Help for package descsuppR

Version:

1.2

License:

Title:

Support Functions for (Reproducible) Descriptive Statistics

Description:

Contains functions to help with generating tables with descriptive statistics. In addition, the package can display results of statistical tests for group comparisons. A wide range of test procedures is supported, and user-defined test functions can be incorporated.

Depends:

foreach

Imports:

plyr, descutils, tibble, dplyr, rlang, DescTools, nparcomp, rankFD, circular, glue, purrr

Suggests:

roxygen2, survival, stringr

Encoding:

UTF-8

Collate:

'descsuppR-package.r' 'tod.r'

RoxygenNote:

7.2.3

NeedsCompilation:

Packaged:

2025-09-24 18:38:18 UTC; kueck2

Author:

Andreas Leha [aut], Fabian Kück [aut, cre]

Maintainer:

Fabian Kück <fabian.kueck@med.uni-goettingen.de>

Repository:

CRAN

Date/Publication:

2025-10-01 07:10:08 UTC

descsuppR

Description

Author(s)

Maintainer: Fabian Kück fabian.kueck@med.uni-goettingen.de

Authors:

Andreas Leha andreas.leha@med.uni-goettingen.de

Conversion to and from 'Time of Day'

Description

Does not safeguard against "26:69".

Usage

as.tod(x)

## S3 method for class 'character'
as.tod(x)

## S3 method for class 'circular'
as.tod(x)

is.tod(x)

## S3 method for class 'tod'
as.double(x, ...)

circular(x, ...)

## Default S3 method:
circular(
  x,
  type = c("angles", "directions"),
  units = c("radians", "degrees", "hours"),
  template = c("none", "geographics", "clock12", "clock24"),
  modulo = c("asis", "2pi", "pi"),
  zero = 0,
  rotation = c("counter", "clock"),
  names = NULL,
  ...
)

## S3 method for class 'tod'
circular(x, ...)

Arguments

x

An object to be converted to or represented as a circular object.

...

Additional arguments passed to methods or lower-level functions.

type

Character string indicating if data represent "angles" or "directions".

units

Character string; the measurement units for the input data ("radians", "degrees", or "hours").

template

Character string specifying a specific template for circular data.

modulo

Character string indicating the modulo arithmetic to be used ("asis", "2pi", "pi").

zero

Numeric; direction assigned as zero (in the specified units).

rotation

Character string; direction of rotation for increasing values ("counter", "clock").

names

Optional character vector of names for the object.

Value

x converted to/from 'tod'

Author(s)

Dr. Andreas Leha

Examples

times <- c("8:53", NA, "22:30")

## some conversions
as.tod(times)
as.numeric(as.tod(times))

is.tod(times)
is.tod(as.tod(times))

buildDescrTbl

Description

Calculate and Present Descriptive Values in Pritable

Usage

buildDescrTbl(
  df,
  tests,
  prmnames,
  prmunits,
  addFactorLevelsToNames = TRUE,
  excel_style = TRUE,
  groupby,
  addungrouped = FALSE,
  dopvals = FALSE,
  ignore_test_errors = FALSE,
  p.adjust.method = "holm",
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  report_tests = FALSE,
  report_testmessages = FALSE,
  pvals_formatting = TRUE,
  pvals_digits = 3,
  pvals_signiflev = 0.05,
  extraLevels = NULL,
  missingName = "missing",
  nonNAsName = "N",
  removeZeroNAs = TRUE,
  removeZeroExtraLevels = TRUE,
  includeNAs = FALSE,
  includeNonNAs = FALSE,
  printOrgAlignment = FALSE,
  useutf8 = "latex",
  verbose = 0,
  without_attrs = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE,
  percentages = "columnwise"
)

Arguments

df

data.frame containing the variables of which to calc the descriptive values

tests

character vector or list of characters or list of functions or list of lists. In each case the i-th element gives the test to perform on the ith variable in the df (excluding stratification variables). The test can either be given as character (name of test function) or as function or as list where the first element is again either character or function and the following elemenst are *named* additional arguments to that test function. The individual function has to accept (at least) the arguments 'values' and 'grouping' which are vectors of equal length. For convenience, this package shipes with some example functions; have a look at those if you want to supply your own. These convenience functions include w.chisq.test w.cor.test, w.fisher.test, w.kruskal.test, w.wilcox.test. the whole list/vector is recycled if too short.

