ordination {ecan}

Helper function for ordination methods

Description

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

library(ggplot2)
library(vegan)
data(dune)
data(dune.env)

df <- 
  table2df(dune) %>%
  dplyr::left_join(tibble::rownames_to_column(dune.env, "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)

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")