Make na.rm = FALSE the default for geomean()

This makes more sense and is in line with mean() from base R. Adapt
tests and update docs.

22 files changed, 296 insertions, 100 deletions

diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd
index f58dea7..0547d61 100644
--- a/man/FOCUS_Step_12_scenarios.Rd
+++ b/man/FOCUS_Step_12_scenarios.Rd
@@ -19,14 +19,14 @@ The text file is not included in the package as its licence is not clear.
   scenario_path <- "inst/extdata/FOCUS_Step_12_scenarios.txt"
   scenarios <- readLines(scenario_path)[9:38]
   FOCUS_Step_12_scenarios <- list()
-  sce <- read.table(text = scenarios, sep = "\\t", header = TRUE, check.names = FALSE,
+  sce <- read.table(text = scenarios, sep = "\t", header = TRUE, check.names = FALSE,
     stringsAsFactors = FALSE)
   FOCUS_Step_12_scenarios$names = sce$Crop
   rownames(sce) <- sce$Crop
   FOCUS_Step_12_scenarios$drift = sce[, 3:11]
   FOCUS_Step_12_scenarios$interception = sce[, 12:15]
   sce_2 <- readLines(scenario_path)[41:46]
-  rd <- read.table(text = sce_2, sep = "\\t")[1:2]
+  rd <- read.table(text = sce_2, sep = "\t")[1:2]
   rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE)
   dimnames(rd_mat) = list(Time = c("Oct-Feb", "Mar-May", "Jun-Sep"),
                           Region = c("North", "South"))
diff --git a/man/FOMC_actual_twa.Rd b/man/FOMC_actual_twa.Rd
index 2c40048..a0c7284 100644
--- a/man/FOMC_actual_twa.Rd
+++ b/man/FOMC_actual_twa.Rd
@@ -9,8 +9,11 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
   18 December 2014, p. 251
 }
 \usage{
-FOMC_actual_twa(alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7,
-  14, 21, 28, 42, 50, 100))
+FOMC_actual_twa(
+  alpha = 1.0001,
+  beta = 10,
+  times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)
+)
 }
 \arguments{
 \item{alpha}{Parameter of the FOMC model}
diff --git a/man/GUS.Rd b/man/GUS.Rd
index adc1bb3..cd1a332 100644
--- a/man/GUS.Rd
+++ b/man/GUS.Rd
@@ -11,10 +11,16 @@ GUS(...)
 
 \method{GUS}{numeric}(DT50, Koc, ...)
 
-\method{GUS}{chent}(chent, degradation_value = "DT50ref",
-  lab_field = "laboratory", redox = "aerobic",
-  sorption_value = "Kfoc", degradation_aggregator = geomean,
-  sorption_aggregator = geomean, ...)
+\method{GUS}{chent}(
+  chent,
+  degradation_value = "DT50ref",
+  lab_field = "laboratory",
+  redox = "aerobic",
+  sorption_value = "Kfoc",
+  degradation_aggregator = geomean,
+  sorption_aggregator = geomean,
+  ...
+)
 