prmnames

names of the variables in df (if needed to be overwritten)

prmunits

units of the variables in df

addFactorLevelsToNames

logical. if TRUE expand 'sex' to 'sex [m/w]'. Defaults to TRUE.

excel_style

logical. if TRUE remove subsequent duplicates from the parameter column (as common in Excel). Default: TRUE

groupby

column of df. do more columns - one for each group. If the df$column is an ordered factor, the order will be respected in the resulting table

addungrouped

logical. if TRUE add a column 'total' with the ungrouped summary statistics. Default: FALSE

dopvals

boolean. if TRUE an additional column containing the p-values comparing the two strata in groubpy. Only implemented for a two-level stratum until now.

ignore_test_errors

logical. If TRUE returns an empty test results (as list).

p.adjust.method

character. if not NULL include an additional column with adjusted p values. see p.adjust.methods for possible values and explanations. Defaults to "holm"

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

report_tests

boolean. if TRUE one additional column in the result table will contain the test, that was performed to calculate the p value. Ignored if dopvals=FALSE

report_testmessages

boolean. if TRUE one additional column in the result table will contain any warnings that appeared while the test was performed. Ignored if dopvals=FALSE

pvals_formatting

boolean. If FALSE report numbers, else report formatted strings (via prettyPvalue)

pvals_digits

integer. Number of digits for p value formatting. Ignored when pvals_formatting==FALSE. Defaults to 2

pvals_signiflev

double. The significance level for bold p value formatting. Ignored when pvals_formatting==FALSE. Defaults to 0.05

extraLevels

named list of lists. Names have to be variable names. Elements have to have to be named list of this form: `some label` = list(idxvec = idxvec, display = logical). Here idxvec needs to be a logical vector of length nrow(df) that specifies the affected rows. If display is TRUE the number of affected rows will be shown under some label.

missingName

character. name of missing values (default: missing)

nonNAsName

character. name of not missing values (default: N)

removeZeroNAs

boolean. if TRUE, rows for missing values containing only 0s are removed from the result.

removeZeroExtraLevels

boolean. if TRUE, rows for ExtraLevels containing only 0s are removed from the result.

includeNAs

boolean. Include number of NAs in the output? Currently only one of either includeNonNAs or includeNAs can be set to TRUE

includeNonNAs

boolean. Include number of not missing values (Non-NAs) in the output? Currently only one of either includeNonNAs or includeNAs can be set to TRUE

printOrgAlignment

boolean. If TRUE, than a row like "<l> <r> <r>" will be included in the result df

useutf8

character. one of c("latex", "utf8", "replace"). if 'latex' (the default) use \pm in the output; if 'replace' use +- in the output, if 'utf8' use the unicode character

verbose

numeric. level of verbosity (0 : silent)

without_attrs

logical. If TRUE return the descriptive table with attrs. Otherwise add df, groupby, and a 'full' (closer to tidy) version of the table as attributes. Defaults to TRUE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

percentages

character. one of c("columnwise", "rowwise"). If 'rowwise', percentages are computed by row. Defaults to "columnwise"

Details

Do a Table containing descriptiva values

Value

formatted data.frame with descriptive values

Author(s)

Andreas Leha

Examples

ttt <- data.frame(data="training set",
                  age=runif(100, 0, 100),
                  sex=sample(c("m","f"), 100, replace=TRUE, prob=c(0.3, 0.7)),
                  score=factor(sample(1:5, 100, replace=TRUE),
                    ordered=TRUE,
                    levels=1:5))
ttt2 <- data.frame(data="test set",
                   age=runif(100, 0, 100),
                   sex=sample(c("m","f"), 100, replace=TRUE, prob=c(0.5,0.5)),
                   score=factor(sample(1:5, 100, replace=TRUE),
                     ordered=TRUE,
                     levels=1:5))

units <- c("years", "", "")
buildDescrTbl(rbind(ttt, ttt2),
              prmunits=units,
              groupby="data",
              includeNAs=TRUE)

buildDescrTbl.intern

Description

Internal wrapper around calc_descr_matrix

Usage

buildDescrTbl.intern(
  df,
  prmnames,
  prmunits,
  addFactorLevelsToNames = TRUE,
  extraLevels = NULL,
  includeNAs = FALSE,
  includeNonNAs = FALSE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE
)

