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Coinertia Analysis#> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 7.830388505 0.085927586 0.002168386 +#> 8.366940629 0.084818255 0.001910769

In this case, the link between the composition of species assemblages and environmental conditions is highly significant.

Coinertia Analysis maximises covariances and thus can handle tables @@ -470,8 +470,8 @@

Coinertia Analysis#> Simulated p-value: 0.001 #> Alternative hypothesis: greater #> -#> Std.Obs Expectation Variance -#> 11.536349363 0.107414725 0.002101926 +#> Std.Obs Expectation Variance +#> 11.39689292 0.10643709 0.00216165

Analysis on instrumental variables @@ -640,7 +640,7 @@

Redundancy Analysis#> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 4.949898690 0.372996568 0.006131435 +#> 5.292976107 0.370986852 0.005418099

Lastly, the summary function also returns information on the eigenvalues and their decomposition. The initial analysis (pca.fish) seeks linear combination of the variables with diff --git a/articles/ChapBetGr.html b/articles/ChapBetGr.html index 33abcff0..18135010 100644 --- a/articles/ChapBetGr.html +++ b/articles/ChapBetGr.html @@ -453,14 +453,14 @@

Between-site analysis#> Observation: 0.4412974 #> #> Based on 999 replicates -#> Simulated p-value: 0.004 +#> Simulated p-value: 0.005 #> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 3.536585195 0.218460129 0.003970154 +#> 3.402123102 0.221177558 0.004186183

The observed value of the criterion is equal to 0.4413, which means that 44% of the total inertia comes from the differences between sites. -The simulated p-value is equal to 0.004, which means that the +The simulated p-value is equal to 0.005, which means that the difference between sites is highly significant.

The following histogram shows the distribution of the values of the criterion computed on permuted tables. The observed value for the @@ -660,7 +660,7 @@

Discriminant Analysis#> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 5.7261170142 0.1291441709 0.0004844328 +#> 5.7228441849 0.1300194291 0.0004782742

The observed value of the criterion is equal to 0.2552, which means that 26% of the total inertia comes from the differences between seasons. The simulated p-value is equal to 0.001, which means diff --git a/articles/ChapBetGr_files/figure-html/unnamed-chunk-15-1.png b/articles/ChapBetGr_files/figure-html/unnamed-chunk-15-1.png index 6805d81a..d3cdb5a9 100644 Binary files a/articles/ChapBetGr_files/figure-html/unnamed-chunk-15-1.png and b/articles/ChapBetGr_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/ChapBetGr_files/figure-html/unnamed-chunk-26-1.png b/articles/ChapBetGr_files/figure-html/unnamed-chunk-26-1.png index 8062d786..7bc83287 100644 Binary files a/articles/ChapBetGr_files/figure-html/unnamed-chunk-26-1.png and b/articles/ChapBetGr_files/figure-html/unnamed-chunk-26-1.png differ diff --git a/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-12-1.png b/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-12-1.png index 9b672b7c..ae24ea1b 100644 Binary files a/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-12-1.png and b/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-21-1.png b/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-21-1.png index ba2b6c5d..fc55e0c5 100644 Binary files a/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-21-1.png and b/articles/ChapEnvVarStruct_files/figure-html/unnamed-chunk-21-1.png differ diff --git a/articles/ChapKtables_files/figure-html/unnamed-chunk-15-1.png b/articles/ChapKtables_files/figure-html/unnamed-chunk-15-1.png index 68d0668b..9527f2d5 100644 Binary files a/articles/ChapKtables_files/figure-html/unnamed-chunk-15-1.png and b/articles/ChapKtables_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/ChapKtables_files/figure-html/unnamed-chunk-20-1.png b/articles/ChapKtables_files/figure-html/unnamed-chunk-20-1.png index 349354e0..ec869952 100644 Binary files a/articles/ChapKtables_files/figure-html/unnamed-chunk-20-1.png and b/articles/ChapKtables_files/figure-html/unnamed-chunk-20-1.png differ diff --git a/articles/ChapKtables_files/figure-html/unnamed-chunk-9-1.png b/articles/ChapKtables_files/figure-html/unnamed-chunk-9-1.png index a8a3807b..748c399f 100644 Binary files a/articles/ChapKtables_files/figure-html/unnamed-chunk-9-1.png and b/articles/ChapKtables_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-17-1.png b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-17-1.png index d6739ca0..912eca32 100644 Binary files a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-17-1.png and b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-20-1.png b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-20-1.png index d85827de..21d15dda 100644 Binary files a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-20-1.png and b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-20-1.png differ diff --git a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-22-1.png b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-22-1.png index 67d06822..1b0575ee 100644 Binary files a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-22-1.png and b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-22-1.png differ diff --git a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-23-1.png b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-23-1.png index 855f3276..bb9580ac 100644 Binary files a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-23-1.png and b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-23-1.png differ diff --git a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-25-1.png b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-25-1.png index 3f3e9f1d..7ec3c61f 100644 Binary files a/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-25-1.png and b/articles/ChapSpeciesStruct_files/figure-html/unnamed-chunk-25-1.png differ diff --git a/pkgdown.yml b/pkgdown.yml index 6b5b0af7..d66059ea 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -14,5 +14,5 @@ articles: papers: papers.html related: related.html faq: faq.html -last_built: 2023-11-16T15:41Z +last_built: 2023-11-17T08:49Z diff --git a/reference/RV.randtest-1.png b/reference/RV.randtest-1.png index 1858f38b..23215c1c 100644 Binary files a/reference/RV.randtest-1.png and b/reference/RV.randtest-1.png differ diff --git a/reference/RV.randtest.html b/reference/RV.randtest.html index 8ddc4ab5..bfddeaf7 100644 --- a/reference/RV.randtest.html +++ b/reference/RV.randtest.html @@ -137,8 +137,8 @@

