add_back_missing_plots_species_combinations: Add back missing plots x species combinations

View source: R/preparing_diversity.R

add_back_missing_plots_species_combinationsR Documentation

Add back missing plots x species combinations

Description

date of creation : 26.01.21 In order to save storage, the diversity dataset for bacteria and soil fungi o not include all combinations of plots x species when a given species was not found in a given plot i.e. they do not contain zeros. They need to be added back in order to gain the complete set of studied plots (missing plots x species are not NA but measured, just the given species was not found). Code from Caterina Penone, for further explanations and rationale see https://github.com/biodiversity-exploratories-synthesis/Synthesis-dataset-manual/blob/main/Synthesis Note : Only the columns Plot and Species are considered, any other columns will be filled with NA. This can cause problems if the dataset is later filtered for e.g. Year. Note : special case if the input dataset does not contain all Plots, if certain plots do not contain any species. This special case is detected and solved in this function.

Usage

add_back_missing_plots_species_combinations(diversity_dataset, all_plots)

Arguments

diversity_dataset

A data.table of soilfuni or bacteria in the format of the synthesis diversity dataset, with at least the columns Plot, Species and value. #' @param all_plots a character vector containing the complete set of plots from the Exploratories. (AEG 1-50, HEG 1-50 and SEG 1-50). Is needed for the subfunction find_and_supplement_missing_plots.

Value

A data.table in the same format as diversity_dataset, but with the previously missing plots x species added back as 0. Note : Only the columns Plot, Species and value are considered, any other columns will be filled with NA.


allanecology/BetaDivMultifun documentation built on Dec. 3, 2022, 12:30 p.m.