 \method{print}{GUS_result}(x, ..., digits = 1)
 }
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index a9e6c49..a198f24 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -4,14 +4,30 @@
 \alias{PEC_soil}
 \title{Calculate predicted environmental concentrations in soil}
 \usage{
-PEC_soil(rate, rate_units = "g/ha", interception = 0,
-  mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L",
-  interval = NA, n_periods = Inf, tillage_depth = 20,
-  leaching_depth = tillage_depth, crop = "annual",
-  cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA,
-  Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL,
+PEC_soil(
+  rate,
+  rate_units = "g/ha",
+  interception = 0,
+  mixing_depth = 5,
+  PEC_units = "mg/kg",
+  PEC_pw_units = "mg/L",
+  interval = NA,
+  n_periods = Inf,
+  tillage_depth = 20,
+  leaching_depth = tillage_depth,
+  crop = "annual",
+  cultivation = FALSE,
+  chent = NA,
+  DT50 = NA,
+  FOMC = NA,
+  Koc = NA,
+  Kom = Koc/1.724,
+  t_avg = 0,
+  t_act = NULL,
   scenarios = c("default", "EFSA_2017", "EFSA_2015"),
-  leaching = scenarios == "EFSA_2017", porewater = FALSE)
+  leaching = scenarios == "EFSA_2017",
+  porewater = FALSE
+)
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index c9f8ed4..98aa868 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -4,9 +4,15 @@
 \alias{PEC_sw_drainage_UK}
 \title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
 \usage{
-PEC_sw_drainage_UK(rate, interception = 0, Koc,
-  latest_application = NULL, soil_DT50 = NULL, model = NULL,
-  model_parms = NULL)
+PEC_sw_drainage_UK(
+  rate,
+  interception = 0,
+  Koc,
+  latest_application = NULL,
+  soil_DT50 = NULL,
+  model = NULL,
+  model_parms = NULL
+)
 }
 \arguments{
 \item{rate}{Application rate in g/ha}
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index dfc3f39..cde3c78 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -4,10 +4,17 @@
 \alias{PEC_sw_drift}
 \title{Calculate predicted environmental concentrations in surface water due to drift}
 \usage{
-PEC_sw_drift(rate, applications = 1, water_depth = 30,
-  drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
-  distances = c(1, 5, 10, 20), rate_units = "g/ha",
-  PEC_units = "µg/L")
+PEC_sw_drift(
+  rate,
+  applications = 1,
+  water_depth = 30,
+  drift_percentages = NULL,
+  drift_data = "JKI",
+  crop = "Ackerbau",
+  distances = c(1, 5, 10, 20),
+  rate_units = "g/ha",
+  PEC_units = "µg/L"
+)
 }
 \arguments{
 \item{rate}{Application rate in units specified below}
diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd
index 237d8cf..5a543c8 100644
--- a/man/PEC_sw_exposit_drainage.Rd
+++ b/man/PEC_sw_exposit_drainage.Rd
@@ -8,10 +8,17 @@ Excel 3.02 spreadsheet available from
   \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3}
 }
 \usage{
-PEC_sw_exposit_drainage(rate, interception = 0, Koc = NA,
-  mobility = c(NA, "low", "high"), DT50 = Inf, t_drainage = 3,
-  V_ditch = 30, V_drainage = c(spring = 10, autumn = 100),
-  dilution = 2)
+PEC_sw_exposit_drainage(
+  rate,
+  interception = 0,
+  Koc = NA,
+  mobility = c(NA, "low", "high"),
+  DT50 = Inf,
+  t_drainage = 3,
+  V_ditch = 30,
+  V_drainage = c(spring = 10, autumn = 100),
+  dilution = 2
+)
 }
 \arguments{
 \item{rate}{The application rate in g/ha}
diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd
index c73270b..a415a63 100644
--- a/man/PEC_sw_exposit_runoff.Rd
+++ b/man/PEC_sw_exposit_runoff.Rd
@@ -8,9 +8,17 @@ Excel 3.02 spreadsheet available from
   \url{https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3}
 }
 \usage{
-PEC_sw_exposit_runoff(rate, interception = 0, Koc, DT50 = Inf,
-  t_runoff = 3, exposit_reduction_version = c("3.02", "3.01a",
-  "3.01a2", "2.0"), V_ditch = 30, V_event = 100, dilution = 2)
+PEC_sw_exposit_runoff(
+  rate,
+  interception = 0,
+  Koc,
+  DT50 = Inf,
+  t_runoff = 3,
+  exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"),
+  V_ditch = 30,
+  V_event = 100,
+  dilution = 2
+)
 }
 \arguments{
 \item{rate}{The application rate in g/ha}
diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index 836ed86..3ad1ad0 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -4,12 +4,25 @@
 \alias{PEC_sw_focus}
 \title{Calculate PEC surface water at FOCUS Step 1}
 \usage{
-PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL,
-  f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
-  region = c("n", "s"), season = c(NA, "of", "mm", "js"),
-  interception = c("no interception", "minimal crop cover",
-  "average crop cover", "full canopy"), met_form_water = TRUE,
-  txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)
+PEC_sw_focus(
+  parent,
+  rate,
+  n = 1,
+  i = NA,
+  comment = "",
+  met = NULL,
+  f_drift = NA,
+  f_rd = 0.1,
+  scenario = FOCUS_Step_12_scenarios$names,
+  region = c("n", "s"),
+  season = c(NA, "of", "mm", "js"),
+  interception = c("no interception", "minimal crop cover", "average crop cover",
+    "full canopy"),
+  met_form_water = TRUE,
+  txt_file = "pesticide.txt",
+  overwrite = FALSE,
+  append = TRUE
+)
 }
 \arguments{
 \item{parent}{A list containing substance specific parameters, e.g.
diff --git a/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd
index 1feb146..bc82ee3 100644
--- a/man/PEC_sw_sed.Rd
+++ b/man/PEC_sw_sed.Rd
@@ -5,9 +5,15 @@
 \title{Calculate predicted environmental concentrations in sediment from surface
 water concentrations}
 \usage{
-PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
-  sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
-  PEC_sed_units = c("µg/kg", "mg/kg"))
+PEC_sw_sed(
+  PEC_sw,
+  percentage = 100,
+  method = "percentage",
+  sediment_depth = 5,
+  water_depth = 30,
+  sediment_density = 1.3,
+  PEC_sed_units = c("µg/kg", "mg/kg")
+)
 }
 \arguments{
 \item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for
diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd
index 30039f2..bdf4c4d 100644
--- a/man/SFO_actual_twa.Rd
+++ b/man/SFO_actual_twa.Rd
@@ -9,8 +9,7 @@ FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
   18 December 2014, p. 251
 }
 \usage{
-SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42,
-  50, 100))
+SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
 }
 \arguments{
 \item{DT50}{The half-life.}
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index f073180..eb3fe38 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -5,31 +5,10 @@
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
 \format{An \code{\link{R6Class}} generator object.}
-\usage{
-TOXSWA_cwa
-}
 \description{
 An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
 Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}.
 }
-\section{Fields}{
-
-\describe{
-\item{\code{filename}}{Length one character vector.}
-
-\item{\code{basedir}}{Length one character vector.}
-
-\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
-
-\item{\code{cwas}}{Dataframe holding the concentrations.}
-
-\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
-
-\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max)
-and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
-for the requested moving window sizes in days.}
-}}
-
 \section{Methods}{
 
