# Copyright (C) 2019 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
# mkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
nafta <- function(ds, title = NA, quiet = FALSE, ...) {
if (length(levels(ds$name)) > 1) {
stop("The NAFTA procedure is only defined for decline data for a single compound")
}
n <- nrow(subset(ds, !is.na(value)))
models <- c("SFO", "IORE", "DFOP")
result <- list(title = title, data = ds)
result$mmkin <- mmkin(models, list(ds), quiet = TRUE, ...)
distimes <- lapply(result$mmkin, function(x) as.numeric(endpoints(x)$distimes["parent", ]))
result$distimes <- matrix(NA, nrow = 3, ncol = 3,
dimnames = list(models, c("DT50", "DT90", "DT50_rep")))
result$distimes["SFO", ] <- distimes[[1]][c(1, 2, 1)]
result$distimes["IORE", ] <- distimes[[2]][c(1, 2, 3)]
result$distimes["DFOP", ] <- distimes[[3]][c(1, 2, 4)]
# Get parameters with statistics
result$parameters <- lapply(result$mmkin, function(x) {
summary(x)$bpar[, c(1, 4:6)]
})
names(result$parameters) <- models
# Compare the sum of squared residuals (SSR) to the upper bound of the
# confidence region of the SSR for the IORE model
result$S <- sapply(result$mmkin, function(x) x$ssr)
names(result$S) <- models
# Equation (3) on p. 3
p <- 3
result$S["IORE"]
result$S_c <- result$S[["IORE"]] * (1 + p/(n - p) * qf(0.5, p, n - p))
result$t_rep <- .evaluate_nafta_results(result$S, result$S_c,
result$distimes, quiet = quiet)
class(result) <- "nafta"
return(result)
}
plot.nafta <- function(x, legend = FALSE, main = "auto", ...) {
if (main == "auto") {
if (is.na(x$title)) main = ""
else main = x$title
}
plot(x$mmkin, ..., legend = legend, main = main)
}
print.nafta <- function(x, quiet = TRUE, digits = 3, ...) {
cat("Sums of squares:\n")
print(x$S)
cat("\nCritical sum of squares for checking the SFO model:\n")
print(x$S_c)
cat("\nParameters:\n")
print(x$parameters, digits = digits)
t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet)
cat("\nDTx values:\n")
print(x$distimes, digits = digits)
cat("\nRepresentative half-life:\n")
print(t_rep)
}
.evaluate_nafta_results <- function(S, S_c, distimes, quiet = FALSE) {
t_SFO <- distimes["IORE", "DT50"]
t_IORE <- distimes["IORE", "DT50_rep"]
t_DFOP2 <- distimes["DFOP", "DT50_rep"]
if (S["SFO"] < S_c) {
if (!quiet) {
message("S_SFO is lower than the critical value S_c, use the SFO model")
}
t_rep <- t_SFO
} else {
if (!quiet) {
message("The SFO model is rejected as S_SFO is equal or higher than the critical value S_c")
}
if (t_IORE < t_DFOP2) {
if (!quiet) {
message("The half-life obtained from the IORE model may be used")
}
t_rep <- t_IORE
} else {
if (!quiet) {
message("The representative half-life of the IORE model is longer than the one corresponding")
message("to the terminal degradation rate found with the DFOP model.")
message("The representative half-life obtained from the DFOP model may be used")
}
t_rep <- t_DFOP2
}
}
return(t_rep)
}
