The goal of the R package rcea is to {{ PLEASE ADD A FEW LINES }}
Installation
You can install the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("david-beauchesne/rcea")Then you can attach the package rcea:
Overview
library(rcea)
library(stars)
#> Loading required package: abind
#> Loading required package: sf
#> Linking to GEOS 3.11.2, GDAL 3.6.3, PROJ 9.2.0; sf_use_s2() is TRUE
# Data
drivers <- rcea:::drivers
vc <- rcea:::vc
sensitivity <- rcea:::sensitivity
metaweb <- rcea:::metaweb
trophic_sensitivity <- rcea::trophic_sensitivity
pal <- viridis::viridis
# Plots
plot(merge(drivers), col = pal)
plot(merge(vc), col = pal(1))
#> Warning in plot.stars(merge(vc), col = pal(1)): breaks="quantile" leads to a
#> single class; maybe try breaks="equal" instead?
# Cumulative footprint
foot_dr <- cea_extract(drivers, cumul_fun = "footprint")
foot_vc <- cea_extract(vc, cumul_fun = "footprint")
plot(foot_dr, col = pal)
plot(foot_vc, breaks = "equal", col = pal)
# Cumulative exposure
expo <- exposure(drivers, vc, "stars")
# Extract specific attributes and evaluate cumulative exposure
dr_sel <- c("driver1","driver5")
vc_sel <- c("vc4","vc7","vc10","vc12")
dat <- cea_extract(expo, dr_sel = dr_sel, vc_sel = vc_sel)
plot(dat["vc4"], col = pal) # Exposure of vc4 to driver1 and driver5
# Cumulative effects assessment (Halpern et al. 2008)
halpern <- cea(drivers, vc, sensitivity, "stars")
# Cumulative effects of all drivers on all vc
dat <- cea_extract(halpern, cumul_fun = "drivers")
plot(merge(dat), breaks = "equal", col = pal)
# Cumulative effects of all drivers on each vc
dat <- cea_extract(halpern, cumul_fun = "vc")
plot(merge(dat), breaks = "equal", col = pal)
# Full cumulative effects
dat <- cea_extract(dat, cumul_fun = "full")
plot(dat, breaks = "equal", col = pal)
# Network-scale cumulative effects assessment (Beauchesne et al. 2021)
beauchesne <- ncea(drivers, vc, sensitivity, metaweb, trophic_sensitivity)
# Net cumulative effects
dat <- cea_extract(beauchesne$net, cumul_fun = "full")
plot(dat, breaks = "equal", col = pal)
# Direct cumulative effects
dat <- cea_extract(beauchesne$direct, cumul_fun = "full")
plot(dat, breaks = "equal", col = pal)
# Indirect cumulative effects
dat <- cea_extract(beauchesne$indirect, cumul_fun = "full")
plot(dat, breaks = "equal", col = pal)
Citation
Please cite this package as:
Beauchesne David (2023) rcea: An R package to perform cumulative effects assessments. R package version 0.0.0.9000.
Code of Conduct
Please note that the rcea project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.