tpaired.krandtest {adespatial} | R Documentation |

This function computes paired t-tests for each species, for abundances observed at time 1 (T1) and time 2 (T2). The test is one-tailed in the direction of the sign (+ or -) of the t statistic.

tpaired.krandtest(mat1, mat2, nperm = 99, list.all = FALSE)

`mat1` |
site-by-species data at time T1 (data.frame or matrix). |

`mat2` |
site-by-species data at time T2 (data.frame or matrix). |

`nperm` |
Number of permutations. Use 999, 9999, or more, to allow for correction of p-values for multiple tests. |

`list.all` |
If |

The species that do not vary in either data set are discarded before calculation of the paired t-tests begins.

p-values should be corrected for multiple testing. Use function `p.adjust`

of
`stats`

: p.adjust(res$t.test$p.param) or p.adjust(res$t.test$p.perm)
Correction methods "holm" (default) and "hochberg" are fine for this type of analysis.

A table with species in rows and 6 columns: "mean(T1-T2)","t.stat","p.param","p.perm","p<=0.05","Sign(T1-T2)" The parametric and permutational p-values are not corrected for multiple tests. A star is shown in column "p<=0.05" if the parametric p-value is <= 0.05.

A list of names of the species tested; their t statistics were not 0.

A list of names of the species not tested because their t-statistics were 0.

Pierre Legendre pierre.legendre@umontreal.ca

Legendre, P. 2019. A temporal beta-diversity index to identify sites that
have changed in exceptional ways in space-time surveys. *Ecology and Evolution*
(in press).

van den Brink, P. J. & C. J. F. ter Braak. 1999. Principal response curves: analysis of
time-dependent multivariate responses of biological community to stress.
*Environmental Toxicology and Chemistry* 18: 138-148.

`tpaired.randtest`

if(require("vegan", quietly = TRUE)) { ## Invertebrate communities subjected to insecticide treatment. ## As an example in their paper on Principal Response Curves (PRC), van den Brink & ter ## Braak (1999) used observations on the abundances of 178 invertebrate species ## (macroinvertebrates and zooplankton) subjected to treatments in 12 mesocosms by the ## insecticide chlorpyrifos. The mesocosms were sampled at 11 occasions. The data, ## available in the {vegan} package, are log-transformed species abundances, ## y.tranformed = loge(10*y+1). ## The data of survey #4 will be compared to those of survey #11 in this example. ## Survey #4 was carried out one week after the insecticide treatment, whereas the ## fauna of the mesocosms was considered to have fully recovered from the treatment ## at the time of survey #11. data(pyrifos) ## The mesocosms had originally been attributed at random to the treatments. However, ## to facilitate presentation of the results, they will be listed here in order of ## increased insecticide doses: {0, 0, 0, 0, 0.1, 0.1, 0.9, 0.9, 6, 6, 44, 44} ## micro g/L. survey4.order = c(38,39,41,47,37,44,40,46,43,48,42,45) survey11.order = c(122,123,125,131,121,128,124,130,127,132,126,129) ## Paired t-tests of differences between survey.4 and survey.11 for the p species res <- tpaired.krandtest(pyrifos[survey4.order,],pyrifos[survey11.order,]) }

[Package *adespatial* version 0.3-14 Index]