 \describe{
@@ -57,3 +36,88 @@ H_sw_R1_stream$moving_windows(c(7, 21))
 print(H_sw_R1_stream)
 }
 \keyword{data}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{filename}}{Length one character vector.}
+
+\item{\code{basedir}}{Length one character vector.}
+
+\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.}
+
+\item{\code{cwas}}{Dataframe holding the concentrations.}
+
+\item{\code{events}}{List of dataframes holding the event statistics for each threshold.}
+
+\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max)
+and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
+for the requested moving window sizes in days.}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{TOXSWA_cwa$new()}}
+\item \href{#method-moving_windows}{\code{TOXSWA_cwa$moving_windows()}}
+\item \href{#method-get_events}{\code{TOXSWA_cwa$get_events()}}
+\item \href{#method-print}{\code{TOXSWA_cwa$print()}}
+\item \href{#method-clone}{\code{TOXSWA_cwa$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new(
+  filename,
+  basedir,
+  zipfile = NULL,
+  segment = "last",
+  substance = "parent",
+  total = FALSE
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-moving_windows"></a>}}
+\subsection{Method \code{moving_windows()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_events"></a>}}
+\subsection{Method \code{get_events()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-print"></a>}}
+\subsection{Method \code{print()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/man/chent_focus_sw.Rd b/man/chent_focus_sw.Rd
index 9830ade..5f595d8 100644
--- a/man/chent_focus_sw.Rd
+++ b/man/chent_focus_sw.Rd
@@ -4,9 +4,18 @@
 \alias{chent_focus_sw}
 \title{Create a chemical compound object for FOCUS Step 1 calculations}
 \usage{
-chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA,
-  DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA,
-  max_soil = 1, max_ws = 1)
+chent_focus_sw(
+  name,
+  Koc,
+  DT50_ws = NA,
+  DT50_soil = NA,
+  DT50_water = NA,
+  DT50_sediment = NA,
+  cwsat = 1000,
+  mw = NA,
+  max_soil = 1,
+  max_ws = 1
+)
 }
 \arguments{
 \item{name}{Length one character vector containing the name}
diff --git a/man/endpoint.Rd b/man/endpoint.Rd
index 204905b..2b66c21 100644
--- a/man/endpoint.Rd
+++ b/man/endpoint.Rd
@@ -8,23 +8,39 @@
 \alias{soil_sorption}
 \title{Retrieve endpoint information from the chyaml field of a chent object}
 \usage{
-endpoint(chent, medium = "soil", type = c("degradation", "sorption"),
-  lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic",
-  "anaerobic"), value = c("DT50ref", "Kfoc", "N"),
-  aggregator = geomean, raw = FALSE, signif = 3)
+endpoint(
+  chent,
+  medium = "soil",
+  type = c("degradation", "sorption"),
+  lab_field = c(NA, "laboratory", "field"),
+  redox = c(NA, "aerobic", "anaerobic"),
+  value = c("DT50ref", "Kfoc", "N"),
+  aggregator = geomean,
+  raw = FALSE,
+  signif = 3
+)
 
