This function allows to test fourth-corner statistics using constrained null
models (for traits and/or environmental variables). If the argument
phyloORorthobasis is specified, random traits are
phylogenetically-constrained to preserve the global autocorrelation (Moran's
I) and the phylogenetic structures at multiple scales. If not, standard
permutations are used. If the argument listwORorthobasis is specified,
random environmental variables are spatially-constrained to preserve the
global autocorrelation (Moran's I) and the spatial structures at multiple
scales. If not, standard permutations are used. Multiscale property is
defined by the power spectrum (i.e. decomposition of the variance of the
original variables) on a basis of orthonormal eigenvectors (Moran's
Eigenvector Maps, MEM).
An object generated by the fourthcorner function.
an object of the class listw (spatial
weights) created by the functions of the spdep package or an object
of class orthobasis
an object of the class phylo (phylogeny)
created by the functions of the ape package or an object of class
orthobasis generated by functions of adephylo
(me.phylo)
an integer indicating the number of replicates
an character specifying which algorithm should be used to
produce spatial replicates (see msr.default).
further arguments of the msr.default function.
An object of class 4thcorner randomized replicates.
Braga, J., Thuiller, W., ter Braak, C.J.F. and Dray, S. (2018) Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait-environment relationships. Ecology, 99:2667-2674.
if(require("ade4", quietly = TRUE) & require("adephylo", quietly = TRUE)
& require("spdep", quietly = TRUE) & require("ape", quietly = TRUE)){
data(mafragh, package = "ade4")
fr1 <- fourthcorner(mafragh$env, mafragh$flo, mafragh$traits$tabQuantitative, nrepet = 49)
phy <- read.tree(text = mafragh$tre)
lw <- nb2listw(mafragh$nb)
fr1.msr <- msr(fr1, listwORorthobasis = lw, phyloORorthobasis = phy)
fr1
fr1.msr
}
#>
#> Attaching package: ‘ape’
#> The following object is masked from ‘package:adegraphics’:
#>
#> zoom
#> Fourth-corner Statistics
#> ------------------------
#> Permutation method msr ( 49 permutations)
#>
#> Adjustment method for multiple comparisons: holm
#> call: msr.4thcorner(x = fr1, listwORorthobasis = lw, phyloORorthobasis = phy)
#>
#> ---
#>
#> Test Stat Obs Std.Obs Alter Pvalue
#> 1 Clay / Lfp r 0.014241856 -0.02354579 two-sided 0.94
#> 2 Silt / Lfp r -0.076256133 -0.88508320 two-sided 0.4
#> 3 Sand / Lfp r 0.063614861 1.06487968 two-sided 0.26
#> 4 K2O / Lfp r 0.031979355 0.22122125 two-sided 0.9
#> 5 Mg++ / Lfp r 0.014982765 0.11196136 two-sided 0.96
#> 6 Na+/100g / Lfp r 0.093499930 1.07691685 two-sided 0.32
#> 7 K+ / Lfp r 0.149968927 1.18174616 two-sided 0.3
#> 8 Conductivity / Lfp r 0.080497038 0.90064013 two-sided 0.38
#> 9 Retention / Lfp r -0.067943687 -0.91942181 two-sided 0.42
#> 10 Na+/l / Lfp r 0.063272819 0.76955442 two-sided 0.42
#> 11 Elevation / Lfp r -0.129537428 -1.25095435 two-sided 0.24
#> 12 Clay / Min height r 0.061180871 1.01291381 two-sided 0.4
#> 13 Silt / Min height r -0.052382325 -0.90909265 two-sided 0.48
#> 14 Sand / Min height r -0.027907397 -0.46567470 two-sided 0.72
#> 15 K2O / Min height r 0.047550545 1.06714650 two-sided 0.34
#> 16 Mg++ / Min height r -0.023023055 -0.55270713 two-sided 0.64
#> 17 Na+/100g / Min height r 0.027191299 0.41929177 two-sided 0.6
#> 18 K+ / Min height r 0.095029793 1.67903999 two-sided 0.1
#> 19 Conductivity / Min height r -0.018899856 -0.57233923 two-sided 0.58
#> 20 Retention / Min height r 0.004165428 0.11766350 two-sided 0.9
#> 21 Na+/l / Min height r -0.046119268 -1.18478048 two-sided 0.24
#> 22 Elevation / Min height r 0.061211127 0.87199828 two-sided 0.42
#> 23 Clay / Max height r 0.010762151 -0.04489317 two-sided 0.98
#> 24 Silt / Max height r -0.030835126 -0.32436846 two-sided 0.76
#> 25 Sand / Max height r 0.027229507 0.65877759 two-sided 0.54
#> 26 K2O / Max height r 0.063923177 1.29519424 two-sided 0.24
#> 27 Mg++ / Max height r 0.010886210 0.15925850 two-sided 0.94
#> 28 Na+/100g / Max height r 0.026525395 0.45085568 two-sided 0.62
#> 29 K+ / Max height r 0.109401849 1.28292558 two-sided 0.24
#> 30 Conductivity / Max height r 0.002446542 -0.20283308 two-sided 0.78
#> 31 Retention / Max height r -0.005456736 -0.03073410 two-sided 1
#> 32 Na+/l / Max height r -0.018577793 -0.71141329 two-sided 0.52
#> 33 Elevation / Max height r 0.033495574 0.64796849 two-sided 0.62
#> Pvalue.adj
#> 1 1
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1
#> 7 1
#> 8 1
#> 9 1
#> 10 1
#> 11 1
#> 12 1
#> 13 1
#> 14 1
#> 15 1
#> 16 1
#> 17 1
#> 18 1
#> 19 1
#> 20 1
#> 21 1
#> 22 1
#> 23 1
#> 24 1
#> 25 1
#> 26 1
#> 27 1
#> 28 1
#> 29 1
#> 30 1
#> 31 1
#> 32 1
#> 33 1
#>
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1