In dilljone/EvoGEAR: EvoGEAR (Evolutionary, BioGeography and Ecology Analyses in R): A package for aiding biogeograpic and eco-evolutionary analyses

knitr::opts_chunk$set(echo = TRUE)

Intro

Purpose of package

EvoGear is being created based on the need to make custom scripts for my current thesis work. Evolutionary geography and ecology analyses require the manipulation of many disparate types of data (Geographic, phylogenetic, occurrence, trait etc.). Further, many standardized datasets or data types (GBIF, IUCN; Shapefiles, point occurence) require some level of manipulation or cleaning before they can be used. While many packages contain several functions for these issues, they are spread throughout many packages, can be difficult to find, or do not produce outputs suitable for these kind of analyses.This package aims to create scripts specifically for data analysis/manipulation for evolutionary biogeography/ecological analyses. Proposed scripts are outlined below

Types of scripts

Occurrence

Occurence datasets are crucial for EvoGeo analyses. However, datasets are messy, in disparate formats, or require some type of manipulation before use. These functions largely deal with cleaning data and data manipulation

Clean_GBIF: Function specific for cleaning Raw GBIF occurrence datasets

clean_occ: Subfunction of Clean_GBIF that can be suited for any point occurrence dataset

KDE_Filter: filter occurence datasets based on Kernel Density Estimates

points2poly: Convert point occurence data into polygons by expanding points into circlesand combining

combine_points_polygons: Combines point occurence data (e.g. GBIF) with polygon data (e.g. IUCN)

Combine_ranges_based_on_tree: iterate through tree and combine polygon ranges together. Need to weight them based on overlapping areas. Troubleshooting sdfasdsf;kladfsskj;ak;jafskj;lagskj;lkj;lj

Phylogenetic

Not sure if I want to keep. These feel somewhat out of place in its current state. Need more functions specifically for phylogenetic/geography stuff

Rogue_taxa: detect rogue taxa across a tree

Instability_index: Instability of particular taxon calculated

Calc_CFI: Consensus Fork Index calculation.

iterate_genbank: Iterate through Genbank based on a vector of search terms (e.g. family) and pull them all into FASTA files

Taxonomic

When using data from many different sources, often the taxonomy will be different between these sources. As such, Taxonomy validation is a useful tool for increasing data coverage and accuracy. These scripts are meant to assist in the taxonomy validation process.

webscrape_frost: Webscraping function for querying AMNH frost amphibians of the world

Several subfunctions here as well

Combinetaxon validates: Combines taxon validation from multiple sources adn identify discrepencies

Identify_syno_problems: Often when working with synonym datasets, you may encounter reciprocal synonym-binomial pairs (e.g. B. aridus -> B. major and B. major -> B. aridus). This function identifies those.

Geographic

Manipulation of bioclim var?

create_map: Creates a map with dissolved interior lines based on user inputted country names

Analyses

Pairwise_Allopatry: detects degree of allopatry/sympatry between all binomial pairs

Allopatry across tree: Still working on this one. Need to think it through more

phylosignalPrep: Combining datasets

Utility

These are functions that are meant for basic utility. Simple data manipulation, metrics, or columns of data

seq_0: Sequence function that includes last records of sequence by function

SPDF -> SF

Convert all objects to simple features (need to create functions that convert them)

combining polygons and stuff was tricky

setting up regions for stuff

getting data ready for BIOGEOBEARS

Should setup data for SDMs as well

Maybe just include the sdm calculation

Alphahull from points

There was some shit you had to do with your polygons cause of clipping or some BS

How about a general function for processing any type of polygon and showing what is missing, what is needed, etc etc?

Attaching trait data to occurence data (shouldnt need as is simple, but is it actually?)

dilljone/EvoGEAR documentation built on May 7, 2023, 5:12 a.m.