In reblake/insectcleanr: Clean Insect Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

insectcleanr

The goal of insectcleanr is to provide functions for building cleaned data tables of insect data. This code package was developed for internal use by a SESYNC pursuit team by SESYNC data science staff.

Publication and Citation

This package has been published on Zenodo. It should be cited with the DOI as:

Rachael E. Blake, & Rebecca Turner. (2021, February 22). reblake/insectcleanr: Initial release (Version 0.1). Zenodo. http://doi.org/10.5281/zenodo.4555787

Installation

You can install the latest version of insectcleanr from GitHub with:

# install.packages("devtools")
devtools::install_github("reblake/insectcleanr")

Example

Example data in this package is courtesy of Morimoto, N., Kiritani, K., Yamamura, K., & Yamanaka, T. (2019). Finding indications of lag time, saturation and trading inflow in the emergence record of exotic agricultural insect pests in Japan. Applied Entomology and Zoology, 54(4), 437-450. DOI:10.1007/s13355-019-00640-2

This is a basic example which shows you how to get accepted taxonomic information for insect taxa from GBIF.

library(insectcleanr)

# list the path(s) to your raw data files
# your path will look different than this; this path loads the example data included in this package
file_list <- system.file("extdata", "Japan_taxa.xlsx", package = "insectcleanr", mustWork = TRUE)

# read in raw data and separate out taxonomic information
taxa_list <- lapply(file_list, separate_taxonomy) %>%
             purrr::reduce(full_join) %>%  # join list of dataframes into one dataframe
             distinct(genus_species) %>%  # get unique taxa names
             arrange(genus_species) %>%  # alphabetical order by taxa name
             select(genus_species) %>%  # select only the column with taxa names
             unlist(., use.names = FALSE)  # make taxa names into a vector

# get accepted taxonomic information from GBIF
taxa_accepted <- lapply(taxa_list, get_accepted_taxonomy)