Beta Diversity Boxplot — beta_diversity

This function calculates beta diversity (shared species, turnover, or nestedness) and generates a ggplot2 boxplot with facets and custom coloring. The user only needs to specify the metadata column(s) to be used for comparisons; the function constructs the comparison pairs internally and removes duplicates (A_vs_B = B_vs_A).

beta_diversity_boxplot(
  table,
  metadata,
  comparison_condition1 = NULL,
  condition1_col,
  condition2_col = NULL,
  color_facets_x = NULL,
  color_axis_x = NULL,
  title_axis_x = "Condition",
  partition = c("shared", "turnover", "nestedness"),
  family = c("sorensen", "jaccard"),
  save_table = TRUE,
  table_filename = "betadiv_table.txt"
)

Arguments

table: Abundance matrix (samples in columns, species/features in rows).
metadata: Data frame with sample metadata. First column must match sample names in table.
comparison_condition1: Optional vector of comparison labels for the first condition.
condition1_col: Column name in metadata for the first condition.
condition2_col: Optional column name in metadata for the second condition (used as facet).
color_facets_x: Optional vector of colors for facet strips. Defaults to RColorBrewer "Set2".
color_axis_x: Optional named vector of colors for x-axis groups. Defaults to RColorBrewer "Set2".
title_axis_x: Title for the x-axis.
partition: Type of beta diversity to compute: "shared", "turnover", or "nestedness".
family: Family for turnover/nestedness calculation: "sorensen" or "jaccard".

Value

A ggplot2 figure object.

Examples

beta_diversity_boxplot(table = table,
                       metadata = metadata,
                       comparison_condition1 = c("fenol_vs_kit"),  
                       condition1_col = "metodo",
                       condition2_col = "edad",
                       title_axis_x = "Samples",
                       partition = "shared", family = "sorensen")
#> Installing package into 'C:/Users/Nestor/AppData/Local/Temp/RtmpaCNPW9/temp_libpath3cfc7e5055bf'
#> (as 'lib' is unspecified)
#> also installing the dependencies 'picante', 'rcdd', 'doSNOW', 'itertools', 'minpack.lm'
#> package 'picante' successfully unpacked and MD5 sums checked
#> package 'rcdd' successfully unpacked and MD5 sums checked
#> package 'doSNOW' successfully unpacked and MD5 sums checked
#> package 'itertools' successfully unpacked and MD5 sums checked
#> package 'minpack.lm' successfully unpacked and MD5 sums checked
#> package 'betapart' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#> 	C:\Users\Nestor\AppData\Local\Temp\RtmpcBYvwG\downloaded_packages
#> Error in table > 0: comparison (>) is possible only for atomic and list types