-soil_DT50(chent, aggregator = geomean, signif = 3,
-  lab_field = "laboratory", value = "DT50ref", redox = "aerobic",
-  raw = FALSE)
+soil_DT50(
+  chent,
+  aggregator = geomean,
+  signif = 3,
+  lab_field = "laboratory",
+  value = "DT50ref",
+  redox = "aerobic",
+  raw = FALSE
+)
 
-soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc",
-  raw = FALSE)
+soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
 
 soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
 
-soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc =
-  geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3),
-  raw = FALSE)
+soil_sorption(
+  chent,
+  values = c("Kfoc", "N"),
+  aggregators = c(Kfoc = geomean, Koc = geomean, N = mean),
+  signif = c(Kfoc = 3, N = 3),
+  raw = FALSE
+)
 }
 \arguments{
 \item{chent}{The chent object to get the information from}
diff --git a/man/geomean.Rd b/man/geomean.Rd
index 2887929..506e64d 100644
--- a/man/geomean.Rd
+++ b/man/geomean.Rd
@@ -4,7 +4,7 @@
 \alias{geomean}
 \title{Calculate the geometric mean}
 \usage{
-geomean(x, na.rm = TRUE)
+geomean(x, na.rm = FALSE)
 }
 \arguments{
 \item{x}{Vector of numbers}
@@ -17,8 +17,9 @@ The geometric mean
 \description{
 Based on some posts in a thread on Stackoverflow
 \url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in}
-This function checks for negative values, removes NA values per default and
-returns 0 if at least one element of the vector is 0.
+This function returns NA if NA values are present and na.rm = FALSE
+(default). If negative values are present, it gives an error message.
+If at least one element of the vector is 0, it returns 0.
 }
 \examples{
 geomean(c(1, 3, 9))
diff --git a/man/one_box.Rd b/man/one_box.Rd
index 3c34dae..a60aa39 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -11,11 +11,9 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 
 \method{one_box}{numeric}(x, ini = 1, ..., t_end = 100, res = 0.01)
 
-\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100,
-  res = 0.01)
+\method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
 
