Type:	Package
Title:	Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Version:	4.4
Date:	2021-10-02
Description:	Note, that the 'PMCMR' package is superset by the novel 'PMCMRplus' package. The 'PMCMRplus' package contains all functions from 'PMCMR' and many more parametric and non-parametric multiple comparison procedures, one-factorial trend tests, as well as improved method functions, such as print, summary and plot. The 'PMCMR' package is no longer maintained, but kept for compatibility of reverse depending packages for some time.
Depends:	R (≥ 3.0.0)
Imports:	stats
Suggests:	multcompView
Encoding:	UTF-8
License:	GPL (≥ 3)
NeedsCompilation:	no
RoxygenNote:	7.1.2
Packaged:	2021-10-02 14:19:45 UTC; thorsten
Author:	Thorsten Pohlert [aut, cre]
Maintainer:	Thorsten Pohlert <thorsten.pohlert@gmx.de>
Repository:	CRAN
Date/Publication:	2021-10-02 15:10:09 UTC

PMCMR-defunct

Description

The functions or methods listed here are no longer part of PMCMR. You will find functions and methods in the PMCMRplus package https://cran.r-project.org/package=PMCMRplus.

Usage

dunn.test.control(x, g, p.adjust.method = p.adjust.methods, ...)

jonckheere.test(x, ...)

## Default S3 method:
jonckheere.test(
  x,
  g,
  alternative = c("monotonic", "increasing", "decreasing"),
  ...
)

posthoc.friedman.conover.test(y, ...)

## Default S3 method:
posthoc.friedman.conover.test(
  y,
  groups,
  blocks,
  p.adjust.method = p.adjust.methods,
  ...
)

posthoc.friedman.nemenyi.test(y, ...)

## Default S3 method:
posthoc.friedman.nemenyi.test(y, groups, blocks, ...)

## S3 method for class 'formula'
posthoc.friedman.nemenyi.test(formula, data, subset, na.action, ...)

durbin.test(y, ...)

## Default S3 method:
durbin.test(y, groups, blocks, ...)

## S3 method for class 'formula'
durbin.test(formula, data, subset, na.action, ...)

posthoc.kruskal.conover.test(x, ...)

## Default S3 method:
posthoc.kruskal.conover.test(x, g, p.adjust.method = p.adjust.methods, ...)

## S3 method for class 'formula'
posthoc.kruskal.conover.test(
  formula,
  data,
  subset,
  na.action,
  p.adjust.method = p.adjust.methods,
  ...
)

posthoc.kruskal.dunn.test(x, ...)

## Default S3 method:
posthoc.kruskal.dunn.test(x, g, p.adjust.method = p.adjust.methods, ...)

## S3 method for class 'formula'
posthoc.kruskal.dunn.test(
  formula,
  data,
  subset,
  na.action,
  p.adjust.method = p.adjust.methods,
  ...
)

posthoc.kruskal.nemenyi.test(x, ...)

## Default S3 method:
posthoc.kruskal.nemenyi.test(x, g, dist = c("Tukey", "Chisquare"), ...)

## S3 method for class 'formula'
posthoc.kruskal.nemenyi.test(
  formula,
  data,
  subset,
  na.action,
  dist = c("Tukey", "Chisquare"),
  ...
)

posthoc.quade.test(y, ...)

## Default S3 method:
posthoc.quade.test(
  y,
  groups,
  blocks,
  dist = c("TDist", "Normal"),
  p.adjust.method = p.adjust.methods,
  ...
)

posthoc.vanWaerden.test(x, ...)

## Default S3 method:
posthoc.vanWaerden.test(x, g, p.adjust.method = p.adjust.methods, ...)

## S3 method for class 'formula'
posthoc.vanWaerden.test(
  formula,
  data,
  subset,
  na.action,
  p.adjust.method = p.adjust.methods,
  ...
)

vanWaerden.test(x, ...)

## Default S3 method:
vanWaerden.test(x, g, ...)

## S3 method for class 'formula'
vanWaerden.test(formula, data, subset, na.action, ...)

Arguments

.Defunct

NA

Deprecated Functions in Package PMCMR

Description

These functions are provided for reverse-dependencies issues of other R-packages. They should no longer be used, as actively maintained functions can be found in the package PMCMRplus. The functions may be defunct as soon as the next release.

Usage

posthoc.durbin.test(y, ...)

## Default S3 method:
posthoc.durbin.test(y, groups, blocks, p.adjust.method = p.adjust.methods, ...)

Arguments

Value

A list with class "PMCMR"

• method The applied method.

• data.nameThe name of the data.

• p.valueThe two-sided p-value according to the student-t-distribution.

• statisticThe estimated quantiles of the student-t-distribution.

• p.adjust.methodThe applied method for p-value adjustment.

Note

The function does not test, whether it is a true BIBD.

This function does not test for ties.

References

W. J. Conover and R. L. Iman (1979), On multiple-comparisons procedures, Tech. Rep. LA-7677-MS, Los Alamos Scientific Laboratory.

W. J. Conover (1999), Practical nonparametric Statistics, 3rd. Edition, Wiley.

Examples

## Not run: 
## Example for an incomplete block design:
## Data from Conover (1999, p. 391).
y <- matrix(c(2, NA, NA, NA, 3, NA, 3, 3,
3, NA, NA, NA,  3, NA, NA,
1,  2, NA, NA, NA,  1,  1, NA,  1,  1,
NA, NA, NA, NA,  2, NA,  2,  1, NA, NA, NA, NA,
3, NA,  2,  1, NA, NA, NA, NA,  3, NA,  2,  2),
ncol=7, nrow=7, byrow=FALSE,
dimnames=list(1:7, LETTERS[1:7]))

posthoc.durbin.test(y)

## End(Not run)

Get Pvalues from PMCMR Objects

Description

Returns a vector of pvalues that includes the names of the pairwise groups (i.e. the null hypothesis). The output can be used by multcompLetters to find homogeneous groups.

Usage

get.pvalues(object, ...)

Arguments

Value

a named vector with p-values

Prints PMCMR objects

Description

print method for class "PMCMR".

Usage

## S3 method for class 'PMCMR'
print(x, ...)

Arguments

Value

The function print.PMCMR returns the lower triangle of the (adjusted) p-values from any of the posthoc tests included in the package PMCMR.

Summarizing PMCMR objects

Description

summary method for class "PMCMR".

Usage

## S3 method for class 'PMCMR'
summary(object, ...)

Arguments

Value

The function summary.PMCMR computes and returns a list of the pairwise comparisons including the H0, the corresponding statistic and the (adjusted) p-value.