ecan

 install.packages("ecan")
 # development
 # install.packages("devtools")
devtools::install_github("matutosi/ecan")

 library(ecan)
 library(vegan)
 #> Loading required package: permute
 #> Loading required package: lattice
 #> This is vegan 2.6-4
 library(dplyr)
 #> 
 #> Attaching package: 'dplyr'
 #> The following objects are masked from 'package:stats':
 #> 
 #> filter, lag
 #> The following objects are masked from 'package:base':
 #> 
 #> intersect, setdiff, setequal, union
 library(stringr)
 library(tibble)
 library(ggplot2)
 data(dune)
 data(dune.env)
 
df <- 
 table2df(dune) %>%
 dplyr::left_join(tibble::rownames_to_column(dune.env, "stand"))
 #> Joining with `by = join_by(stand)`
 
sp_dammy <- 
 tibble::tibble("species" = colnames(dune), 
 "dammy_1" = stringr::str_sub(colnames(dune), 1, 1),
 "dammy_6" = stringr::str_sub(colnames(dune), 6, 6))
 
df <- 
 df %>%
 dplyr::left_join(sp_dammy)
 #> Joining with `by = join_by(species)`
 
df
 #> # A tibble: 197 ×ばつ 10
 #> stand species abundance A1 Moisture Manage...1 Use Manure dammy_1 dammy_6
 #> <chr> <chr> <dbl> <dbl> <ord> <fct> <ord> <ord> <chr> <chr> 
 #> 1 1 Achimill 1 2.8 1 SF Hayp... 4 A i 
 #> 2 1 Elymrepe 4 2.8 1 SF Hayp... 4 E e 
 #> 3 1 Lolipere 7 2.8 1 SF Hayp... 4 L e 
 #> 4 1 Poaprat 4 2.8 1 SF Hayp... 4 P a 
 #> 5 1 Poatriv 2 2.8 1 SF Hayp... 4 P i 
 #> 6 2 Achimill 3 3.5 1 BF Hayp... 2 A i 
 #> 7 2 Alopgeni 2 3.5 1 BF Hayp... 2 A e 
 #> 8 2 Bellpere 3 3.5 1 BF Hayp... 2 B e 
 #> 9 2 Bromhord 4 3.5 1 BF Hayp... 2 B o 
 #> 10 2 Elymrepe 4 3.5 1 BF Hayp... 2 E e 
 #> # ... with 187 more rows, and abbreviated variable name 1​Management

div <- 
 shdi(df) %>%
 dplyr::left_join(select_one2multi(df, "stand"))
 #> Joining with `by = join_by(stand)`
 
group <- "Management"
div_index <- "s"
div %>%
 ggplot(aes(x = .data[[group]], y = .data[[div_index]])) + 
 geom_boxplot(outlier.shape = NA) + # do not show outer point
 geom_jitter(height = 0, width = 0.1)

