vlindersRarefaction

Installation

You can install the development version of vlindersRarefaction from GitHub with:

# install.packages("devtools")
devtools::install_github("PietrH/vlindersRarefaction")

Scope

This simple and experimental package converts a dataframe with a known format to the format the iNEXT package expects for abundance and incidence frequency data.

The package was written with exactly this file in mind as a draft, with little flexibility. This means that your file will need the following columns as a minimum:

date
species_name
year
number

Any number of extra columns can be provided to split the rarefaction on, these are called assemblages in the context of iNEXT.

#> Rows: 2,976
#> Columns: 5
#> $ date         <date> 2009-06-19, 2009-07-01, 2009-08-13, 2009-08-30, 2010-06-…
#> $ species_name <chr> "Bruine huismot", "Oranje iepentakvlinder", "Oranje worte…
#> $ year         <dbl> 2009, 2009, 2009, 2009, 2010, 2010, 2010, 2010, 2010, 201…
#> $ number       <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
#> $ MicroMacro   <chr> "Micro", "Macro", "Macro", "Macro", "Macro", "Macro", "Ma…

This is a basic example on how you can plug this package into iNEXT:

library(vlindersRarefaction)

## convert to formats iNEXT is expecting, then calculate rarefaction curves
rare_out_inc <-
  iNEXT::iNEXT(convert_to_incidence_freq(warande),
               datatype = "incidence_freq",
               nboot = 2 # for speed
               )
rare_out_abun <-
  iNEXT::iNEXT(convert_to_abundance(warande),
               datatype = "abundance",
               nboot = 2 # for speed
               )
## and plot them:
iNEXT::ggiNEXT(rare_out_abun) + ggplot2::ggtitle("Abundance based")
#> Warning in ggiNEXT.iNEXT(rare_out_abun): invalid color.var setting, the iNEXT
#> object do not consist multiple assemblages, change setting as Order.q

iNEXT::ggiNEXT(rare_out_inc) + ggplot2::ggtitle("Incidence based")
#> Warning in ggiNEXT.iNEXT(rare_out_inc): invalid color.var setting, the iNEXT
#> object do not consist multiple assemblages, change setting as Order.q

Now with an assemblage set:

# Let's generate some random area's for the observations to belong to.
warande_gebieden <- warande %>% 
  dplyr::mutate(gebied =
                  sample(
                    c("gebied_a", "gebied_b"),
                    nrow(warande),
                    replace = TRUE)
  )

rare_out_inc_gebied <-
  iNEXT::iNEXT(convert_to_incidence_freq(warande_gebieden, gebied),
               datatype = "incidence_freq",
               nboot = 2 # for speed
               )

rare_out_abun_micromacro <- 
    iNEXT::iNEXT(convert_to_abundance(warande, MicroMacro),
               datatype = "abundance",
               nboot = 2 # for speed
               )

## and plot them:
iNEXT::ggiNEXT(rare_out_inc_gebied) + ggplot2::ggtitle("Incidence based, with areas")

iNEXT::ggiNEXT(rare_out_abun_micromacro) + ggplot2::ggtitle("Abundance based, split on Micro/Macro")