Version 1.0.0

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 \(\Delta \Delta \text{Ct}\) 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
• Basic calculation of sample sizes and detection rates