-\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100,
-  res = 0.01)
+\method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01)
 }
 \arguments{
 \item{x}{When numeric, this is the half-life to be used for an exponential
diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd
index fdc99fe..6684fa4 100644
--- a/man/pfm_degradation.Rd
+++ b/man/pfm_degradation.Rd
@@ -4,9 +4,14 @@
 \alias{pfm_degradation}
 \title{Calculate a time course of relative concentrations based on an mkinmod model}
 \usage{
-pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
-  log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365,
-  by = step_days))
+pfm_degradation(
+  model = "SFO",
+  DT50 = 1000,
+  parms = c(k_parent_sink = log(2)/DT50),
+  years = 1,
+  step_days = 1,
+  times = seq(0, years * 365, by = step_days)
+)
 }
 \arguments{
 \item{model}{The degradation model to be used. Either a parent only model like
diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd
index f06d3c7..7eeb3fc 100644
--- a/man/plot.TOXSWA_cwa.Rd
+++ b/man/plot.TOXSWA_cwa.Rd
@@ -4,10 +4,18 @@
 \alias{plot.TOXSWA_cwa}
 \title{Plot TOXSWA surface water concentrations}
 \usage{
-\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t",
-  "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default",
-  add = FALSE, threshold_factor = 1000, thin_low = 1,
-  total = FALSE, LC_TIME = "C", ...)
+\method{plot}{TOXSWA_cwa}(
+  x,
+  time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"),
+  xlab = "default",
+  ylab = "default",
+  add = FALSE,
+  threshold_factor = 1000,
+  thin_low = 1,
+  total = FALSE,
+  LC_TIME = "C",
+  ...
+)
 }
 \arguments{
 \item{x}{The TOXSWA_cwa object to be plotted.}
diff --git a/man/plot.one_box.Rd b/man/plot.one_box.Rd
index a212c11..35e7bf7 100644
--- a/man/plot.one_box.Rd
+++ b/man/plot.one_box.Rd
@@ -4,9 +4,16 @@
 \alias{plot.one_box}
 \title{Plot time series of decline data}
 \usage{
-\method{plot}{one_box}(x, xlim = range(time(x)), ylim = c(0, max(x)),
-  xlab = "Time", ylab = "Residue", max_twa = NULL,
-  max_twa_var = dimnames(x)[[2]][1], ...)
+\method{plot}{one_box}(
+  x,
+  xlim = range(time(x)),
+  ylim = c(0, max(x)),
+  xlab = "Time",
+  ylab = "Residue",
+  max_twa = NULL,
+  max_twa_var = dimnames(x)[[2]][1],
+  ...
+)
 }
 \arguments{
 \item{x}{The object of type \code{\link{one_box}} to be plotted}
diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd
index ccd403a..b6ee4f6 100644
--- a/man/read.TOXSWA_cwa.Rd
+++ b/man/read.TOXSWA_cwa.Rd
@@ -4,9 +4,16 @@
 \alias{read.TOXSWA_cwa}
 \title{Read TOXSWA surface water concentrations}
 \usage{
-read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL,
-  segment = "last", substance = "parent", total = FALSE,
-  windows = NULL, thresholds = NULL)
+read.TOXSWA_cwa(
+  filename,
+  basedir = ".",
+  zipfile = NULL,
+  segment = "last",
+  substance = "parent",
+  total = FALSE,
+  windows = NULL,
+  thresholds = NULL
+)
 }
 \arguments{
 \item{filename}{The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd
index 007f00d..44ab2be 100644
--- a/man/sawtooth.Rd
+++ b/man/sawtooth.Rd
@@ -4,8 +4,12 @@
 \alias{sawtooth}
 \title{Create decline time series for multiple applications}
 \usage{
-sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0,
-  (n - 1) * i, length.out = n), amount = 1))
+sawtooth(
+  x,
+  n = 1,
+  i = 365,
+  applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1)
+)
 }
 \arguments{
 \item{x}{A \code{\link{one_box}} object}
diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
index 47b7e33..7135d0d 100644
--- a/man/set_nd_nq.Rd
+++ b/man/set_nd_nq.Rd
@@ -7,8 +7,14 @@
 \usage{
 set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
 
-set_nd_nq_focus(res_raw, lod, loq = NA, set_first_sample_nd = TRUE,
-  first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE)
+set_nd_nq_focus(
+  res_raw,
+  lod,
+  loq = NA,
+  set_first_sample_nd = TRUE,
+  first_sample_nd_value = 0,
+  ignore_below_loq_after_first_nd = TRUE
+)
 }
 \arguments{
 \item{res_raw}{Character vector of a residue time series, or matrix of