Enable markdown and rebuild docs

21 files changed, 132 insertions, 132 deletions

diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd
index e153fbe..3ec7987 100644
--- a/man/EFSA_washoff_2017.Rd
+++ b/man/EFSA_washoff_2017.Rd
@@ -9,10 +9,10 @@ A matrix containing wash-off factors, currently only for some selected crops
 }
 \source{
 European Food Safety Authority (2017) EFSA guidance document for
-  predicting environmental concentrations of active substances of plant
-  protection products and transformation products of these active substances
-  in soil. \emph{EFSA Journal} \bold{15}(10) 4982
-  doi:10.2903/j.efsa.2017.4982
+predicting environmental concentrations of active substances of plant
+protection products and transformation products of these active substances
+in soil. \emph{EFSA Journal} \bold{15}(10) 4982
+doi:10.2903/j.efsa.2017.4982
 }
 \description{
 Subset of EFSA crop washoff default values
diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
index 53d1d3c..302aa75 100644
--- a/man/FOCUS_GW_scenarios_2012.Rd
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -11,15 +11,15 @@ An object of class \code{list} of length 2.
 FOCUS_GW_scenarios_2012
 }
 \description{
-Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The 
+Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The
 soil definitions are from page 46ff. from FOCUS (2012).
 }
 \examples{
 FOCUS_GW_scenarios_2012
 }
 \references{
-FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. 
- FOrum for the Co-ordination of pesticde fate models and their USe. 
- http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
+FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1.
+FOrum for the Co-ordination of pesticde fate models and their USe.
+http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf
 }
 \keyword{datasets}
diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd
index 02963bf..fca98e3 100644
--- a/man/FOCUS_Step_12_scenarios.Rd
+++ b/man/FOCUS_Step_12_scenarios.Rd
@@ -6,9 +6,9 @@
 \title{Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator}
 \format{
 A list containing the scenario names in a character vector called 'names',
-  the drift percentiles in a matrix called 'drift', interception percentages in
-  a matrix called 'interception' and the runoff/drainage percentages for Step 2
-  calculations in a matrix called 'rd'.
+the drift percentiles in a matrix called 'drift', interception percentages in
+a matrix called 'interception' and the runoff/drainage percentages for Step 2
+calculations in a matrix called 'rd'.
 }
 \description{
 The data were extracted from the scenario.txt file using the R code shown below.
diff --git a/man/FOMC_actual_twa.Rd b/man/FOMC_actual_twa.Rd
index a0c7284..dd8e4d3 100644
--- a/man/FOMC_actual_twa.Rd
+++ b/man/FOMC_actual_twa.Rd
@@ -5,8 +5,8 @@
 \title{Actual and maximum moving window time average concentrations for FOMC kinetics}
 \source{
 FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
-  18 December 2014, p. 251
+Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+18 December 2014, p. 251
 }
 \usage{
 FOMC_actual_twa(
diff --git a/man/GUS.Rd b/man/GUS.Rd
index cd1a332..93f52a5 100644
--- a/man/GUS.Rd
+++ b/man/GUS.Rd
@@ -36,14 +36,14 @@ be conducted under use conditions.}
 
 \item{Koc}{The sorption constant normalised to organic carbon. Gustafson
 does not mention the nonlinearity of the sorption constant commonly
-found and usually described by Freundlich sorption, therefore it is 
+found and usually described by Freundlich sorption, therefore it is
 unclear at which reference concentration the Koc should be observed
 (and if the reference concentration would be in soil or in porewater).}
 
 \item{chent}{If a chent is given with appropriate information present in its
 chyaml field, this information is used, with defaults specified below.}
 
-\item{degradation_value}{Which of the available degradation values should 
+\item{degradation_value}{Which of the available degradation values should
 be used?}
 
 \item{lab_field}{Should laboratory or field half-lives be used? This
@@ -70,7 +70,7 @@ be Koc values at a concentration of 1 mg/L in the water phase.}
 }
 \value{
 A list with the DT50 and Koc used as well as the resulting score
-  of class GUS_result
+of class GUS_result
 }
 \description{
 The groundwater ubiquity score GUS is calculated according to
diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd
index e7efd6c..391e25b 100644
--- a/man/PEC_soil.Rd
+++ b/man/PEC_soil.Rd
@@ -127,16 +127,16 @@ true for the TWA concentrations given for the same example in the EFSA guidance
 from 2017 (p. 92).
 
