Version 1.0.0
CRAN release: 2024-07-12
The ‘WES’ R package v1.0.0 migrated from the ‘es’ R package v1.0.0 on July 03, 2024
Welcome to the first release of the ‘WES’ R package! Version 1.0.0 contains a collection of basic features that aim to make analyzing environmental sampling data easier and more reproducible. The functionality we have included to kick off the package includes:
- Detailed descriptions of standard data formats for environmental sampling data and standard curve assays. The functionality of the package requires data to follow these formats.
- Functions for the absolute and relative quantification of qPCR data which include:
- Calculating the number of gene copies using Ct values and a standard curve assay
- Calculating the ΔΔCt method for the fold-change in gene expression relative to a reference gene. An efficiency-weighted version is also included.
- Estimation of the percentile amplification efficiency using a standard curve assay.
- Functions for downloading covariate data from several open-source APIs and methods for relating these data to environmental sampling observations. These data include:
- Climate
- Data from Open-Meteo Historical Weather API
- cumulative precipitation
- accumulated thermal units
- Evaporative Stress Index (ESI)
- Topology and hydrology
- Data from Amazon Web Services (AWS) API
- elevation
- slope
- aspect
- flow accumulation
- stream networks
- drainage catchments
- Local population
- Data from WorldPop
- Population counts in drainage catchments
- Population counts within radius
- Administrative boundaries
- Data from geoBoundaries
- Place names of sampling sites
- Climate
- Basic calculation of sample sizes and detection rates