Arguments

df

data.frame containing the variables of which to calc the descriptive values

prmnames

names of the variables in df (if needed to be overwritten)

prmunits

units of the variables in df

addFactorLevelsToNames

logical. if TRUE expand 'sex' to 'sex [m/w]'. Defaults to TRUE.

extraLevels

includeNAs

boolean. Include number of NAs in the output? Currently only one of either includeNonNAs or includeNAs can be set to TRUE

includeNonNAs

boolean. Include number of not missing values (Non-NAs) in the output? Currently only one of either includeNonNAs or includeNAs can be set to TRUE

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

Value

matrix with descriptive values

Author(s)

Andreas Leha

calc_descr

Description

calc descriptive values

Usage

calc_descr(
  x,
  xname,
  extraLevels = NULL,
  includeNAs = TRUE,
  includeNonNAs = FALSE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE
)

Arguments

x

vector of which to calc the descriptive values

xname

name of the varible holding values in x

extraLevels

includeNAs

boolean. include the number of NAs in the output?

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

Details

create a descriptive values containing data.frame.

Value

data.frame of character describing x

Author(s)

Andreas Leha

calc_descr_long

Description

change the description into the long format

Usage

calc_descr_long(
  x,
  xname,
  extraLevels = NULL,
  includeNAs = FALSE,
  includeNonNAs = FALSE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE
)

Arguments

x

vector of which to calc the descriptive values

xname

the name of the variable encoded in x

extraLevels

includeNAs

logical. include the number of NAs in the output?

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

Details

only for internal use.

Value

data.frame of character describing x

Author(s)

Andreas Leha

calc_descr_long

Description

change the description into the long format

Usage

calc_descr_long_old(
  x,
  xname,
  includeNAs = FALSE,
  includeNonNAs = FALSE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14
)

Arguments

x

vector of which to calc the descriptive values

xname

the name of the variable encoded in x

includeNAs

boolean. include the number of NAs in the output?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

Details

only for internal use.

Value

data.frame of character describing x

Author(s)

Andreas Leha

calc_descr_matrix

Description

Wrapper for single vectors

Usage

calc_descr_matrix(
  ttt,
  format = "long",
  extraLevels = NULL,
  includeNAs = FALSE,
  includeNonNAs = FALSE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE
)

Arguments

ttt

the data.frame

format

in c("long", "wide")

extraLevels

includeNAs

boolean. include number of NAs in the output?

includeNonNAs

boolean. include number of non-NAs in the output?

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

Details

calls the one dimensional functions

Value

matrix containing the descriptive values

Author(s)

Andreas Leha

calc_descr

Description

calc descriptive values

Usage

calc_descr_old(
  x,
  xname,
  extraLevels = NULL,
  includeNAs = TRUE,
  orderedAsUnordered = FALSE,
  factorlevellimit = 14,
  show.minmax = TRUE,
  show.IQR = FALSE,
  sd_digits = "by_mean",
  descr_digits = 2,
  significant_digits = TRUE
)

Arguments

x

vector of which to calc the descriptive values

xname

name of the varible holding values in x

extraLevels

includeNAs

boolean. include the number of NAs in the output?

orderedAsUnordered

logical. treat ordered factors as unordered factors?

factorlevellimit

integer. for factors with more than factorlevellimit levels, not all levels are printed

show.minmax

logical. if TRUE show minimum and maximum for numeric variables. Defaults to TRUE.

show.IQR

logical. if TRUE show 25% and 75% quantiles for numeric variables. Defaults to FALSE.

sd_digits

character. one of c("by_mean", "fixed"). If 'by_mean', the number of decimal places of the standard deviation is limited by the number of decimal places of the mean.

descr_digits

integer. Number of digits for formatting of descriptive values. Defaults to 2.

significant_digits

boolean. if TRUE, the number of significant digits of is given by descr_digits. Otherwise the number of decimal places is fixed.