 According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be
-  taken into account for the EFSA 2017 scenarios, using the evaluation depth
-  (here mixing depth) as the depth of the layer from which leaching takes
-  place.  However, as the amount leaching below the evaluation depth
-  (often 5 cm) will partly be mixed back during tillage, the default in this function
-  is to use the tillage depth for the calculation of the leaching rate.
+taken into account for the EFSA 2017 scenarios, using the evaluation depth
+(here mixing depth) as the depth of the layer from which leaching takes
+place.  However, as the amount leaching below the evaluation depth
+(often 5 cm) will partly be mixed back during tillage, the default in this function
+is to use the tillage depth for the calculation of the leaching rate.
 
 If temperature information is available in the selected scenarios, as
-  e.g. in the EFSA scenarios, the DT50 for groundwater modelling
-  (destination 'PECgw') is taken from the chent object, otherwise the DT50
-  with destination 'PECsoil'.
+e.g. in the EFSA scenarios, the DT50 for groundwater modelling
+(destination 'PECgw') is taken from the chent object, otherwise the DT50
+with destination 'PECsoil'.
 }
 \examples{
 PEC_soil(100, interception = 0.25)
@@ -166,22 +166,22 @@ results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_a
 }
 \references{
 EFSA Panel on Plant Protection Products and their Residues (2012)
-  Scientific Opinion on the science behind the guidance for scenario
-  selection and scenario parameterisation for predicting environmental
-  concentrations of plant protection products in soil. \emph{EFSA Journal}
-  \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562
-
-  EFSA (European Food Safety Authority) 2017) EFSA guidance document for
-  predicting environmental concentrations of active substances of plant
-  protection products and transformation products of these active substances
-  in soil. \emph{EFSA Journal} \bold{15}(10) 4982
-  doi:10.2903/j.efsa.2017.4982
-
-  EFSA (European Food Safety Authority) (2015) EFSA guidance document for
-  predicting environmental concentrations of active substances of plant
-  protection products and transformation products of these active substances
-  in soil. \emph{EFSA Journal} \bold{13}(4) 4093
-  doi:10.2903/j.efsa.2015.4093
+Scientific Opinion on the science behind the guidance for scenario
+selection and scenario parameterisation for predicting environmental
+concentrations of plant protection products in soil. \emph{EFSA Journal}
+\bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562
+
+EFSA (European Food Safety Authority) 2017) EFSA guidance document for
+predicting environmental concentrations of active substances of plant
+protection products and transformation products of these active substances
+in soil. \emph{EFSA Journal} \bold{15}(10) 4982
+doi:10.2903/j.efsa.2017.4982
+
+EFSA (European Food Safety Authority) (2015) EFSA guidance document for
+predicting environmental concentrations of active substances of plant
+protection products and transformation products of these active substances
+in soil. \emph{EFSA Journal} \bold{13}(4) 4093
+doi:10.2903/j.efsa.2015.4093
 }
 \author{
 Johannes Ranke
diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd
index 98aa868..f3d6169 100644
--- a/man/PEC_sw_drainage_UK.Rd
+++ b/man/PEC_sw_drainage_UK.Rd
@@ -42,13 +42,13 @@ PEC_sw_drainage_UK(150, Koc = 100)
 }
 \references{
 HSE's Chemicals Regulation Division (CRD) Active substance
-  PECsw calculations (for UK specific authorisation requests)
-  \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm}
-  accessed 2019-09-27
+PECsw calculations (for UK specific authorisation requests)
+\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm}
+accessed 2019-09-27
 
