Remove copyright headers, update TOXSWA_cwa test

- The window column of the windows component of a TOXSWA_cwa object is not
a factor any more, but a character vector.
- testthat::expect_equal_to_reference is replaced by
testthat::expect_known_output, so we can have git diff show what has
changed

11 files changed, 5 insertions, 192 deletions

diff --git a/R/FOMC_actual_twa.R b/R/FOMC_actual_twa.R
index dc869b5..0ccf315 100644
--- a/R/FOMC_actual_twa.R
+++ b/R/FOMC_actual_twa.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2018  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Actual and maximum moving window time average concentrations for FOMC kinetics
 #'
 #' @param alpha Parameter of the FOMC model
diff --git a/R/GUS.R b/R/GUS.R
index 4a6532d..040857a 100644
--- a/R/GUS.R
+++ b/R/GUS.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Groundwater ubiquity score based on Gustafson (1989)
 #' 
 #' The groundwater ubiquity score GUS is calculated according to
diff --git a/R/PEC_soil.R b/R/PEC_soil.R
index 541184f..b29ff13 100644
--- a/R/PEC_soil.R
+++ b/R/PEC_soil.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015,2016,2018,2019  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 # Register global variables
 if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier",
                                                        "soil_scenario_data_EFSA_2015",
diff --git a/R/PEC_sw_drainage_UK.R b/R/PEC_sw_drainage_UK.R
index 3be4c97..d773f40 100644
--- a/R/PEC_sw_drainage_UK.R
+++ b/R/PEC_sw_drainage_UK.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
 #'
 #' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
diff --git a/R/PEC_sw_drift.R b/R/PEC_sw_drift.R
index 261706c..6fcaecf 100644
--- a/R/PEC_sw_drift.R
+++ b/R/PEC_sw_drift.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Calculate predicted environmental concentrations in surface water due to drift
 #'
 #' This is a basic, vectorised form of a simple calculation of a contaminant
diff --git a/R/PEC_sw_sed.R b/R/PEC_sw_sed.R
index a4a3d6a..2865ab7 100644
--- a/R/PEC_sw_sed.R
+++ b/R/PEC_sw_sed.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Calculate predicted environmental concentrations in sediment from surface
 #' water concentrations
 #'
diff --git a/R/SFO_actual_twa.R b/R/SFO_actual_twa.R
index 0d2015b..63a53f3 100644
--- a/R/SFO_actual_twa.R
+++ b/R/SFO_actual_twa.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015,2018  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Actual and maximum moving window time average concentrations for SFO kinetics
 #'
 #' @param DT50 The half-life.
diff --git a/R/SSLRC_mobility_classification.R b/R/SSLRC_mobility_classification.R
index 602f166..b78de98 100644
--- a/R/SSLRC_mobility_classification.R
+++ b/R/SSLRC_mobility_classification.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015,2018,2019  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Determine the SSLRC mobility classification for a chemical substance from its Koc
 #'
 #' This implements the method specified in the UK data requirements handbook and was
diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R
index 5b1e8f2..42cdd35 100644
--- a/R/TOXSWA_cwa.R
+++ b/R/TOXSWA_cwa.R
@@ -1,19 +1,3 @@
-# Copyright (C) 2014,2015,2016,2017,2018  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
 if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa"))
 
 #' Read TOXSWA surface water concentrations
diff --git a/R/geomean.R b/R/geomean.R
index 04328c8..34c5caf 100644
--- a/R/geomean.R
+++ b/R/geomean.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015,2020  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Calculate the geometric mean
 #'
 #' Based on some posts in a thread on Stackoverflow
diff --git a/R/twa.R b/R/twa.R
index 59fc73a..886351d 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -1,28 +1,10 @@
-# Copyright (C) 2016,2017  Johannes Ranke
-
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program 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/>
-
 #' Create a time series of decline data
 #'
 #' @param x When numeric, this is the half-life to be used for an exponential
 #'   decline. When a character string specifying a parent decline model is given
 #'   e.g. \code{FOMC}, \code{parms} must contain the corresponding parameters.
 #'   If x is an \code{\link{mkinfit}} object, the decline is calculated from this
-#'   object.  
+#'   object.
 #' @param ini The initial amount. If x is an \code{\link{mkinfit}} object, and
 #'   ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 #'   must be numeric. If it has length one, it is used for the parent and
@@ -93,7 +75,7 @@ one_box.character <- function(x, ini = 1, parms, ...,
 
   t_out <- seq(0, t_end, by = res)
   pred <- mkinpredict(m, odeparms = parms, odeini = c(parent = ini),
-                      outtimes = t_out, solution_type = "analytical")[-1]
+    outtimes = t_out, solution_type = "analytical")[, -1, drop = FALSE]
   result <- ts(pred, 0, t_end, frequency = 1/res)
   class(result) <- c("one_box", "ts")
   return(result)
@@ -118,7 +100,7 @@ one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) {
   else solution_type = "deSolve"
 
   tmp <- mkinpredict(fit$mkinmod, odeparms = fit$bparms.ode, odeini = odeini,
-    outtimes = t_out, solution_type = solution_type)[-1]
+    outtimes = t_out, solution_type = solution_type)[, -1, drop = FALSE]
   result <- ts(tmp, 0, t_end, frequency = 1/res)
   class(result) <- c("one_box", "ts")
   return(result)
@@ -172,7 +154,7 @@ plot.one_box <- function(x,
 
 #' Create decline time series for multiple applications
 #'
-#' If the application pattern is specified in \code{applications}, 
+#' If the application pattern is specified in \code{applications},
 #' \code{n} and \code{i} are disregarded.
 #' @param x A \code{\link{one_box}} object
 #' @param n The number of applications. If \code{applications} is specified, \code{n} is ignored
@@ -260,7 +242,7 @@ twa.one_box <- function(x, window = 21)
 #' for finding the maximum. It is therefore recommended to check this using
 #' \code{\link{plot.one_box}} using the window size for the argument
 #' \code{max_twa}.
-#' 
+#'
 #' The method working directly on fitted \code{\link{mkinfit}} objects uses the
 #' equations given in the PEC soil section of the FOCUS guidance and is restricted
 #' SFO, FOMC and DFOP models and to the parent compound