Adding LICENSE and minor script revisions

.gitignore

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 .RData
 .Ruserdata
 .DS_Store
-data/raw/*
 documents/*
 scripts/archived_scripts/*

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 Evan A. Eskew
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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-# United States amphibian imports from 1999 to 2021
+# Amphibian imports into the United States from 1999 to 2021
 
 This repository contains code, data, and figures that support:
 
 Connelly, P.J., N. Ross, O.C. Stringham, and E.A. Eskew. 2023. Ongoing amphibian trade into the United States threatens salamander biodiversity.
 
-The global amphibian trade is closely linked to wildlife disease issues because of potential for spread of either of the two fungi responsible for amphibian chytridiomycosis, *Batrachochytrium dendrobatidis* (*Bd*) or *Batrachochytrium salamandrivorans* (*Bsal*). A primary aim of this project was evaluate the efficacy of a [2016 wildlife trade policy](https://www.federalregister.gov/documents/2016/01/13/2016-00452/injurious-wildlife-species-listing-salamanders-due-to-risk-of-salamander-chytrid-fungus) that sought to reduce the likelihood of *Bsal* introduction to the United States by banning the import of 20 salamander genera. To address this question and describe patterns in amphibian imports more generally, we collated and cleaned a dataset of United States amphibian imports from 1999 to 2021, building off [previous EcoHealth Alliance efforts to curate the United States Fish and Wildlife Service's Law Enforcement Management Information System (LEMIS) data](https://doi.org/10.1038/s41597-020-0354-5). The full, cleaned dataset, with taxonomy reconciled to the [AmphibiaWeb nomenclature](https://amphibiaweb.org/taxonomy/AWtaxonomy.html) is [available in this repository](/data/cleaned/harmonized_amphibian_LEMIS_1999_to_2021.csv).
+The global amphibian trade is closely linked to wildlife disease issues because of the potential for spread of either of the two fungi responsible for amphibian chytridiomycosis, *Batrachochytrium dendrobatidis* (*Bd*) or *Batrachochytrium salamandrivorans* (*Bsal*). A primary aim of this project was evaluate the efficacy of a [2016 wildlife trade policy](https://www.federalregister.gov/documents/2016/01/13/2016-00452/injurious-wildlife-species-listing-salamanders-due-to-risk-of-salamander-chytrid-fungus) that sought to reduce the likelihood of *Bsal* introduction to the United States by banning the import of 20 salamander genera. To address this question and describe patterns in amphibian imports more generally, we collated and cleaned a dataset of amphibian imports into the United States from 1999 to 2021, building off [previous EcoHealth Alliance efforts to curate the United States Fish and Wildlife Service's Law Enforcement Management Information System (LEMIS) data](https://doi.org/10.1038/s41597-020-0354-5). The full, cleaned dataset, with taxonomy reconciled to the [AmphibiaWeb nomenclature](https://amphibiaweb.org/taxonomy/AWtaxonomy.html) is [available in this repository](/data/cleaned/harmonized_amphibian_LEMIS_1999_to_2021.csv).
 
 --- 
 
 ### Repository Structure
 
 - [`/data`](/data) contains all raw and cleaned data files
-	- [`/cleaned`](/data/cleaned) contains cleaned versions of all three LEMIS data subsets that are combined in this analysis as well as [the full, cleaned dataset](/data/cleaned/harmonized_amphibian_LEMIS_1999_to_2021.csv) 
-	- [`/lacey_act`](/data/lacey_act) contains a list of the taxa listed under the 2016 Lacey Act interim ruling
+	- [`/cleaned`](/data/cleaned) contains cleaned versions of all three LEMIS data subsets that are combined in this analysis as well as [the full, cleaned dataset](/data/cleaned/harmonized_amphibian_LEMIS_1999_to_2021.csv)
 	- [`/raw`](/data/raw) contains the raw LEMIS data that is cleaned and combined in this analysis
-	- [`/reference`](/data/reference) contains a table with information on potential *Bsal* carrier taxa, as gathered from the literature
+	- [`/reference`](/data/reference) contains tables with information on *Bsal* carrier taxa, as gathered from the literature, and the taxa listed under the 2016 Lacey Act interim ruling
 	- [`/taxonomy`](/data/taxonomy) contains AmphibiaWeb taxonomic information as well as tables used to clean the LEMIS taxonomic data
 - [`/misc`](/misc) contains the footer image used in this README page
 - [`/outputs`](/outputs) contains all figures output from the [`05_amphibian_trade_analyses.R`](/scripts/05_amphibian_trade_analyses.R) script