-  Drainage PECs Version 1.0 (2015) Spreadsheet published at
-  \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx}
-  accessed 2019-09-27
+Drainage PECs Version 1.0 (2015) Spreadsheet published at
+\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx}
+accessed 2019-09-27
 }
 \author{
 Johannes Ranke
diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd
index 92e0f77..9fd733e 100644
--- a/man/PEC_sw_drift.Rd
+++ b/man/PEC_sw_drift.Rd
@@ -26,7 +26,7 @@ PEC_sw_drift(
 \item{drift_percentages}{Percentage drift values for which to calculate PECsw.
 'drift_data' and 'distances' if not NULL.}
 
-\item{drift_data}{Source of drift percentage data. If 'JKI', the [drift_data_JKI]
+\item{drift_data}{Source of drift percentage data. If 'JKI', the \link{drift_data_JKI}
 included in the package is used. If 'RF', the Rautmann formula is used, if
 implemented for the crop type and number of applications}
 
diff --git a/man/PEC_sw_exposit_drainage.Rd b/man/PEC_sw_exposit_drainage.Rd
index 5a543c8..e2294bf 100644
--- a/man/PEC_sw_exposit_drainage.Rd
+++ b/man/PEC_sw_exposit_drainage.Rd
@@ -5,7 +5,7 @@
 \title{Calculate PEC surface water due to drainage as in Exposit 3}
 \source{
 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}
+\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(
@@ -43,12 +43,12 @@ autumn/winter/early spring.}
 }
 \value{
 A list containing the following components
-  \describe{
-    \item{perc_runoff}{The runoff percentages for dissolved and bound substance}
-    \item{runoff}{A matrix containing dissolved and bound input for the different distances}
-    \item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
-      for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
-  }
+\describe{
+\item{perc_runoff}{The runoff percentages for dissolved and bound substance}
+\item{runoff}{A matrix containing dissolved and bound input for the different distances}
+\item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
+for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
+}
 }
 \description{
 This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file,
diff --git a/man/PEC_sw_exposit_runoff.Rd b/man/PEC_sw_exposit_runoff.Rd
index a415a63..03dbb4b 100644
--- a/man/PEC_sw_exposit_runoff.Rd
+++ b/man/PEC_sw_exposit_runoff.Rd
@@ -5,7 +5,7 @@
 \title{Calculate PEC surface water due to runoff and erosion as in Exposit 3}
 \source{
 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}
+\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(
@@ -45,12 +45,12 @@ and the bound fraction.}
 }
 \value{
 A list containing the following components
-  \describe{
-    \item{perc_runoff}{The runoff percentages for dissolved and bound substance}
-    \item{runoff}{A matrix containing dissolved and bound input for the different distances}
-    \item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
-      for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
-  }
+\describe{
+\item{perc_runoff}{The runoff percentages for dissolved and bound substance}
+\item{runoff}{A matrix containing dissolved and bound input for the different distances}
+\item{PEC_sw_runoff}{A matrix containing PEC values for dissolved and bound substance
+for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.}
+}
 }
 \description{
 This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file,
diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd
index f23423b..973b1fa 100644
--- a/man/PEC_sw_focus.Rd
+++ b/man/PEC_sw_focus.Rd
@@ -26,7 +26,7 @@ PEC_sw_focus(
 }
 \arguments{
 \item{parent}{A list containing substance specific parameters, e.g.
-conveniently generated by [chent_focus_sw].}
+conveniently generated by \link{chent_focus_sw}.}
 
 \item{rate}{The application rate in g/ha. Overriden when
 applications are given explicitly}
@@ -38,20 +38,20 @@ applications are given explicitly}
 \item{comment}{A comment for the input file}
 
 \item{met}{A list containing metabolite specific parameters.  e.g.
-conveniently generated by [chent_focus_sw].  If not NULL,
+conveniently generated by \link{chent_focus_sw}.  If not NULL,
 the PEC is calculated for this compound, not the parent.}
 
