knitr::opts_chunk$set(echo = TRUE)
An R package to implement and test the ECOSTAT toolkit for estimating nutrient boundaries.
Implements and tests the ECOSTAT toolkit for estimating nutrient boundaries. R functions have been created that replicate the original scripts by Geoff Phillips.
ecostattoolkit can be installed directly from GitHub using the install_github
function in package devtools
# install.packages("devtools") devtools::install_github("andrewdolman/ecostattoolkit")
library(ecostattoolkit) library(dplyr) library(tidyr)
filename <- system.file("extdata", "DataTemplate_Example1.csv", package = "ecostattoolkit") dat <- read.csv(filename) status_boundaries <- c("HG" = 0.8, "GM" = 0.6, "MP" = 0.4) # min and max nutrient value used for model nut.min <- 1 nut.max <- 138 dat$status <- cut(dat$EQR, breaks = rev(c(Inf, status_boundaries, -Inf)), labels = rev(c("High", "Good", "Moderate", "Poor"))) dat$x.u <- log10(dat$P) dat$y.u <- dat$EQR knitr::kable(head(dat))
dat_sub <- filter(dat, Exclude_P == 0, P <= nut.max, P >= nut.min) boundaries <- boundaries_all(dat_sub) boundaries <- dplyr::mutate_if(boundaries, is.numeric, dplyr::funs(round(10^., 0))) %>% select(-MP) knitr::kable(boundaries)
Run script
source(system.file("extdata", "TKit_20170208_CORRECTED/TKit_fit_lin_mod1.R", package = "ecostattoolkit"))
# Collect results script.res <- data.frame( Method = c(rep("OLS1_YonX", 2), rep("OLS2_XonY", 2), rep("RMA", 2)), Boundary = c("GM", "HG", "GM", "HG", "GM", "HG"), Value = c(GM.mod1, HG.mod1, GM.mod2, HG.mod2, GM.mod4, HG.mod4), stringsAsFactors = TRUE) script.res %>% tidyr::spread(Boundary, Value) %>% dplyr::select(Method, HG, GM) %>% arrange(Method) %>% knitr::kable(.)
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