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Diffstat (limited to 'R/nafta.R')
-rw-r--r-- | R/nafta.R | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/R/nafta.R b/R/nafta.R new file mode 100644 index 00000000..102a9ad6 --- /dev/null +++ b/R/nafta.R @@ -0,0 +1,105 @@ +# 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, ...) { + cat("Parameters:\n") + print(x$parameters) + t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet) + cat("\nDTx values:\n") + print(round((x$distimes), digits = 0)) + 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 to the terminal degradation rate found with the DFOP model.") + message("The reprentative half-life obtained from the DFOP model may be used") + } + t_rep <- t_DFOP2 + } + } + return(t_rep) +} |