Details

create a descriptive values containing data.frame.

Value

data.frame of character describing x

Author(s)

Andreas Leha

Convert Grouping Column Values into Headings with ddply

Description

For each unique value in the specified column of a data frame, creates a "subtable" where that value is moved as a group heading (first row) and the column is blanked for the remaining rows. Optionally, can "move along" specified metadata columns, shifting their first element to the last row.

Usage

convertColumnHeading(df, col, movealong = NULL)

Arguments

df

A data frame to be processed.

col

Character. Name of the column in df to use for grouping and converting to headings.

movealong

Optional character vector of column names. For each group, these columns are rotated, placing their first value after the last row.

Details

The function uses plyr::ddply to split the data frame by the levels of col. For each group, - Moves the grouping value to a heading (top row) - Adds an empty row for formatting - Optionally rotates metadata columns specified in movealong This can be useful for preparing tables for presentation or reporting.

Value

A data frame formatted with expanded headings per group.

Author(s)

Andreas Leha

Examples

df <- data.frame(Group = c("A", "A", "B", "B"), Data = 1:4, Meta = c("x", "y", "z", "w"))
convertColumnHeading(df, "Group")
convertColumnHeading(df, "Group", movealong = "Meta")

descrSurvEstimate

Description

build a description table for survival estimates

Usage

descrSurvEstimate(
  S,
  strata,
  stratorder,
  survname = "survival time",
  evaltimes = c(3, 5),
  evaltimeunits = "years",
  digits = 2,
  includeNAs = TRUE,
  includeNonNAs = TRUE,
  missingName = "missing",
  nonNAsName = "N",
  stratheader = TRUE,
  pval = FALSE,
  pvals_formatting = TRUE,
  pvals_digits = 2,
  pvals_signiflev = 0.05,
  hr = FALSE
)

Arguments

S

survival objects from Surv

strata

a list of vectors containing strata. If the vectors are ordered factors the columns will be used in the given order.

stratorder

(list of) character vector for the order of the reported columns. Overrides any order of strata

survname

the name of the survival time, e.g. 'DFS'

evaltimes

numeric vector. for which times to calculate the survival estimate

evaltimeunits

the unit of the survival times (years, months, ...)

digits

round to

includeNAs

boolean. Include number of NAs in the output?

includeNonNAs

Logical; if TRUE, include a column reporting the number of non-missing (non-NA) observations in the output table. Default is TRUE.

missingName

character. name of the rows with missing numbers. Defaults to "missing".

nonNAsName

Character string; the name to use as the column heading for the number of non-missing (non-NA) values. Default is "N".

stratheader

boolean. print the stratheader? Turn off for inclusion into a bigger table

pval

boolean. if TRUE, the p value from a cox model is printed in a separate column

pvals_formatting

boolean. If FALSE report numbers, else report formatted strings (via prettyPvalue)

pvals_digits

integer. Number of digits for p value formatting. Ignored when pvals_formatting==FALSE. Defaults to 2

pvals_signiflev

double. The significance level for bold p value formatting. Ignored when pvals_formatting==FALSE. Defaults to 0.05

hr

boolean. if TRUE, the hazard ratio (with confidence interval) is printed as well. (only has an effect if pval==TRUE)

Details

calculate the survival estimates at the specified times and return a nicely formatted table

Value

a character matrix

Author(s)

Andreas Leha

Examples

if (require("survival")) {

  S <- Surv(aml$time, aml$status)

  descrSurvEstimate(S,
                    evaltimes=c(19, 24),
                    evaltimeunits="months")
}

Extract the hours/minutes Component of time-of-day

Description

Extract the hours/minutes Component of time-of-day

Usage

hours.tod(x)

minutes.tod(x)

Arguments

x

vector of class tod

Value

numeric vector of length length(x) with hours/minutes

Author(s)

Dr. Andreas Leha

Examples

times <- as.tod(c("8:53", NA, "22:30"))
hours.tod(times)
minutes.tod(times)