 ind_val(df, group = "Moisture", row_data = TRUE)
 #> $relfrq
 #> 1 2 3 4
 #> Achimill 0.7142857 0.50 0.0000000 0.0
 #> Elymrepe 0.4285714 0.50 0.0000000 0.5
 #> Lolipere 1.0000000 0.75 0.1428571 0.5
 #> Poaprat 1.0000000 1.00 0.2857143 0.5
 #> Poatriv 0.7142857 0.75 0.4285714 1.0
 #> Alopgeni 0.1428571 0.50 0.4285714 1.0
 #> Bellpere 0.4285714 0.75 0.0000000 0.0
 #> Bromhord 0.4285714 0.50 0.0000000 0.0
 #> Scorautu 0.8571429 1.00 0.8571429 1.0
 #> Trifrepe 0.8571429 0.75 0.7142857 1.0
 #> Agrostol 0.0000000 0.50 0.8571429 1.0
 #> Bracruta 0.7142857 0.75 0.7142857 1.0
 #> Cirsarve 0.0000000 0.25 0.0000000 0.0
 #> Sagiproc 0.1428571 0.25 0.4285714 1.0
 #> Anthodor 0.4285714 0.50 0.1428571 0.0
 #> Planlanc 0.7142857 0.50 0.0000000 0.0
 #> Rumeacet 0.4285714 0.00 0.0000000 1.0
 #> Trifprat 0.4285714 0.00 0.0000000 0.0
 #> Juncbufo 0.1428571 0.00 0.1428571 1.0
 #> Eleopalu 0.0000000 0.00 0.7142857 0.0
 #> Juncarti 0.0000000 0.00 0.5714286 0.5
 #> Ranuflam 0.0000000 0.00 0.8571429 0.0
 #> Vicilath 0.2857143 0.25 0.0000000 0.0
 #> Hyporadi 0.1428571 0.25 0.1428571 0.0
 #> Chenalbu 0.0000000 0.00 0.1428571 0.0
 #> Comapalu 0.0000000 0.00 0.2857143 0.0
 #> Callcusp 0.0000000 0.00 0.4285714 0.0
 #> Airaprae 0.0000000 0.25 0.1428571 0.0
 #> Salirepe 0.1428571 0.00 0.2857143 0.0
 #> Empenigr 0.0000000 0.00 0.1428571 0.0
 #> 
 #> $relabu
 #> 1 2 3 4
 #> Achimill 0.48780488 0.5121951 0.00000000 0.00000000
 #> Elymrepe 0.25531915 0.2978723 0.00000000 0.44680851
 #> Lolipere 0.46204620 0.3927393 0.05280528 0.09240924
 #> Poaprat 0.35036496 0.3576642 0.08759124 0.20437956
 #> Poatriv 0.24806202 0.2713178 0.15503876 0.32558140
 #> Alopgeni 0.02846975 0.2241993 0.19928826 0.54804270
 #> Bellpere 0.40000000 0.6000000 0.00000000 0.00000000
 #> Bromhord 0.39506173 0.6049383 0.00000000 0.00000000
 #> Scorautu 0.33922261 0.2226148 0.24028269 0.19787986
 #> Trifrepe 0.27636364 0.2290909 0.18909091 0.30545455
 #> Agrostol 0.00000000 0.2818792 0.38926174 0.32885906
 #> Bracruta 0.29197080 0.1532847 0.24817518 0.30656934
 #> Cirsarve 0.00000000 1.0000000 0.00000000 0.00000000
 #> Sagiproc 0.05161290 0.2258065 0.18064516 0.54193548
 #> Anthodor 0.33333333 0.5185185 0.14814815 0.00000000
 #> Planlanc 0.70588235 0.2941176 0.00000000 0.00000000
 #> Rumeacet 0.50000000 0.0000000 0.00000000 0.50000000
 #> Trifprat 1.00000000 0.0000000 0.00000000 0.00000000
 #> Juncbufo 0.06060606 0.0000000 0.09090909 0.84848485
 #> Eleopalu 0.00000000 0.0000000 1.00000000 0.00000000
 #> Juncarti 0.00000000 0.0000000 0.50000000 0.50000000
 #> Ranuflam 0.00000000 0.0000000 1.00000000 0.00000000
 #> Vicilath 0.63157895 0.3684211 0.00000000 0.00000000
 #> Hyporadi 0.19047619 0.3333333 0.47619048 0.00000000
 #> Chenalbu 0.00000000 0.0000000 1.00000000 0.00000000
 #> Comapalu 0.00000000 0.0000000 1.00000000 0.00000000
 #> Callcusp 0.00000000 0.0000000 1.00000000 0.00000000
 #> Airaprae 0.00000000 0.5384615 0.46153846 0.00000000
 #> Salirepe 0.27272727 0.0000000 0.72727273 0.00000000
 #> Empenigr 0.00000000 0.0000000 1.00000000 0.00000000
 #> 
 #> $indval
 #> 1 2 3 4
 #> Achimill 0.348432056 0.25609756 0.000000000 0.00000000
 #> Elymrepe 0.109422492 0.14893617 0.000000000 0.22340426
 #> Lolipere 0.462046205 0.29455446 0.007543612 0.04620462
 #> Poaprat 0.350364964 0.35766423 0.025026069 0.10218978
 #> Poatriv 0.177187154 0.20348837 0.066445183 0.32558140
 #> Alopgeni 0.004067107 0.11209964 0.085409253 0.54804270
 #> Bellpere 0.171428571 0.45000000 0.000000000 0.00000000
 #> Bromhord 0.169312169 0.30246914 0.000000000 0.00000000
 #> Scorautu 0.290762241 0.22261484 0.205956588 0.19787986
 #> Trifrepe 0.236883117 0.17181818 0.135064935 0.30545455
 #> Agrostol 0.000000000 0.14093960 0.333652924 0.32885906
 #> Bracruta 0.208550574 0.11496350 0.177267987 0.30656934
 #> Cirsarve 0.000000000 0.25000000 0.000000000 0.00000000
 #> Sagiproc 0.007373272 0.05645161 0.077419355 0.54193548
 #> Anthodor 0.142857143 0.25925926 0.021164021 0.00000000
 #> Planlanc 0.504201681 0.14705882 0.000000000 0.00000000
