The goal of biosampleR is to provide a simple set of functions togenerate common biodiversity measures from count data, along withconfidence intervals around these measures using bootstrapping. Thepackage also provides functions to assess the effect of sampling efforton the precision of these measures.
You can install the development version of biosampleR fromGitHub with:
# install.packages("devtools")devtools::install_github("csim063/biosampleR")Or you can install the stable version of biosampleR fromCRAN with (the package is not yeton CRAN):
install.packages("biosampleR")The the functions in the package may be used in a single workflow asfollows:
library(biosampleR)# Import count datadf<- BCI#Using the BCI dataset from the vegan package as an example# Calculate biodiversity measures with confidence intervals# (both per site and overall for all sites)stats<-get_sample_stats(df)# Generate subsamples of a data frame with a number of sites between a minimum# and maximum value.ss<-generate_subsamples(df,min_sites =1,max_sites =5,step =1,reps =2)# Calculate change in variance of biodiversity measures with increasing sampling effortdata<-unlist(ss,recursive =FALSE)data<-do.call(rbind, data)calc_delta_var(data,col_name ="richness",site_name ="num_sites",rep_name ="rep",visualize =TRUE)Please note that thespectre package is releasedwith a Contributor Code of Conduct. By contributing to this project, youagree to abide by its terms.
To see how to contribute to this project, please see the Contributingguidelines.