NEWS

compareGroups 4.9.1 (2024-10-30)

bug fixed in cGroupsWUI()

compareGroups 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

compareGroups 4.8.0 (2024-01-29)

<comparegroups.eu> URL replaced by <isubirana.github.io/compareGroups>
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

compareGroups 4.7.2 (2023-10-11)

export2md: table format bug fixed in exporting to HTML when nmax=FALSE

compareGroups 4.7.1 (2023-08-22)

version info fixed (DESCRIPTION vs MAN)
missing functions in alias argument from compareGroups-internals.Rd document incorporated

compareGroups 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

compareGroups 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

compareGroups 4.5.3

compareGroups: bug fixed in Xext when data contains a single variable

compareGroups 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.

compareGroups 4.5.1 (2021-03-29)

export2md: add bottom header line when compiling to PDF.

compareGroups 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.

compareGroups 4.4.6 (2020-12-04)

NAMESPACE: functions from importFrom(flextable,...) have been dropped.

compareGroups 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

compareGroups 4.4.4 (2020-08-25)

SNPassoc moved from Depends to Suggests

compareGroups 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

compareGroups 4.4.2

bug fixed when exporting tables to PDF in cGroupsWUI()

compareGroups 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

compareGroups 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).

compareGroups 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.

compareGroups 4.3.0

export2word supports stratified tables
Risk Ratios are now computed. See riskratio argument from compareGroups function.

compareGroups 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

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 3.4.0 (2018-05-18)

compareGroups now handles tibble objects

compareGroups 3.3.4 (2018-04-22)

bug fixed when checking vignette v3.3.3
bug fixed for Hmisc::label in examples and vignette

compareGroups 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.

compareGroups 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.

compareGroups 3.0.1 (2015-05-13)

cGroupsWUI: udpates and improvements in the aspect of the GUI web based application.

compareGroups 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.

compareGroups 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.

compareGroups 2.0.4 (2014-05-02)

2014-05-02

JSS paper citation included, in compareGroups.Rd and in createTable.Rd help files.

compareGroups 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.

compareGroups 2.0.2 (2014-03-26)

2014-03-26

fixed: +/- symbol

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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.

compareGroups 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

compareGroups 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

compareGroups 0.1-2

2010-07-27

MAIN CHANGE: submitted to CRAN.
package no more available in www.regicor.org

compareGroups 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

compareGroups 0.1-0

2010-06-22

'compareGroups' created and uploaded in www.regicor.org