tolerance: Species tolerances and sample heterogeneities

In vegan: Community Ecology Package

Description

Species tolerances and sample heterogeneities.

Usage

tolerance(x, ...)

## S3 method for class 'cca'
tolerance(x, choices = 1:2, which = c("species","sites"),
          scaling = "species", useN2 = FALSE, hill = FALSE, ...)

Arguments

x	object of class "cca".
choices	numeric; which ordination axes to compute tolerances and heterogeneities for. Defaults to axes 1 and 2.
which	character; one of "species" or "sites", indicating whether species tolerances or sample heterogeneities respectively are computed.
scaling	character or numeric; the ordination scaling to use. See scores.cca for details.
hill	logical; if scaling is a character, these control whether Hill's scaling is used for (C)CA respectively. See scores.cca for details.
useN2	logical; should the bias in the tolerances / heterogeneities be reduced via scaling by Hill's N2?
...	arguments passed to other methods.

Details

Function to compute species tolerances and site heterogeneity measures from unimodal ordinations (CCA & CA). Implements Eq 6.47 and 6.48 from the Canoco 4.5 Reference Manual (pages 178-179).

Value

Matrix of tolerances/heterogeneities with some additional attributes.

Author(s)

Gavin L. Simpson

Examples

data(dune)
data(dune.env)
mod <- cca(dune ~ ., data = dune.env)

## defaults to species tolerances
tolerance(mod)

## sample heterogeneities for CCA axes 1:6
tolerance(mod, which = "sites", choices = 1:6)

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4

Species Tolerance

Scaling: 2

               CCA1      CCA2
Achimill 0.32968099 0.9241988
Agrostol 0.93670069 0.9238455
Airaprae 1.04694096 0.5889849
Alopgeni 0.72227472 0.3760138
Anthodor 1.00596787 0.8338212
Bellpere 0.32891011 0.9962790
Bromhord 0.27740999 0.6236199
Chenalbu 0.00000000 0.0000000
Cirsarve 0.00000000 0.0000000
Comapalu 0.47185632 0.8029414
Eleopalu 0.50344134 0.9384960
Elymrepe 0.35119963 0.5642491
Empenigr 0.00000000 0.0000000
Hyporadi 1.05840696 0.7523003
Juncarti 0.78397702 1.0686743
Juncbufo 0.69275956 0.6180830
Lolipere 0.51006235 0.8278177
Planlanc 0.36040676 0.6962294
Poaprat  0.58184277 0.9547104
Poatriv  0.78695928 0.7433503
Ranuflam 0.56576326 1.1725628
Rumeacet 0.58715663 0.8751491
Sagiproc 0.70922180 1.1153129
Salirepe 0.98530179 0.1077917
Scorautu 1.04355761 1.0724439
Trifprat 0.03045846 0.3651949
Trifrepe 1.21543364 0.9115613
Vicilath 0.24853962 0.6194084
Bracruta 1.03787313 1.0958331
Callcusp 0.57882025 1.0418623


Sample Heterogeneity

Scaling: 2

        CCA1      CCA2      CCA3      CCA4      CCA5      CCA6
1  0.2350112 0.8611530 1.7964571 0.4445499 2.4235732 0.5496289
2  0.7100754 0.4136311 0.8151643 0.6311751 1.0467901 0.2514646
3  0.5076492 0.7279717 0.8306874 0.5590739 0.3904998 0.9162012
4  0.5955037 0.6901907 0.7931255 0.4873638 0.3966068 0.8700581
5  0.6001048 0.5614830 1.1481560 0.3569604 0.4423909 1.9420043
6  0.7272637 0.6867342 1.6068628 0.7778498 0.9187843 0.4938865
7  0.6478967 0.4993262 0.7207318 0.3817131 0.4130713 0.7228173
8  0.8563491 0.5498552 0.4217718 0.3370226 0.3013276 0.9535190
9  0.5599722 0.7399384 0.4170304 1.0535541 1.4612437 0.7626183
10 0.5210280 0.5806978 0.5856634 0.4174860 1.8559344 0.8890262
11 0.4489323 0.6016877 0.3317371 1.8780211 1.2965939 2.1953737
12 0.4948094 1.1084494 0.5226746 1.5064446 0.5703077 1.1561020
13 0.6998985 0.8859365 0.4215474 0.8582272 0.5673698 0.5186678
14 1.5925779 0.6747926 0.8927360 1.6798300 0.3480218 0.1575892
15 1.0107648 0.5294221 1.0975629 1.7632888 0.2240900 0.3727240
16 0.8031479 0.6058313 0.4871527 0.4227451 0.5341256 0.6990815
17 0.5936276 1.5142792 0.5137979 1.0224938 1.7931775 0.6261853
18 0.5689409 1.4067575 0.6398557 0.4983399 0.4364791 0.6590394
19 1.1330387 0.9816332 1.1242398 0.7238920 0.5577662 0.7036044
20 0.6737757 1.4458326 1.4380928 1.0959027 0.4142423 0.5332460

vegan documentation built on May 2, 2019, 5:51 p.m.