jranke / pfm

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@@ -1,20 +1,3 @@
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 1 - # Copyright (C) 2015 Johannes Ranke 2 - # Contact: jranke@uni-bremen.de 3 - # This file is part of the R package pfm 4 - 5 - # This program is free software: you can redistribute it and/or modify it under 6 - # the terms of the GNU General Public License as published by the Free Software 7 - # Foundation, either version 3 of the License, or (at your option) any later 8 - # version. 9 - 10 - # This program is distributed in the hope that it will be useful, but WITHOUT 11 - # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 12 - # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 13 - # details. 14 - 15 - # You should have received a copy of the GNU General Public License along with 16 - # this program. If not, see  17 - 18 1 #' Calculate predicted environmental concentrations in surface water due to drift 19 2 #' 20 3 #' This is a basic, vectorised form of a simple calculation of a contaminant

@@ -1,20 +1,3 @@
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 1 - # Copyright (C) 2015,2020 Johannes Ranke 2 - # Contact: jranke@uni-bremen.de 3 - # This file is part of the R package pfm 4 - 5 - # This program is free software: you can redistribute it and/or modify it under 6 - # the terms of the GNU General Public License as published by the Free Software 7 - # Foundation, either version 3 of the License, or (at your option) any later 8 - # version. 9 - 10 - # This program is distributed in the hope that it will be useful, but WITHOUT 11 - # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 12 - # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 13 - # details. 14 - 15 - # You should have received a copy of the GNU General Public License along with 16 - # this program. If not, see  17 - 18 1 #' Calculate the geometric mean 19 2 #' 20 3 #' Based on some posts in a thread on Stackoverflow

@@ -1,28 +1,10 @@
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 1 - # Copyright (C) 2016,2017 Johannes Ranke 2 - 3 - # Contact: jranke@uni-bremen.de 4 - # This file is part of the R package pfm 5 - 6 - # This program is free software: you can redistribute it and/or modify it under 7 - # the terms of the GNU General Public License as published by the Free Software 8 - # Foundation, either version 3 of the License, or (at your option) any later 9 - # version. 10 - 11 - # This program is distributed in the hope that it will be useful, but WITHOUT 12 - # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 13 - # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 14 - # details. 15 - 16 - # You should have received a copy of the GNU General Public License along with 17 - # this program. If not, see  18 - 19 1 #' Create a time series of decline data 20 2 #' 21 3 #' @param x When numeric, this is the half-life to be used for an exponential 22 4 #' decline. When a character string specifying a parent decline model is given 23 5 #' e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters. 24 6 #' If x is an \code{\link{mkinfit}} object, the decline is calculated from this 25 - #' object.  7 + #' object. 26 8 #' @param ini The initial amount. If x is an \code{\link{mkinfit}} object, and 27 9 #' ini is 'model', the fitted initial concentrations are used. Otherwise, ini 28 10 #' must be numeric. If it has length one, it is used for the parent and
@@ -93,7 +75,7 @@
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 93 75 94 76  t_out <- seq(0, t_end, by = res) 95 77  pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = ini), 96 -  outtimes = t_out, solution_type = "analytical")[-1] 78 +  outtimes = t_out, solution_type = "analytical")[, -1, drop = FALSE] 97 79  result <- ts(pred, 0, t_end, frequency = 1/res) 98 80  class(result) <- c("one_box", "ts") 99 81  return(result)
@@ -118,7 +100,7 @@
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 118 100  else solution_type = "deSolve" 119 101 120 102  tmp <- mkinpredict(fit$mkinmod, odeparms = fit$bparms.ode, odeini = odeini, 121 -  outtimes = t_out, solution_type = solution_type)[-1] 103 +  outtimes = t_out, solution_type = solution_type)[, -1, drop = FALSE] 122 104  result <- ts(tmp, 0, t_end, frequency = 1/res) 123 105  class(result) <- c("one_box", "ts") 124 106  return(result)
@@ -172,7 +154,7 @@
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 172 154 173 155 #' Create decline time series for multiple applications 174 156 #' 175 - #' If the application pattern is specified in \code{applications},  157 + #' If the application pattern is specified in \code{applications}, 176 158 #' \code{n} and \code{i} are disregarded. 177 159 #' @param x A \code{\link{one_box}} object 178 160 #' @param n The number of applications. If \code{applications} is specified, \code{n} is ignored
@@ -260,7 +242,7 @@
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 260 242 #' for finding the maximum. It is therefore recommended to check this using 261 243 #' \code{\link{plot.one_box}} using the window size for the argument 262 244 #' \code{max_twa}. 263 - #'  245 + #' 264 246 #' The method working directly on fitted \code{\link{mkinfit}} objects uses the 265 247 #' equations given in the PEC soil section of the FOCUS guidance and is restricted 266 248 #' SFO, FOMC and DFOP models and to the parent compound

