jranke / pfm

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

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

@@ -1,28 +1,10 @@
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# Copyright (C) 2016,2017  Johannes Ranke
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# Contact: jranke@uni-bremen.de
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# This file is part of the R package pfm
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# This program is free software: you can redistribute it and/or modify it under
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# the terms of the GNU General Public License as published by the Free Software
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# Foundation, either version 3 of the License, or (at your option) any later
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# version.
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# This program is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
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# details.
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# You should have received a copy of the GNU General Public License along with
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# this program. If not, see <http://www.gnu.org/licenses/>
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#' Create a time series of decline data
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#'
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#' @param x When numeric, this is the half-life to be used for an exponential
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#'   decline. When a character string specifying a parent decline model is given
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#'   e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
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#'   If x is an \code{\link{mkinfit}} object, the decline is calculated from this
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#'   object.  
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#'   object.
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#' @param ini The initial amount. If x is an \code{\link{mkinfit}} object, and
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#'   ini is 'model', the fitted initial concentrations are used. Otherwise, ini
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#'   must be numeric. If it has length one, it is used for the parent and
@@ -93,7 +75,7 @@
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  t_out <- seq(0, t_end, by = res)
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  pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = ini),
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                      outtimes = t_out, solution_type = "analytical")[-1]
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    outtimes = t_out, solution_type = "analytical")[, -1, drop = FALSE]
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  result <- ts(pred, 0, t_end, frequency = 1/res)
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  class(result) <- c("one_box", "ts")
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  return(result)
@@ -118,7 +100,7 @@
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  else solution_type = "deSolve"
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  tmp <- mkinpredict(fit$mkinmod, odeparms = fit$bparms.ode, odeini = odeini,
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    outtimes = t_out, solution_type = solution_type)[-1]
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    outtimes = t_out, solution_type = solution_type)[, -1, drop = FALSE]
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  result <- ts(tmp, 0, t_end, frequency = 1/res)
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  class(result) <- c("one_box", "ts")
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  return(result)
@@ -172,7 +154,7 @@
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#' Create decline time series for multiple applications
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#'
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#' If the application pattern is specified in \code{applications}, 
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#' If the application pattern is specified in \code{applications},
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#' \code{n} and \code{i} are disregarded.
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#' @param x A \code{\link{one_box}} object
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#' @param n The number of applications. If \code{applications} is specified, \code{n} is ignored
@@ -260,7 +242,7 @@
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#' for finding the maximum. It is therefore recommended to check this using
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#' \code{\link{plot.one_box}} using the window size for the argument
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#' \code{max_twa}.
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#' 
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#'
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#' The method working directly on fitted \code{\link{mkinfit}} objects uses the
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#' equations given in the PEC soil section of the FOCUS guidance and is restricted
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#' SFO, FOMC and DFOP models and to the parent compound

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

@@ -1,20 +1,3 @@
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# Copyright (C) 2015  Johannes Ranke
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# Contact: jranke@uni-bremen.de
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# 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
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# the terms of the GNU General Public License as published by the Free Software
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# Foundation, either version 3 of the License, or (at your option) any later
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# version.
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# This program is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
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# details.
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# You should have received a copy of the GNU General Public License along with
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# this program. If not, see <http://www.gnu.org/licenses/>
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#' Calculate a time course of relative concentrations based on an mkinmod model
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#'
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#' @import mkin
@@ -30,19 +13,19 @@
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#' @author Johannes Ranke
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#' @examples
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#' head(pfm_degradation("SFO", DT50 = 10))
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pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50),
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                            years = 1, step_days = 1,
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                            times = seq(0, years * 365, by = step_days))
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pfm_degradation <- function(model = "SFO",
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  DT50 = 1000, parms = c(k_parent = log(2)/DT50),
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  years = 1, step_days = 1,
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  times = seq(0, years * 365, by = step_days))
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{
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  if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
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    model <- mkinmod(parent = list(type = model))
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  }
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  initial_state = c(1, rep(0, length(model$diffs) - 1))
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  names(initial_state) <- names(model$diffs)
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  time_course <- mkinpredict(model, odeparms = parms, 
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                             odeini = initial_state,
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                             outtimes = times,
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                             solution_type = ifelse(length(model$spec) == 1,
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                                                    "analytical", "deSolve"))
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    odeini = initial_state,
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    outtimes = times,
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    solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve"))
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  invisible(time_course)
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}

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Learn more Showing 1 files with coverage changes found.

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Files Coverage
R -0.32% 68.80%
Project Totals (17 files) 68.80%
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