processModis: Process MODIS files from Google Earth Engine

Description Usage Arguments Details Value References

Description

Combine MODIS files and split into species-level files.

Usage

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processModis(species.col, obs.table, read.wd, write.wd, aux.wd, keep, drop,
  cores)

Arguments

species.col

Character vector specifying the column that contains the species names. Will be used to split files. IMPORTANT: ebirdr generally uses file names as organizational/naming structure. It's possible that the species names do not match the file names, for instance if the analysis is using a different taxonomy than eBird. If this is the case, and if the raw MODIS files contain the OBS_ID, the this argument can be set to NULL, and a 'obs.table' passed instead. See below.

obs.table

Data frame with 'OBS_ID' as the first column, and the 'correct.species' that observation belongs to as the second column. If this approach is used, then 'correct.species' must be one of the values in keep. This argument can be missing if species.col is provided.

read.wd

Path to the read directory, where the files to be prepped are found.

write.wd

Path to the write directory.

aux.wd

Path to directory where the sample size summary file will be saved.

keep

Character vector of columns to keep in the output files.

drop

Should points that were not assigned complete MODIS values be dropped? Default is TRUE.

cores

How many cores to use for parallel processing.

Details

This function works by first binding all the files together in read.wd, then dropping to all but the specified columns in keep, optionally dropping incomplete records, then splitting into species-level files and saving out.

Value

Nothing to workspace. Saves out two files. First to aux.wd is a data frame summarizing per species sample sizes. Next are species-level csv files with matched MODIS data. Spaces in the species names will be removed.

References

Team eBird.


eliotmiller/ebirdr documentation built on May 14, 2019, 10:33 a.m.