@@ -1,20 +1,3 @@
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 1 - # Copyright (C) 2015 Johannes Ranke 2 - # Contact: jranke@uni-bremen.de 3 - # This file is part of the R package pfm 4 - 5 - # This program is free software: you can redistribute it and/or modify it under 6 - # the terms of the GNU General Public License as published by the Free Software 7 - # Foundation, either version 3 of the License, or (at your option) any later 8 - # version. 9 - 10 - # This program is distributed in the hope that it will be useful, but WITHOUT 11 - # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 12 - # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 13 - # details. 14 - 15 - # You should have received a copy of the GNU General Public License along with 16 - # this program. If not, see  17 - 18 1 #' Groundwater ubiquity score based on Gustafson (1989) 19 2 #'  20 3 #' The groundwater ubiquity score GUS is calculated according to
@@ -24,7 +7,6 @@
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 24 7 #' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple 25 8 #' method for assessing pesticide leachability. \emph{Environmental 26 9 #' toxicology and chemistry} \bold{8}(4) 339–57. 27 - #' @inheritParams endpoint 28 10 #' @param DT50 Half-life of the chemical in soil. Should be a field 29 11 #' half-life according to Gustafson (1989). However, leaching to the sub-soil 30 12 #' can not completely be excluded in field dissipation experiments and Gustafson

@@ -1,20 +1,3 @@
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 1 - # Copyright (C) 2015 Johannes Ranke 2 - # Contact: jranke@uni-bremen.de 3 - # This file is part of the R package pfm 4 - 5 - # This program is free software: you can redistribute it and/or modify it under 6 - # the terms of the GNU General Public License as published by the Free Software 7 - # Foundation, either version 3 of the License, or (at your option) any later 8 - # version. 9 - 10 - # This program is distributed in the hope that it will be useful, but WITHOUT 11 - # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 12 - # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 13 - # details. 14 - 15 - # You should have received a copy of the GNU General Public License along with 16 - # this program. If not, see  17 - 18 1 #' Calculate a time course of relative concentrations based on an mkinmod model 19 2 #' 20 3 #' @import mkin
@@ -30,19 +13,19 @@
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 30 13 #' @author Johannes Ranke 31 14 #' @examples 32 15 #' head(pfm_degradation("SFO", DT50 = 10)) 33 - pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), 34 -  years = 1, step_days = 1, 35 -  times = seq(0, years * 365, by = step_days)) 16 + pfm_degradation <- function(model = "SFO", 17 +  DT50 = 1000, parms = c(k_parent = log(2)/DT50), 18 +  years = 1, step_days = 1, 19 +  times = seq(0, years * 365, by = step_days)) 36 20 { 37 21  if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) { 38 22  model <- mkinmod(parent = list(type = model)) 39 23  } 40 24  initial_state = c(1, rep(0, length(model$diffs) - 1)) 41 25  names(initial_state) <- names(model$diffs) 42 26  time_course <- mkinpredict(model, odeparms = parms,  43 -  odeini = initial_state, 44 -  outtimes = times, 45 -  solution_type = ifelse(length(model$spec) == 1, 46 -  "analytical", "deSolve")) 27 +  odeini = initial_state, 28 +  outtimes = times, 29 +  solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve")) 47 30  invisible(time_course) 48 31 }

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