Examples#> Simulated p-value: 0.01 #> Alternative hypothesis: greater #> -#> Std.Obs Expectation Variance -#> 10.094484207 0.085766796 0.001305924 +#> Std.Obs Expectation Variance +#> 8.264931596 0.081784023 0.001990854 plot(rv1)

diff --git a/reference/RV.rtest-1.png b/reference/RV.rtest-1.png index eda0e4b8..7f16c1e1 100644 Binary files a/reference/RV.rtest-1.png and b/reference/RV.rtest-1.png differ diff --git a/reference/RV.rtest.html b/reference/RV.rtest.html index 8a61bcec..e9fa465c 100644 --- a/reference/RV.rtest.html +++ b/reference/RV.rtest.html @@ -138,7 +138,7 @@

Examples#> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 10.061852300 0.081836655 0.001342883 +#> 10.263405354 0.082418665 0.001286586 plot(rv1) diff --git a/reference/RVintra.randtest-1.png b/reference/RVintra.randtest-1.png index a5eff4ae..5e931407 100644 Binary files a/reference/RVintra.randtest-1.png and b/reference/RVintra.randtest-1.png differ diff --git a/reference/RVintra.randtest.html b/reference/RVintra.randtest.html index bed4bfcd..e06121dc 100644 --- a/reference/RVintra.randtest.html +++ b/reference/RVintra.randtest.html @@ -145,7 +145,7 @@

Examples#> Alternative hypothesis: greater #> #> Std.Obs Expectation Variance -#> 4.552475340 0.223137927 0.003272742 +#> 4.490804097 0.221541332 0.003404609 plot(rv1) diff --git a/reference/Rplot002.png b/reference/Rplot002.png index f66c30a6..27fc42d6 100644 Binary files a/reference/Rplot002.png and b/reference/Rplot002.png differ diff --git a/reference/Rplot003.png b/reference/Rplot003.png index bcb0ca16..d2ebb39a 100644 Binary files a/reference/Rplot003.png and b/reference/Rplot003.png differ diff --git a/reference/Rplot004.png b/reference/Rplot004.png index 7f4ed8d0..9a2c915d 100644 Binary files a/reference/Rplot004.png and b/reference/Rplot004.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index d9d581ae..7099a524 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index 03b53542..487a4960 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index 2ee9b3d4..b209ed2d 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index 3ddcb850..c4b8a457 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/Rplot011.png b/reference/Rplot011.png index 533063cf..34a5aaee 100644 Binary files a/reference/Rplot011.png and b/reference/Rplot011.png differ diff --git a/reference/Rplot012.png b/reference/Rplot012.png index e07b16db..d52fd981 100644 Binary files a/reference/Rplot012.png and b/reference/Rplot012.png differ diff --git a/reference/Rplot013.png b/reference/Rplot013.png index 1de49557..3b04aede 100644 Binary files a/reference/Rplot013.png and b/reference/Rplot013.png differ diff --git a/reference/Rplot014.png b/reference/Rplot014.png index a8c5af49..b558d37b 100644 Binary files a/reference/Rplot014.png and b/reference/Rplot014.png differ diff --git a/reference/Rplot015.png b/reference/Rplot015.png index 7bfd04c0..447079e4 100644 Binary files a/reference/Rplot015.png and b/reference/Rplot015.png differ diff --git a/reference/add.scatter-1.png b/reference/add.scatter-1.png index efe34ce1..60fc897a 100644 Binary files a/reference/add.scatter-1.png and b/reference/add.scatter-1.png differ diff --git a/reference/as.taxo-1.png b/reference/as.taxo-1.png index 925e2c4f..b4ff080f 100644 Binary files a/reference/as.taxo-1.png and b/reference/as.taxo-1.png differ diff --git a/reference/bicenter.wt.html b/reference/bicenter.wt.html index ff19d963..7fbf2755 100644 --- a/reference/bicenter.wt.html +++ b/reference/bicenter.wt.html @@ -127,7 +127,7 @@

Examples w <- matrix(1:20, 5, 4) sum(bicenter.wt(w, runif(5), runif(4))^2) -#> [1] 1.676329e-29 +#> [1] 2.228532e-29