Basic Functions on time-of-day Vectors

Description

These shoud just do whatever the same function does for character vectors

Usage

## S3 method for class 'tod'
length(x)

## S3 method for class 'tod'
x[i, ...]

## S3 replacement method for class 'tod'
x[i, ...] <- value

## S3 method for class 'tod'
x[[i, ...]]

## S3 replacement method for class 'tod'
x[[i, ...]] <- value

## S3 method for class 'tod'
c(...)

Arguments

x

vector of class tod

i

integer of indices

...

to match the generics' arguments

value

of type tod. to be inserted

Value

as expected

Author(s)

Dr. Andreas Leha

Examples

times <- c("8:53", NA, "22:30")
times <- as.tod(times)

length(times)
times[1]
times[1] <- "07:00"
c(times, times)

Descriptive Statistics for time-of-day Vectors

Description

Functions to calculate descriptve values for timo-of-day vectors. The heavy lifting is done by the circular package.

Usage

## S3 method for class 'tod'
mean(x, ...)

sd(x, ...)

## Default S3 method:
sd(x, na.rm = FALSE, ...)

## S3 method for class 'tod'
sd(x, na.rm = FALSE, ...)

## S3 method for class 'tod'
median(x, na.rm = FALSE, ...)

## S3 method for class 'tod'
min(..., na.rm = FALSE)

## S3 method for class 'tod'
max(..., na.rm = FALSE)

## S3 method for class 'tod'
quantile(x, ...)

Arguments

x

vector of class tod

...

additional args passed on to base stats or circular stats functions

na.rm

often passed through to correponding functions in the circular packages. Otherwise logitcal. Defaults to FALSE.

Details

These functions are meant to provide the least surprising descriptive values.

Value

descriptive values as would be returned for non-circular numeric vectors

Author(s)

Dr. Andreas Leha

Examples

times <- as.tod(c("21:53", NA, "22:30", "23:10", "23:58", "00:15", "01:01"))

mean(times)
mean(times, na.rm = TRUE)

pred.survfit

Description

X-years prediction

Usage

pred.survfit(Sfit, time)

Arguments

Sfit

a survfit object

time

the time to calculate the estimate

Details

Calculate the X-years estimate of a survfit

Value

the estimate

Author(s)

Andreas Leha

Replace German Umlaute

Description

Replace German Umlaute

Usage

replaceGermanUmlauts(txt)

Arguments

txt

character. within this txt the German umlauts will be replaced

Value

character. version of txt with all 'Umlaute' and 'scharfes s' replaced.

Author(s)

Andreas Leha

Examples

replaceGermanUmlauts("gefräßig")

Collect Warnings From Runnning testfun

Description

wrap this around 'correlation' tests to get output formatted for buildDescrTbl

Usage

testWrapper(testfun, values, grouping, ignore_test_errors = FALSE, ...)

Arguments

testfun

character or function. Which function to call.

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

ignore_test_errors

logical. If TRUE returns an empty test results (as list).

...

additional parameters. are passed on to the testfun

Details

This function is called by buildDescrTbl in order to generate the comparison p values. Basically it just calls the provided testfun. Main purpose is, that it collects warnings and returns them as well.

Value

list. the results from testfun plus the element 'warnings' containing all warnings collected from the run of testfun. the results from testfun are assumed to be of type list and are additionally assumed to contain at least the elements 'p.value' and 'method'.

Author(s)

Andreas Leha

Cochran-Armitage Test for Trend

Description

Wrapper for CochranArmitageTest which is a test for trend in binomial proportions across the levels of a single variable

Usage

w.CochraneArmitageTrend.test(values, grouping, ...)

Arguments

values

vector. The values to compare. Will be passed to circular to be converted to circular format

grouping

of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the CochranArmitageTest

Value

the value of CochranArmitageTest

Author(s)

Dr. Andreas Leha

JonckheereTerpstraTest with unified interface

Description

JonckheereTerpstraTest with unified interface

Usage

w.JonckheereTerpstraTest(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the JonckheereTerpstraTest

Details

just a call to JonckheereTerpstraTest that unifies the api to other tests

Value

the value JonckheereTerpstraTest

Author(s)

Fabian Kück

ANOVA with unified interface

Description

One-way ANOVA that unifies the api to other tests

Usage

w.anova.test(values, grouping, na.rm = TRUE, ...)

