Tools for Analyzing Wastewater and Environmental Sampling Data
Apply PCR amplification efficiency estimation to a data.frame
Apply the delta delta Ct calculation to a data.frame
Calculate delta delta Ct
Calculate number of target copies
Calculate sample sizes
Convert coordinates to ISO country code
Download administrative boundaries from geoBoundaries API
Download DEM from AWS Terrain Tiles
Download WorldPop population raster data
Estimate PCR amplification efficiency
Get population counts within catchments of sampling sites
Get administrative data for a set of points
Get elevation data
Get Evaporative Stress Index (ESI) data
Request metadata from GeoBoundaries API
Get hydrological data
Get population counts within a radius of sampling sites
Get precipitation data
Get river discharge data
Get temperature data
Provides reproducible functions for collating and analyzing data from environmental sampling studies. Environmental Sampling (ES) of infectious diseases involves collecting samples from various sources (such as sewage, water, air, soil, or surfaces) to monitor the presence of pathogens in the environment. Analysis of ES data often requires the calculation of Real-Time Quantitative PCR (qPCR) variables, normalizing ES observations, and analyzing sampling site characteristics. To help reduce the complexity of these analyses we have implemented tools that assist with establishing standardized ES data formats, absolute and relative quantification of qPCR data, estimation of qPCR amplification efficiency, and collating open-source spatial data for sampling sites.