 \item{f_drift}{The fraction of the application rate reaching the waterbody
 via drift. If NA, this is derived from the scenario name and the number
 of applications via the drift data defined by the
-[FOCUS_Step_12_scenarios]}
+\link{FOCUS_Step_12_scenarios}}
 
 \item{f_rd}{The fraction of the amount applied reaching the waterbody via
-runoff/drainage. At Step 1, it is assumed to be 10%, be it the
+runoff/drainage. At Step 1, it is assumed to be 10\%, be it the
 parent or a metabolite}
 
 \item{scenario}{The name of the scenario. Must be one of the scenario
-names given in [FOCUS_Step_12_scenarios]}
+names given in \link{FOCUS_Step_12_scenarios}}
 
 \item{region}{'n' for Northern Europe or 's' for Southern Europe. If NA, only
 Step 1 PECsw are calculated}
@@ -86,11 +86,11 @@ to be used with the FOCUS calculator.
 }
 \note{
 The formulas for input to the waterbody via runoff/drainage of the
-  parent and subsequent formation of the metabolite in water is not
-  documented in the model description coming with the calculator. As one would
-  expect, this appears to be (as we get the same results) calculated by
-  multiplying the application rate with the molar weight
-  correction and the formation fraction in water/sediment systems.
+parent and subsequent formation of the metabolite in water is not
+documented in the model description coming with the calculator. As one would
+expect, this appears to be (as we get the same results) calculated by
+multiplying the application rate with the molar weight
+correction and the formation fraction in water/sediment systems.
 
 Step 2 is not implemented.
 }
@@ -107,10 +107,10 @@ PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1)
 }
 \references{
 FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
- FOrum for the Co-ordination of pesticde fate models and their USe.
- http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf
+FOrum for the Co-ordination of pesticde fate models and their USe.
+http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic\%20FOCUS_SWS_vc1.4.pdf
 
 Website of the Steps 1 and 2 calculator at the Joint Research
-  Center of the European Union:
-  http://esdac.jrc.ec.europa.eu/projects/stepsonetwo
+Center of the European Union:
+http://esdac.jrc.ec.europa.eu/projects/stepsonetwo
 }
diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd
index bdf4c4d..1652b82 100644
--- a/man/SFO_actual_twa.Rd
+++ b/man/SFO_actual_twa.Rd
@@ -5,8 +5,8 @@
 \title{Actual and maximum moving window time average concentrations for SFO kinetics}
 \source{
 FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 
-  18 December 2014, p. 251
+Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+18 December 2014, p. 251
 }
 \usage{
 SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))
diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd
index 797332b..43de457 100644
--- a/man/SSLRC_mobility_classification.Rd
+++ b/man/SSLRC_mobility_classification.Rd
@@ -11,7 +11,7 @@ SSLRC_mobility_classification(Koc)
 }
 \value{
 A list containing the classification and the percentage of the
-  compound transported per 10 mm drain water
+compound transported per 10 mm drain water
 }
 \description{
 This implements the method specified in the UK data requirements handbook and was
@@ -23,13 +23,13 @@ SSLRC_mobility_classification(10000)
 }
 \references{
 HSE's Chemicals Regulation Division (CRD) Active substance
-  PECsw calculations (for UK specific authorisation requests)
-  \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm}
-  accessed 2019-09-27
+PECsw calculations (for UK specific authorisation requests)
+\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm}
+accessed 2019-09-27
 
