Package 'PMCMR'

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

object	either an object of class "PMCMR", usually, a result of a call to any of the posthoc-tests included in the package PMCMR. Or an object of class "pairwise.htest", a result of a call to pairwise.prop.test, pairwise.t.test or pairwise.wilcox.test.
...	further arguments, currently ignored.

Value

a named vector with p-values

---

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

x	a numeric vector of data values, or a list of numeric data vectors.
g	a vector or factor object giving the group for the corresponding elements of x. Ignored if x is a list.
p.adjust.method	Method for adjusting p values (see p.adjust).
...	further arguments to be passed to or from methods.
alternative	The alternative hypothesis.
y	either a numeric vector of data values, or a data matrix.
groups	a vector giving the group for the corresponding elements of y if this is a vector; ignored if y is a matrix. If not a factor object, it is coerced to one.
blocks	a vector giving the block for the corresponding elements of y if this is a vector; ignored if y is a matrix. If not a factor object, it is coerced to one
formula	a formula of the form a ~ b | c, where a, b and c give the data values and corresponding groups and blocks, respectively.
data	an optional matrix or data frame (or similar: see model.frame) containing the variables in the formula formula. By default the variables are taken from environment(formula).
subset	an optional vector specifying a subset of observations to be used.
na.action	a function which indicates what should happen when the data contain NAs. Defaults to getOption("na.action").´
dist	the test distribution

.Defunct

NA

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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

y	either a numeric vector of data values, or a data matrix.
...	further arguments to be passed to or from methods.
groups	a vector giving the group for the corresponding elements of y if this is a vector; ignored if y is a matrix. If not a factor object, it is coerced to one.
blocks	a vector giving the block for the corresponding elements of y if this is a vector; ignored if y is a matrix. If not a factor object, it is coerced to one.
p.adjust.method	Method for adjusting p values (see p.adjust).

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)

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Prints PMCMR objects

Description

print method for class "PMCMR".

Usage

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

Arguments

x	an object of class "PMCMR", usually, a result of a call to any of the posthoc-tests included in the package PMCMR.
...	further arguments, currently ignored.

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.

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Summarizing PMCMR objects

Description

summary method for class "PMCMR".

Usage

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

Arguments

object	an object of class "PMCMR", usually, a result of a call to any of the posthoc-tests included in the package PMCMR.
...	further arguments, currently ignored.

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.

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