jonckheereTest() R function from [PMCMRplus]

Testing against Ordered Alternatives (Jonckheere-Terpstra Test)

Performs the Jonckheere-Terpstra test for testing against ordered alternatives.


jonckheereTest(x, ...)

## Default S3 method:
jonckheereTest(
  x,
  g,
  alternative = c("two.sided", "greater", "less"),
  continuity = FALSE,
  ...
)

## S3 method for class 'formula'
jonckheereTest(
  formula,
  data,
  subset,
  na.action,
  alternative = c("two.sided", "greater", "less"),
  continuity = FALSE,
  ...
)

Arguments

x: a numeric vector of data values, or a list of numeric data vectors.
...: further arguments to be passed to or from methods.
g: a vector or factor object giving the group for the corresponding elements of "x". Ignored with a warning if "x" is a list.
alternative: the alternative hypothesis. Defaults to "two.sided".
continuity: logical indicator whether a continuity correction shall be performed. Defaults to FALSE.
formula: a formula of the form response ~ group where response gives the data values and group a vector or factor of the corresponding groups.
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").

Returns

A list with class "htest" containing the following components:

method: a character string indicating what type of test was performed.
data.name: a character string giving the name(s) of the data.
statistic: the estimated quantile of the test statistic.
p.value: the p-value for the test.
parameter: the parameters of the test statistic, if any.
alternative: a character string describing the alternative hypothesis.
estimates: the estimates, if any.
null.value: the estimate under the null hypothesis, if any.

Details

The null hypothesis, H $_0: \theta_1 = \theta_2 = \ldots = \theta_k$

is tested against a simple order hypothesis, Hc(" $_\\mathrm{A}: \\theta_1 \\le \\theta_2 \\le \\ldots \\le\n$ ", " $\\theta_k,~\\theta_1 < \\theta_k$ ").

The p-values are estimated from the standard normal distribution.

Note

jonckheereTest(x, g, alternative = "two.sided", continuity = TRUE) is equivalent to

cor.test(x, as.numeric(g), method = "kendall", alternative ="two.sided", continuity = TRUE)

Factor labels for g must be assigned in such a way, that they can be increasingly ordered from zero-dose control to the highest dose level, e.g. integers {0, 1, 2, ..., k} or letters {a, b, c, ...}. Otherwise the function may not select the correct values for intended zero-dose control.

It is safer, to i) label the factor levels as given above, and to ii) sort the data according to increasing dose-levels prior to call the function (see order, factor).

Source

The code for the computation of the standard deviation for the Jonckheere-Terpstra test in the presence of ties was taken from:

Kloke, J., McKean, J. (2016) list("npsm"): Package for Nonparametric Statistical Methods using R. R package version 0.5. https://CRAN.R-project.org/package=npsm

Examples


## Example from Sachs (1997, p. 402)
x <- c(106, 114, 116, 127, 145,
       110, 125, 143, 148, 151,
       136, 139, 149, 160, 174)
g <- gl(3,5)
levels(g) <- c("A", "B", "C")

## Chacko's test
chackoTest(x, g)

## Cuzick's test
cuzickTest(x, g)

## Johnson-Mehrotra test
johnsonTest(x, g)

## Jonckheere-Terpstra test
jonckheereTest(x, g)

## Le's test
leTest(x, g)

## Spearman type test
spearmanTest(x, g)

## Murakami's BWS trend test
bwsTrendTest(x, g)

## Fligner-Wolfe test
flignerWolfeTest(x, g)

## Shan-Young-Kang test
shanTest(x, g)

References

Jonckheere, A. R. (1954) A distribution-free k-sample test against ordered alternatives. Biometrica 41 , 133–145.

Kloke, J., McKean, J. W. (2015) Nonparametric statistical methods using R. Boca Raton, FL: Chapman & Hall/CRC.

jonckheereTest function