Skip to contents

Compare All Diversity Indices Side by Side

Source: R/compare_indices.R
compare_indices.Rd

Computes all available diversity indices for one or more communities and returns them in a single data frame. Optionally produces a grouped bar plot for visual comparison.

Usage

compare_indices(
  communities,
  tax_tree,
  correction = c("none", "miller_madow", "grassberger", "chao_shen"),
  plot = FALSE
)

Arguments

communities

A named list of community vectors (named numeric), or a single named numeric vector. When a single vector is provided, it is wrapped in a list with name "Community".

tax_tree

A data frame representing the taxonomic hierarchy, as produced by build_tax_tree.

correction

Bias correction for the Shannon index. One of "none" (default), "miller_madow", "grassberger", or "chao_shen". Passed to shannon(). See shannon() for details.

plot

Logical. If TRUE and ggplot2 is available, returns a list with both the data frame and a ggplot object. Default is FALSE.

Value

If plot = FALSE, a data frame with communities as rows and indices as columns. If plot = TRUE, a list with two elements:

table

The data frame of index values.

plot

A ggplot object showing a grouped bar chart.

Details

The function calculates the following indices:

  • Shannon: Shannon-Wiener entropy (shannon)

  • Simpson: Gini-Simpson index (simpson)

  • Delta: Clarke & Warwick taxonomic diversity (delta)

  • Delta_star: Clarke & Warwick taxonomic distinctness (delta_star)

  • AvTD: Average taxonomic distinctness (avtd)

  • VarTD: Variation in taxonomic distinctness (vartd)

  • uTO: Unweighted taxonomic diversity (Ozkan pTO, all levels)

  • TO: Weighted taxonomic diversity (Ozkan pTO, all levels)

  • uTO_plus: Unweighted taxonomic distance (Ozkan pTO, all levels)

  • TO_plus: Weighted taxonomic distance (Ozkan pTO, all levels)

  • uTO_max: Unweighted taxonomic diversity (informative levels)

  • TO_max: Weighted taxonomic diversity (informative levels)

  • uTO_plus_max: Unweighted taxonomic distance (informative levels)

  • TO_plus_max: Weighted taxonomic distance (informative levels)

See also

shannon, simpson, delta, delta_star, avtd, vartd, ozkan_pto, pto_components

Examples

tax <- build_tax_tree(
  species = c("sp1", "sp2", "sp3", "sp4"),
  Genus   = c("G1", "G1", "G2", "G2"),
  Family  = c("F1", "F1", "F1", "F2"),
  Order   = c("O1", "O1", "O1", "O1")
)

# Single community
comm <- c(sp1 = 10, sp2 = 20, sp3 = 15, sp4 = 5)
compare_indices(comm, tax)
#> taxdiv -- Index Comparison
#>   Communities: 1 
#>   Indices: Shannon, Simpson, Delta, Delta_star, AvTD, VarTD, uTO, TO, uTO_plus, TO_plus, uTO_max, TO_max, uTO_plus_max, TO_plus_max 
#> 
#>  Community N_Species  Shannon Simpson    Delta Delta_star AvTD    VarTD
#>  Community         4 1.279854     0.7 1.326531   1.857143    2 0.666667
#>       uTO       TO uTO_plus  TO_plus  uTO_max   TO_max uTO_plus_max TO_plus_max
#>  3.413215 5.066836  4.04615 5.837909 3.413215 5.066836      4.04615    5.837909

# Multiple communities
comm_list <- list(
  Site_A = c(sp1 = 10, sp2 = 20, sp3 = 15, sp4 = 5),
  Site_B = c(sp1 = 5, sp2 = 5, sp3 = 5, sp4 = 5)
)
compare_indices(comm_list, tax)
#> taxdiv -- Index Comparison
#>   Communities: 2 
#>   Indices: Shannon, Simpson, Delta, Delta_star, AvTD, VarTD, uTO, TO, uTO_plus, TO_plus, uTO_max, TO_max, uTO_plus_max, TO_plus_max 
#> 
#>  Community N_Species  Shannon Simpson    Delta Delta_star AvTD    VarTD
#>     Site_A         4 1.279854    0.70 1.326531   1.857143    2 0.666667
#>     Site_B         4 1.386294    0.75 1.578947   2.000000    2 0.666667
#>       uTO       TO uTO_plus  TO_plus  uTO_max   TO_max uTO_plus_max TO_plus_max
#>  3.413215 5.066836  4.04615 5.837909 3.413215 5.066836      4.04615    5.837909
#>  4.046150 5.837909  4.04615 5.837909 4.046150 5.837909      4.04615    5.837909