Helper function for ordination methods

Usage

ordination(tbl, o_method, d_method = NULL, ...)

ord_plot(ord, score = "st_scores", x = 1, y = 2)

ord_add_group(ord, score = "st_scores", df, indiv, group)

ord_extract_score(ord, score = "st_scores", row_name = NULL)

Arguments

tbl: A community data matrix. rownames: stands. colnames: species.
o_method: A string of ordination method. "pca", "ca", "dca", "pcoa", or "nmds". "fspa" is removed, because package dave was archived.
d_method: A string of distance method. "correlation", "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis", "chisq", "chord", "aitchison", or "robust.aitchison".
...: Other parameters for PCA.
ord: A result of ordination().
score: A string to specify score for plot. "st_scores" means stands and "sp_scores" species.
x, y: A column number for x and y axis.
df: A data.frame to be added into ord scores
indiv, group, row_name: A string to specify indiv, group, row_name column in df.

Value

ordination() returns result of ordination. $st_scores: scores for stand. $sp_scores: scores for species. $eig_val: eigen value for stand. $results_raw: results of original ordination function. $ordination_method: o_method. $distance_method: d_method. ord_plot() returns ggplot2 object. ord_extract_score() extracts stand or species scores from ordination result. ord_add_group() adds group data.frame into ordination scores.

Examples

# \donttest{
library(ggplot2)
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.6-8
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 <- dplyr::left_join(df, sp_dammy)
#> Joining with `by = join_by(species)`

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_pca_sp <- 
  ord_add_group(ord_pca, 
  score = "sp_scores", df, indiv = "species", group = "dammy_1")
#> Joining with `by = join_by(species)`
# }