 #> Rumeacet 0.214285714 0.00000000 0.000000000 0.50000000
 #> Trifprat 0.428571429 0.00000000 0.000000000 0.00000000
 #> Juncbufo 0.008658009 0.00000000 0.012987013 0.84848485
 #> Eleopalu 0.000000000 0.00000000 0.714285714 0.00000000
 #> Juncarti 0.000000000 0.00000000 0.285714286 0.25000000
 #> Ranuflam 0.000000000 0.00000000 0.857142857 0.00000000
 #> Vicilath 0.180451128 0.09210526 0.000000000 0.00000000
 #> Hyporadi 0.027210884 0.08333333 0.068027211 0.00000000
 #> Chenalbu 0.000000000 0.00000000 0.142857143 0.00000000
 #> Comapalu 0.000000000 0.00000000 0.285714286 0.00000000
 #> Callcusp 0.000000000 0.00000000 0.428571429 0.00000000
 #> Airaprae 0.000000000 0.13461538 0.065934066 0.00000000
 #> Salirepe 0.038961039 0.00000000 0.207792208 0.00000000
 #> Empenigr 0.000000000 0.00000000 0.142857143 0.00000000
 #> 
 #> $maxcls
 #> Achimill Elymrepe Lolipere Poaprat Poatriv Alopgeni Bellpere Bromhord 
 #> 1 4 1 2 4 4 2 2 
 #> Scorautu Trifrepe Agrostol Bracruta Cirsarve Sagiproc Anthodor Planlanc 
 #> 1 4 3 4 2 4 2 1 
 #> Rumeacet Trifprat Juncbufo Eleopalu Juncarti Ranuflam Vicilath Hyporadi 
 #> 4 1 4 3 3 3 1 2 
 #> Chenalbu Comapalu Callcusp Airaprae Salirepe Empenigr 
 #> 3 3 3 2 3 3 
 #> 
 #> $indcls
 #> Achimill Elymrepe Lolipere Poaprat Poatriv Alopgeni Bellpere 
 #> 0.34843206 0.22340426 0.46204620 0.35766423 0.32558140 0.54804270 0.45000000 
 #> Bromhord Scorautu Trifrepe Agrostol Bracruta Cirsarve Sagiproc 
 #> 0.30246914 0.29076224 0.30545455 0.33365292 0.30656934 0.25000000 0.54193548 
 #> Anthodor Planlanc Rumeacet Trifprat Juncbufo Eleopalu Juncarti 
 #> 0.25925926 0.50420168 0.50000000 0.42857143 0.84848485 0.71428571 0.28571429 
 #> Ranuflam Vicilath Hyporadi Chenalbu Comapalu Callcusp Airaprae 
 #> 0.85714286 0.18045113 0.08333333 0.14285714 0.28571429 0.42857143 0.13461538 
 #> Salirepe Empenigr 
 #> 0.20779221 0.14285714 
 #> 
 #> $pval
 #> Achimill Elymrepe Lolipere Poaprat Poatriv Alopgeni Bellpere Bromhord 
 #> 0.240 0.417 0.062 0.378 0.502 0.053 0.131 0.190 
 #> Scorautu Trifrepe Agrostol Bracruta Cirsarve Sagiproc Anthodor Planlanc 
 #> 0.797 0.698 0.383 0.614 0.286 0.072 0.311 0.107 
 #> Rumeacet Trifprat Juncbufo Eleopalu Juncarti Ranuflam Vicilath Hyporadi 
 #> 0.092 0.136 0.004 0.024 0.214 0.001 0.699 1.000 
 #> Chenalbu Comapalu Callcusp Airaprae Salirepe Empenigr 
 #> 1.000 0.449 0.072 0.755 0.594 1.000 
 #> 
 #> $error
 #> [1] 0
 #> 
 #> attr(,"class")
 #> [1] "indval"
 ind_val(df, group = "Management")
 #> Joining with `by = join_by(numeric_Management)`
 #> # A tibble: 30 ×ばつ 4
 #> Management species ind.val p.value
 #> <fct> <chr> <dbl> <dbl>
 #> 1 SF Elymrepe 0.188 0.684
 #> 2 SF Alopgeni 0.547 0.038
 #> 3 SF Agrostol 0.472 0.054
 #> 4 SF Cirsarve 0.167 1 
 #> 5 SF Sagiproc 0.241 0.514
 #> 6 SF Chenalbu 0.167 1 
 #> 7 BF Achimill 0.386 0.118
 #> 8 BF Lolipere 0.45 0.07 
 #> 9 BF Poaprat 0.379 0.188
 #> 10 BF Bellpere 0.362 0.126
 #> # ... with 20 more rows
 ind_val(df, group = "Use")
 #> Joining with `by = join_by(numeric_Use)`
 #> # A tibble: 30 ×ばつ 4
 #> Use species ind.val p.value
 #> <ord> <chr> <dbl> <dbl>
 #> 1 Haypastu Elymrepe 0.292 0.288
 #> 2 Haypastu Lolipere 0.259 0.796
 #> 3 Haypastu Poaprat 0.288 0.824
 #> 4 Haypastu Poatriv 0.451 0.118
 #> 5 Haypastu Alopgeni 0.359 0.184
 #> 6 Haypastu Agrostol 0.269 0.589
 #> 7 Haypastu Cirsarve 0.125 1 
 #> 8 Haypastu Sagiproc 0.178 0.8 
 #> 9 Haypastu Juncbufo 0.118 0.848
 #> 10 Haypastu Chenalbu 0.125 1 
 #> # ... with 20 more rows
 ind_val(df, group = "Manure")
 #> Joining with `by = join_by(numeric_Manure)`
 #> # A tibble: 30 ×ばつ 4
 #> Manure species ind.val p.value
 #> <ord> <chr> <dbl> <dbl>
 #> 1 4 Elymrepe 0.5 0.048
 #> 2 4 Lolipere 0.351 0.211
 #> 3 4 Poaprat 0.315 0.28 
 #> 4 4 Bellpere 0.248 0.469
 #> 5 4 Cirsarve 0.333 0.279
 #> 6 2 Achimill 0.309 0.262
 #> 7 2 Poatriv 0.299 0.394
 #> 8 2 Bromhord 0.173 0.703
 #> 9 2 Anthodor 0.178 0.763
 #> 10 2 Rumeacet 0.522 0.041
 #> # ... with 20 more rows

