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