InputOccDataSummary: InputOccDataSummary

In GPowney/TrendSummaries: TrendSummaries - summarising occupancy model outputs

Description

THIS FUNCTION IS STILL UNDER REVIEW - This function takes .rdata files created by the Data_cleaning.function and calculates how many species have records in each region follwoing the data cleaning process. Furthermore, this function can be used to extract the first and last year of data for each species following the data cleaning process.

Usage

InputOccDataSummary(
  indata = "data/model_runs/",
  output_path = "output/",
  minNyear = 2,
  minNrecs = 50,
  save_name = "cirrus",
  outhwaite_spp_clean = TRUE,
  species_year_summary = TRUE
)

Arguments

indata	The file path to a folder contain .rdata output files from the Data_cleaning.function
output_path	The file path for the location where we want to save the outputs
minNyear	The minimum number of years of records a site needs to be included in the final modelled dataset
minNrecs	The total (across all regions) minimum number of records a species needs to be included in the final modelled dataset
save_name	the name of the file to be saved
outhwaite_spp_clean	Set to TRUE or FALSE. ONly include species included in Outhwaite's data paper
species_year_summary	Do you want to save a file that extracts the year of the first and last record for the each species. This is calculated post occupancy model filtering, e.g. site with < X years dropped.

Value

A .csv file summarising the number of species included for each region from the cleaned dataset

GPowney/TrendSummaries documentation built on Nov. 15, 2021, 6:14 p.m.