Arguments

values

vector. The values to compare (age, gene expression, ...)

grouping

vector ef the same length as values. treated as factor giving the group membership

na.rm

logcical. if TRUE (default) the values are subset to only non-missing and finite values

...

additional parameters. are passed on to lm()

Value

the value of anova augmented by 'p.value' and 'method'

Author(s)

Dr. Andreas Leha

chisq.test with unified interface

Description

chisq.test with unified interface

Usage

w.chisq.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the chisq.test

Details

just a call to chisq.test that unifies the api to other tests

Value

the value chisq.test

Author(s)

Andreas Leha

cor.test with unified interface

Description

cor.test with unified interface

Usage

w.cor.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the cor.test

Details

just a call to cor.test that unifies the api to other tests

Value

the value cor.test

Author(s)

Andreas Leha

fisher.test with unified interface

Description

fisher.test with unified interface

Usage

w.fisher.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the fisher.test

Details

just a call to fisher.test that unifies the api to other tests computes the exact p-value if possible and simulates the p-value otherwise

Value

the value fisher.test

Author(s)

Andreas Leha

kruskal.test with unified interface

Description

kruskal.test with unified interface

Usage

w.kruskal.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the kruskal.test

Details

just a call to kruskal.test that unifies the api to other tests

Value

the value kruskal.test

Author(s)

Andreas Leha

no test

Description

no test but unified interface

Usage

w.no.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. unused

Details

just returns NA. Included as pass through for non-testable variables

Value

Author(s)

Andreas Leha

npar.t.test with unified interface

Description

npar.t.test with unified interface

Usage

w.npar.t.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the npar.t.test

Details

just a call to npar.t.test that unifies the api to other tests computes the ordinary Brunner-Munzel test for group sizes > 9 and the studentized permutation test version otherwise

Value

the value npar.t.test

Author(s)

Fabian Kück

npar.t.test with unified interface

Description

npar.t.test with unified interface

Usage

w.npar.t.test.permu(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the npar.t.test

Details

just a call to npar.t.test that unifies the api to other tests computes the the studentized permutation test version of the Brunner-Munzel test

Value

the value npar.t.test

Author(s)

Fabian Kück

prop.trend.test with unified interface

Description

prop.trend.test with unified interface

Usage

w.prop.trend.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the prop.trend.test

Details

just a call to prop.trend.test that unifies the api to other tests

Value

the value prop.trend.test

Author(s)

Fabian Kück

rankFD with unified interface

Description

rankFD with unified interface

Usage

w.rankFD.mid.ranks(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the rankFD

Details

just a call to rankFD with effect="weighted" that unifies the api to other tests

Value

the value rankFD

Author(s)

Fabian Kück

rankFD with unified interface

Description

rankFD with unified interface

Usage

w.rankFD.pseudo.ranks(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the rankFD

Details

just a call to rankFD that unifies the api to other tests

Value

the value rankFD

Author(s)

Fabian Kück

t.test with unified interface

Description

just a call to t.test that unifies the api to other tests

Usage

w.t.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the t.test

Value

the value of t.test

Author(s)

Andreas Leha

Watson-Williams Test of Homogeneity of Means

Description

just a call to watson.williams.test that unifies the api to other tests

Usage

w.watson.williams.test(values, grouping, ...)

Arguments

values

vector. The values to compare. Will be passed to circular to be converted to circular format

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the watson.williams.test

Value

the value of watson.williams.test

Author(s)

Dr. Andreas Leha

wilcox.test with unified interface

Description

wilcox.test with unified interface

Usage

w.wilcox.test(values, grouping, ...)

Arguments

values

vector. The values to compare (age, toxicity score, gene expression, ...)

grouping

vector of the same length as values. treated as factor giving the group membership

...

additional parameters. are passed on to the wilcox.test

Details

just a call to wilcox.test that unifies the api to other tests

Value

the value wilcox.test

Author(s)

Andreas Leha