as response variables in order to compute appropiate p-values for a cohort (time-to-response) studies. - plot.compareGroups: perform appropiate plots when response is of class 'Surv' (kaplan-meier, etc.) - export2html: new function created to export tables to HTML format - plot.compareGroups: new internal functions created to draw proper plots for survival class variables - createTable: new argument 'show.p.overall'. - createTable: change default value for 'show.p.all' argument to FALSE. - export2csv and export2html: new argument created which is the same as 'which.table' in 'export2latex' function - plot.compareGroups: bug fixed in performing shapiro-Wilks test on >5000 size sample. - export2latex: new arguments 'caption' and 'loc.caption' added. - argument silent set to TRUE in all functions where try have been applied. Changes in version 0.1-5 2010-08-20 - print.createTable: lines in header and botoom of the tables are printed, using some characters from integer2ascii function of oce package. - print.createTable, export2latex, export2csv: new argument 'nmax' added. - export2latex: environment longtable is used, instead of table. - compareGroups: new argument 'simplify' added. - MAIN change: it is possible not to specify any grouping variable, and descriptives for all sample are performed without p-values. - print.createTable, export2latex, export2csv: bug fixed when row-variables with no data present. - plot.compareGroups method now plots barplots for categorical variable, as well as bivariate plots (row-variables vs grouping variable). - [.summary.compareGroups method deleted and new [.compareGroups method created instead. - export2csv: now writes the N (sample size) for each group in the header line. - createTable: argument 'hide' changed, now the user can specify either the position of the cateogory to be hidden or the name of this category. - createTable: new argument 'hide.no' added, that allows the user to specify which category to be hidden for all 2-level row-variables. - createTable: bug fixed, when only 1 row-variable and show.all=FALSE. - print.createTable changed: 'which.table' argument added that specifyies which table is printed (descr, avail or both). By default, only 'descr' table is printed. - export2latex: 'which.table' argument added add an argument that specifyies which table is printed (descr, avail or both). By default, only 'descr' table is printed. - export2latex: 'file' argument can be missing. In this case, LaTex code is printed in the R console. This function returns the LaTeX code like print.xtable does. - export2latex: 'size' argument added. - compareGroups.formula: bug fixed in removing variables using '-'. - compare.i: bug fixed in p-value for multiple comparison for a normal row-variable. - createTable: automatacally detects if grouping variable is an ordered factor to display p-trend. Changes in version 0.1-4 (2011-04-26) 2010-07-30 - print.compareGroups: fix a bug, significant p-values codes 0.01 has been replaced by 0.1 - export2latex: substitute some special character ($, <, >, >=, <=, &, ...) in the grouping variable label, and '&' for row-variables and group levels. - compareGroups.default: added an option to specify different quantiles from Q1 and Q3 (min and max for example) for non-normal variables. - [.summary.compareGroups method Changes in version 0.1-3 (2010-07-29) 2010-07-27 - fixed a bug in 'print.createTable', 'export2csv' and 'export2latex' functions when there is only one row-variable Changes in version 0.1-2 2010-07-27 - MAIN CHANGE: submitted to CRAN. - package no more available in www.regicor.org Changes in version 0.1-1 2010-07-26 - fixed a bug in 'print.createTable', 'export2csv' and 'export2latex' functions when there is only one group - some words changed in help documentation Changes in version 0.1-0 2010-06-22 - 'compareGroups' created and uploaded in www.regicor.org