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Summary Table on Traits (Missingness, Range, etc.)

Source: R/fb_table_trait_summary.R
fb_table_trait_summary.Rd

This function outputs a data.frame that summarises the species by trait table to have many information in a glance. This can then return a data.frame or a nicely formatted knitr::kable() for inclusion in an Rmarkdown document.

Usage

fb_table_trait_summary(species_traits, kable = FALSE)

Arguments

species_traits

a data.frame with species in rows and traits as columns. NOTE: The first column should be named "species" and contain species names. The other columns should be named according to trait names.

kable

TRUE or FALSE Should function returns a knitr::kable()? defaults FALSE

Value

a data.frame with the following columns:

  • trait_name: a character column with the trait name as indicated in species_traits

  • trait_type: the nature of the trait (numeric, categorical, or ordered)

  • number_non_missing: the total number of non-NA trait values

  • proportion_non_missing: the proportion of non-NA trait values

  • trait_range: for numerical traits, the range of values

  • trait_mean_sd: for numerical traits, the mean plus-minus the standard deviation

  • number_distinct: for non-numerical traits, the number of categories

  • list_distinct: for non-numerical traits, the list of categories

Examples

# Get a data.frame back
fb_table_trait_summary(woodiv_traits)
#>     trait_name trait_type number_non_missing proportion_non_missing trait_range
#> 1 plant_height    numeric                 24                  100 %  1.37-49.64
#> 2    seed_mass    numeric                 23                   96 % 7.61-626.19
#> 3          sla    numeric                 17                   71 %   0.51-10.6
#> 4 wood_density    numeric                 17                   71 %   0.28-0.65
#>      trait_mean_sd number_distinct list_distinct
#> 1  18.78 +/- 11.76              NA          <NA>
#> 2 62.25 +/- 125.44              NA          <NA>
#> 3    4.77 +/- 2.18              NA          <NA>
#> 4    0.49 +/- 0.09              NA          <NA>

# Get a kable (to use in Rmd documents)
fb_table_trait_summary(woodiv_traits, TRUE)
#> 
#> 
#> Table: Summary of trait data
#> 
#> |  Trait Name  | Nature of Trait | Number of Non-Missing Values| Proportion of Non-Missing Values| Range of Trait | Trait Mean +/- SD | Number of Distinct Values|List of Distinct Values |
#> |:------------:|:---------------:|----------------------------:|--------------------------------:|:--------------:|:-----------------:|-------------------------:|:-----------------------|
#> | plant_height |     numeric     |                           24|                            100 %|   1.37-49.64   |  18.78 +/- 11.76  |                        NA|NA                      |
#> |  seed_mass   |     numeric     |                           23|                             96 %|  7.61-626.19   | 62.25 +/- 125.44  |                        NA|NA                      |
#> |     sla      |     numeric     |                           17|                             71 %|   0.51-10.6    |   4.77 +/- 2.18   |                        NA|NA                      |
#> | wood_density |     numeric     |                           17|                             71 %|   0.28-0.65    |   0.49 +/- 0.09   |                        NA|NA                      |