TSCF estimation equations, update docs

Briggs et al. (1982) and Dettenmaier et al. (2009)

11 files changed, 78 insertions, 16 deletions

diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd
index f2e8c1c..2334d7f 100644
--- a/man/EFSA_GW_interception_2014.Rd
+++ b/man/EFSA_GW_interception_2014.Rd
@@ -4,7 +4,9 @@
 \name{EFSA_GW_interception_2014}
 \alias{EFSA_GW_interception_2014}
 \title{Subset of EFSA crop interception default values for groundwater modelling}
-\format{A matrix containing interception values, currently only for some selected crops}
+\format{
+A matrix containing interception values, currently only for some selected crops
+}
 \source{
 European Food Safety Authority (2014) EFSA Guidance Document for
 evaluating laboratory and field dissipation studies to obtain DegT50 values
diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd
index b1ab30f..e153fbe 100644
--- a/man/EFSA_washoff_2017.Rd
+++ b/man/EFSA_washoff_2017.Rd
@@ -4,7 +4,9 @@
 \name{EFSA_washoff_2017}
 \alias{EFSA_washoff_2017}
 \title{Subset of EFSA crop washoff default values}
-\format{A matrix containing wash-off factors, currently only for some selected crops}
+\format{
+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
diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd
index 4529816..53d1d3c 100644
--- a/man/FOCUS_GW_scenarios_2012.Rd
+++ b/man/FOCUS_GW_scenarios_2012.Rd
@@ -4,7 +4,9 @@
 \name{FOCUS_GW_scenarios_2012}
 \alias{FOCUS_GW_scenarios_2012}
 \title{A very small subset of the FOCUS Groundwater scenario definitions}
-\format{An object of class \code{list} of length 2.}
+\format{
+An object of class \code{list} of length 2.
+}
 \usage{
 FOCUS_GW_scenarios_2012
 }
diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd
index 0547d61..02963bf 100644
--- a/man/FOCUS_Step_12_scenarios.Rd
+++ b/man/FOCUS_Step_12_scenarios.Rd
@@ -4,10 +4,12 @@
 \name{FOCUS_Step_12_scenarios}
 \alias{FOCUS_Step_12_scenarios}
 \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',
+\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'.}
+  calculations in a matrix called 'rd'.
+}
 \description{
 The data were extracted from the scenario.txt file using the R code shown below.
 The text file is not included in the package as its licence is not clear.
diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd
index eb3fe38..6a95a0b 100644
--- a/man/TOXSWA_cwa.Rd
+++ b/man/TOXSWA_cwa.Rd
@@ -4,7 +4,9 @@
 \name{TOXSWA_cwa}
 \alias{TOXSWA_cwa}
 \title{R6 class for holding TOXSWA water concentration data and associated statistics}
-\format{An \code{\link{R6Class}} generator object.}
+\format{
+An \code{\link{R6Class}} generator object.
+}
 \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}}.
@@ -67,6 +69,7 @@ for the requested moving window sizes in days.}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
 \subsection{Method \code{new()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new(
@@ -82,6 +85,7 @@ for the requested moving window sizes in days.}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-moving_windows"></a>}}
+\if{latex}{\out{\hypertarget{method-moving_windows}{}}}
 \subsection{Method \code{moving_windows()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}}
@@ -90,6 +94,7 @@ for the requested moving window sizes in days.}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-get_events"></a>}}
+\if{latex}{\out{\hypertarget{method-get_events}{}}}
 \subsection{Method \code{get_events()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}}
@@ -98,6 +103,7 @@ for the requested moving window sizes in days.}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-print"></a>}}
+\if{latex}{\out{\hypertarget{method-print}{}}}
 \subsection{Method \code{print()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}}
@@ -106,6 +112,7 @@ for the requested moving window sizes in days.}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
 \subsection{Method \code{clone()}}{
 The objects of this class are cloneable with this method.
 \subsection{Usage}{
diff --git a/man/TSCF.Rd b/man/TSCF.Rd
new file mode 100644
index 0000000..e4cefdc
--- /dev/null
+++ b/man/TSCF.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/TSCF.R
+\name{TSCF}
+\alias{TSCF}
+\title{Estimation of the transpiration stream concentration factor}
+\usage{
+TSCF(log_Kow, method = c("briggs82", "dettenmaier09"))
+}
+\arguments{
+\item{log_Kow}{The decadic logarithm of the octanol-water partition constant}
+
+\item{method}{Short name of the estimation method.}
+}
+\description{
+The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured
+log Kow for neutral pH must be available in order to apply the Briggs
+equation. It is not clarified when it can be regarded reliable, but the
+equation is stated to be produced for non-ionic compounds, suggesting that
+the compound should not be ionogenic (weak acid/base)
+or ionic.
+}
+\details{
+The Dettenmaier equation is given to show that other views on the subject exist.
+}
+\examples{
+plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1))
+TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09")
+curve(TSCF_2, -1, 5, add = TRUE, lty = 2)
+legend("topright", lty = 1:2, bty = "n",
+  legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)"))
+}
+\references{
+FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments.
+ 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/drift_data_JKI.Rd b/man/drift_data_JKI.Rd
index 090910f..181eca6 100644
--- a/man/drift_data_JKI.Rd
+++ b/man/drift_data_JKI.Rd
@@ -5,9 +5,11 @@
 \alias{drift_data_JKI}
 \title{Deposition from spray drift expressed as percent of the applied dose as
 published by the JKI}
-\format{A list currently containing matrices with spray drift percentage
+\format{
+A list currently containing matrices with spray drift percentage
 data for field crops (Ackerbau), and Pome/stone fruit, early and late
-(Obstbau frueh, spaet).}
+(Obstbau frueh, spaet).
+}
 \source{
 JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved
 from
diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd
index 3f072df..0bd2827 100644
--- a/man/perc_runoff_exposit.Rd
+++ b/man/perc_runoff_exposit.Rd
@@ -3,7 +3,8 @@
 \name{perc_runoff_exposit}
 \alias{perc_runoff_exposit}
 \title{Runoff loss percentages as used in Exposit 3}
-\format{A data frame with percentage values for the dissolved fraction and the fraction
+\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}
@@ -11,7 +12,8 @@
       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}
diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd
index 016f9dd..0aa50c1 100644
--- a/man/perc_runoff_reduction_exposit.Rd
+++ b/man/perc_runoff_reduction_exposit.Rd
@@ -4,14 +4,16 @@
 \name{perc_runoff_reduction_exposit}
 \alias{perc_runoff_reduction_exposit}
 \title{Runoff reduction percentages as used in Exposit}
-\format{A named list of data frames with reduction percentage values for the
+\format{
+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}
-  }}
+  }
+}
 \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}
diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd
index 64c00a8..dfad4aa 100644
--- a/man/soil_scenario_data_EFSA_2015.Rd
+++ b/man/soil_scenario_data_EFSA_2015.Rd
@@ -4,9 +4,11 @@
 \name{soil_scenario_data_EFSA_2015}
 \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, 
+\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.}
+  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
diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd
index aeaacac..f6de290 100644
--- a/man/soil_scenario_data_EFSA_2017.Rd
+++ b/man/soil_scenario_data_EFSA_2017.Rd
@@ -4,9 +4,11 @@
 \name{soil_scenario_data_EFSA_2017}
 \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, 
+\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.}
+  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