 library(ggdendro)
 library(dendextend)
 #> Registered S3 method overwritten by 'dendextend':
 #> method from 
 #> rev.hclust vegan
 #> 
 #> ---------------------
 #> Welcome to dendextend version 1.16.0
 #> Type citation('dendextend') for how to cite the package.
 #> 
 #> Type browseVignettes(package = 'dendextend') for the package vignette.
 #> The github page is: https://github.com/talgalili/dendextend/
 #> 
 #> Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
 #> You may ask questions at stackoverflow, use the r and dendextend tags: 
 #> https://stackoverflow.com/questions/tagged/dendextend
 #> 
 #> To suppress this message use: suppressPackageStartupMessages(library(dendextend))
 #> ---------------------
 #> 
 #> Attaching package: 'dendextend'
 #> The following object is masked from 'package:ggdendro':
 #> 
 #> theme_dendro
 #> The following object is masked from 'package:permute':
 #> 
 #> shuffle
 #> The following object is masked from 'package:stats':
 #> 
 #> cutree
 
cls <- cluster(dune, c_method = "average", d_method = "euclidean")
ggdendro::ggdendrogram(cls)

 
indiv <- "stand"
group <- "Use"
 
ggdendro::ggdendrogram(cls_add_group(cls, df, indiv, group))
 #> Joining with `by = join_by(stand)`

 
col <- cls_color(cls, df, indiv, group)
 #> Joining with `by = join_by(stand)`
 #> Joining with `by = join_by(Use)`
cls <- 
 cls_add_group(cls, df, indiv, group) %>%
 stats::as.dendrogram()
 #> Joining with `by = join_by(stand)`
 labels_colors(cls) <- gray(0)
 
 plot(cls)
dendextend::colored_bars(colors = col, cls, group, y_shift = 0, y_scale = 3)
 par(new = TRUE)
 plot(cls)

ord_dca <- ordination(dune, o_method = "dca")
ord_pca <-
 df %>%
 df2table() %>%
 ordination(o_method = "pca")
 
ord_dca_st <- 
 ord_extract_score(ord_dca, score = "st_scores")
 
ord_dca_st %>%
 ggplot(aes(DCA1, DCA2, label = rownames(.))) +
 geom_text()

 
 
indiv <- "species"
group <- "dammy_1"
ord_pca_sp <- 
 ord_add_group(ord_pca, score = "sp_scores", df, indiv, group)
 #> Joining with `by = join_by(species)`
 
ord_pca_sp %>%
 ggplot(aes(PC1, PC2, label = rownames(.))) +
 geom_point(aes(col = .data[[group]]), alpha = 0.4, size = 7) +
 geom_text() +
 theme_bw()