-  Drainage PECs Version 1.0 (2015) Spreadsheet published at
-  \url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx}
-  accessed 2019-09-27
+Drainage PECs Version 1.0 (2015) Spreadsheet published at
+\url{https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC\%20sw-sed\%20(drainage).xlsx}
+accessed 2019-09-27
 }
 \author{
 Johannes Ranke
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index de83ec2..0923f10 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -94,7 +94,7 @@ Create a TOXSWA_cwa object from a file
 \if{html}{\out{<a id="method-TOXSWA_cwa-moving_windows"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-moving_windows}{}}}
 \subsection{Method \code{moving_windows()}}{
-Add to the `windows` field described above.
+Add to the \code{windows} field described above.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
 }
@@ -115,7 +115,7 @@ suspended matter will be used.}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-get_events}{}}}
 \subsection{Method \code{get_events()}}{
 Populate a datataframe with event information for the specified
-threshold value.  The resulting dataframe is stored in the `events`
+threshold value.  The resulting dataframe is stored in the \code{events}
 field of the object.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
@@ -136,7 +136,7 @@ suspended matter will be used.}
 \if{html}{\out{<a id="method-TOXSWA_cwa-print"></a>}}
 \if{latex}{\out{\hypertarget{method-TOXSWA_cwa-print}{}}}
 \subsection{Method \code{print()}}{
-Print a `TOXSWA_cwa` object
+Print a \code{TOXSWA_cwa} object
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
 }
diff --git a/man/TSCF.Rd b/man/TSCF.Rd
index e4cefdc..71cd692 100644
--- a/man/TSCF.Rd
+++ b/man/TSCF.Rd
@@ -31,7 +31,7 @@ legend("topright", lty = 1:2, bty = "n",
 }
 \references{
 FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments.
- Version 2.2, May 2014
+Version 2.2, May 2014
 Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake
 by plant roots. Environ. Sci. Technol 43, 324 - 329
 }
diff --git a/man/endpoint.Rd b/man/endpoint.Rd
index 2b66c21..41c6a24 100644
--- a/man/endpoint.Rd
+++ b/man/endpoint.Rd
@@ -53,10 +53,10 @@ soil_sorption(
 
 \item{redox}{If not NA, are we looking for aerobic or anaerobic data}
 
-\item{value}{The name of the value we want. The list given in the 
+\item{value}{The name of the value we want. The list given in the
 usage section is not exclusive}
 
-\item{aggregator}{The aggregator function. Can be mean, 
+\item{aggregator}{The aggregator function. Can be mean,
 \code{\link{geomean}}, or identity, for example.}
 
 \item{raw}{Should the number(s) be returned as stored in the chent
@@ -71,10 +71,10 @@ about precision?}
 }
 \value{
 The result from applying the aggregator function to
-  the values converted to a numeric vector, rounded to the
-  given number of significant digits, or, if raw = TRUE,
-  the values as a character value, retaining any implicit
-  information on precision that may be present.
+the values converted to a numeric vector, rounded to the
+given number of significant digits, or, if raw = TRUE,
+the values as a character value, retaining any implicit
+information on precision that may be present.
 }
 \description{
 R6 class objects of class chent represent chemical entities
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 0a8dcca..43ad50e 100644
--- a/man/max_twa.Rd
+++ b/man/max_twa.Rd
@@ -32,10 +32,10 @@ max_twa(pred_FOMC)
 }
 \references{
 FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
 \code{\link{twa}}
diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd
index 0bd2827..a3d19a6 100644
--- a/man/perc_runoff_exposit.Rd
+++ b/man/perc_runoff_exposit.Rd
@@ -5,18 +5,18 @@
 \title{Runoff loss percentages as used in Exposit 3}
 \format{
 A data frame with percentage values for the dissolved fraction and the fraction
-  bound to eroding particles, with Koc classes used as row names
-  \describe{
-    \item{Koc_lower_bound}{The lower bound of the Koc class}
-    \item{dissolved}{The percentage of the applied substance transferred to an
-      adjacent water body in the dissolved phase}
-    \item{bound}{The percentage of the applied substance transferred to an
-      adjacent water body bound to eroding particles}
-  }
+bound to eroding particles, with Koc classes used as row names
+\describe{
+\item{Koc_lower_bound}{The lower bound of the Koc class}
+\item{dissolved}{The percentage of the applied substance transferred to an
+adjacent water body in the dissolved phase}
+\item{bound}{The percentage of the applied substance transferred to an
+adjacent water body bound to eroding particles}
+}
 }
 \source{
 Excel 3.02 spreadsheet available from
-  \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
+\url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
 }
 \description{
 A table of the loss percentages used in Exposit 3 for the twelve different Koc classes
diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd
index 93016b7..b9ea059 100644
--- a/man/perc_runoff_reduction_exposit.Rd
+++ b/man/perc_runoff_reduction_exposit.Rd
@@ -9,17 +9,17 @@ A named list of data frames with reduction percentage values for the
 dissolved fraction and the fraction bound to eroding particles, with
 vegetated buffer widths as row names. The names of the list items are the Exposit versions
 from which the values were taken.
-  \describe{
-    \item{dissolved}{The reduction percentage for the dissolved phase}
-    \item{bound}{The reduction percentage for the particulate phase}
-  }
+\describe{
+\item{dissolved}{The reduction percentage for the dissolved phase}
+\item{bound}{The reduction percentage for the particulate phase}
+}
 }
 \source{
 Excel 3.02 spreadsheet available from
-  \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
+\url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html}
 
-  Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published).
-  The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.
+Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published).
+The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.
 }
 \usage{
 perc_runoff_reduction_exposit
diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd
index dfad4aa..0e7f374 100644
--- a/man/soil_scenario_data_EFSA_2015.Rd
+++ b/man/soil_scenario_data_EFSA_2015.Rd
@@ -5,20 +5,20 @@
 \alias{soil_scenario_data_EFSA_2015}
 \title{Properties of the predefined scenarios from the EFSA guidance from 2015}
 \format{
-A data frame with one row for each scenario. Row names are the scenario codes, 
-  e.g. CTN for the Northern scenario for the total concentration in soil. Columns are 
-  mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
+A data frame with one row for each scenario. Row names are the scenario codes,
+e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
+mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
 }
 \source{
 EFSA (European Food Safety Authority) (2015)
-  EFSA guidance document for predicting environmental concentrations
-  of active substances of plant protection products and transformation products of these
-  active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093
-  doi:10.2903/j.efsa.2015.4093
+EFSA guidance document for predicting environmental concentrations
+of active substances of plant protection products and transformation products of these
+active substances in soil. \emph{EFSA Journal} \bold{13}(4) 4093
+doi:10.2903/j.efsa.2015.4093
 }
 \description{
-Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the 
-concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the 
+Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the
+concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the
 scenario and model adjustment factors from p. 15 and p. 17 are included.
 }
 \examples{
diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd
index f6de290..626ada3 100644
--- a/man/soil_scenario_data_EFSA_2017.Rd
+++ b/man/soil_scenario_data_EFSA_2017.Rd
@@ -5,20 +5,20 @@
 \alias{soil_scenario_data_EFSA_2017}
 \title{Properties of the predefined scenarios from the EFSA guidance from 2017}
 \format{
-A data frame with one row for each scenario. Row names are the scenario codes, 
-  e.g. CTN for the Northern scenario for the total concentration in soil. Columns are 
-  mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
+A data frame with one row for each scenario. Row names are the scenario codes,
+e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
+mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
 }
 \source{
 EFSA (European Food Safety Authority) (2017)
-  EFSA guidance document for predicting environmental concentrations
-  of active substances of plant protection products and transformation products of these
-  active substances in soil. \emph{EFSA Journal} \bold{15}(10) 4982
-  doi:10.2903/j.efsa.2017.4982
+EFSA guidance document for predicting environmental concentrations
+of active substances of plant protection products and transformation products of these
+active substances in soil. \emph{EFSA Journal} \bold{15}(10) 4982
+doi:10.2903/j.efsa.2017.4982
 }
 \description{
-Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the 
-concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the 
+Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the
+concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the
 scenario and model adjustment factors from p. 16 and p. 18 are included.
 }
 \examples{