Add simplest PEC soil calcs, use testthat

15 files changed, 163 insertions, 10 deletions

diff --git a/Makefile b/GNUmakefile
index db1ade6..93708a6 100644
--- a/Makefile
+++ b/GNUmakefile
@@ -18,6 +18,8 @@ usage:
 
 pkgfiles = pkg/DESCRIPTION \
 	   pkg/inst/testdata/* \
+		 pkg/tests/testthat.R \
+		 pkg/tests/testthat/* \
 	   pkg/R/*
 
 clean:
@@ -33,14 +35,24 @@ roxygen:
 $(TGZ): $(pkgfiles)
 	@echo "Building package..."
 	sed -i -e "s/Date:.*/Date: $(DATE)/" pkg/DESCRIPTION
-	"$(R_HOME)/bin/Rscript" -e 'library(roxygen2); roxygenize("pkg")' > roxygen.log 2>&1 || cat roxygen.log
+	"$(R_HOME)/bin/Rscript" -e 'library(roxygen2); roxygenize("pkg")' 2>&1 | tee roxygen.log
 	git log --no-merges -M --date=iso pkg/ > pkg/ChangeLog
 	"$(R_HOME)/bin/R" CMD build pkg > build.log 2>&1
 	@echo "DONE."
 
 build: $(TGZ)
 
+test: build
+	@echo "Running testthat tests..."
+	"$(R_HOME)/bin/Rscript" -e 'library(devtools); devtools::test("pkg")' 2>&1 | tee roxygen.log
+	@echo "DONE."
+
 check: build
+	@echo "Running check..."
+	"$(R_HOME)/bin/R" CMD check $(TGZ)
+	@echo "DONE."
+
+crancheck: build
 	@echo "Running CRAN check..."
 	"$(R_HOME)/bin/R" CMD check --as-cran $(TGZ)
 	@echo "DONE."
diff --git a/README.rmd b/README.rmd
index 77364fb..c87014f 100644
--- a/README.rmd
+++ b/README.rmd
@@ -33,7 +33,11 @@ library(devtools)
 install_github("jranke/pfm", subdir = "pkg", quick = TRUE)
 ```
 
-To read in and analyse a cwa file:
+## Use
+
+# Analyse TOXSWA output
+
+Read in and analyse a cwa file:
 
 ```{r}
 library(pfm)
@@ -43,3 +47,13 @@ example_cwa$get_events(c(20, 100))
 example_cwa$moving_windows(c(7, 21))
 print(example_cwa)
 ```
+
+# Calculate PEC soil
+
+Simple PEC soil calculation for an application rate of 100 g/ha and
+25% interception, assuming complete mixing into 5 cm and a soil bulk
+density of 1.5 kg/L, output in mg/kg:
+
+```{r}
+PEC_soil(100, int = 0.25)
+```
diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 29e36e7..a327ae1 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -1,11 +1,14 @@
 Package: pfm
 Type: Package
 Title: Utilities for pesticide fate modelling
-Version: 0.1-1
-Date: 2015-01-23
-Authors@R: "Johannes Ranke <jranke@uni-bremen.de> [aut, cre, cph]"
-Description: Utilities for dealing with data from FOCUS software tools.
+Version: 0.1-2
+Date: 2015-04-22
+Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", 
+                  role = c("aut", "cre", "cph"))
+Description: Utilities for simple PEC calculations and for dealing with data
+  from some FOCUS pesticide fate modelling software.
 Depends: R6
+Suggests: testthat
 License: GPL
 LazyLoad: yes
 LazyData: yes
diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 4b55df5..dd140d0 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -1,6 +1,7 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2 (4.1.0.9001): do not edit by hand
 
 S3method(plot,TOXSWA_cwa)
+export(PEC_soil)
 export(TOXSWA_cwa)
 export(read.TOXSWA_cwa)
 importFrom(R6,R6Class)
diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R
new file mode 100644
index 0000000..3dbc2eb
--- /dev/null
+++ b/pkg/R/PEC_soil.R
@@ -0,0 +1,45 @@
+# 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 soil
+#'
+#' This is a basic, vectorised form of a simple calculation of a contaminant
+#' concentration in bulk soil based on complete, instantaneous mixing.
+#'
+#' @param rate Application rate in units specified below
+#' @param rate_units Defaults to g/ha
+#' @param interception The fraction of the application rate that does not reach the soil
+#' @param mixing_depth Mixing depth in cm
+#' @param bulk_density Bulk density of the soil. Defaults to 1.5 kg/L, or 1500 kg/m3
+#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported
+#' @return The predicted concentration in soil
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' PEC_soil(100, interception = 0.25)
+PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
+                     mixing_depth = 5, bulk_density = 1.5,
+                     PEC_units = "mg/kg")
+{
+  rate_to_soil = (1 - interception) * rate
+  rate_units = match.arg(rate_units)
+  PEC_units = match.arg(PEC_units)
+  soil_volume = 100 * 100 * (mixing_depth/100)   # in m3
+  soil_mass = soil_volume * bulk_density * 1000  # in kg
+  PEC_soil = rate_to_soil * 1000 / soil_mass     # in mg/kg
+  return(PEC_soil)
+}
diff --git a/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd
new file mode 100644
index 0000000..76ffd4b
--- /dev/null
+++ b/pkg/man/PEC_soil.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_soil.R
+\name{PEC_soil}
+\alias{PEC_soil}
+\title{Calculate predicted environmental concentrations in soil}
+\usage{
+PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
+  bulk_density = 1.5, PEC_units = "mg/kg")
+}
+\arguments{
+\item{rate}{Application rate in units specified below}
+
+\item{rate_units}{Defaults to g/ha}
+
+\item{interception}{The fraction of the application rate that does not reach the soil}
+
+\item{mixing_depth}{Mixing depth in cm}
+
+\item{bulk_density}{Bulk density of the soil. Defaults to 1.5 kg/L, or 1500 kg/m3}
+
+\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported}
+}
+\value{
+The predicted concentration in soil
+}
+\description{
+This is a basic, vectorised form of a simple calculation of a contaminant
+concentration in bulk soil based on complete, instantaneous mixing.
+}
+\examples{
+PEC_soil(100, interception = 0.25)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd
index c4d573b..5aa8bfc 100644
--- a/pkg/man/TOXSWA_cwa.Rd
+++ b/pkg/man/TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \docType{class}
 \name{TOXSWA_cwa}
diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd
index 9136c10..1dddb78 100644
--- a/pkg/man/plot.TOXSWA_cwa.Rd
+++ b/pkg/man/plot.TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \name{plot.TOXSWA_cwa}
 \alias{plot.TOXSWA_cwa}
diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd
index ded0a39..f67455f 100644
--- a/pkg/man/read.TOXSWA_cwa.Rd
+++ b/pkg/man/read.TOXSWA_cwa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
 % Please edit documentation in R/TOXSWA_cwa.R
 \name{read.TOXSWA_cwa}
 \alias{read.TOXSWA_cwa}
diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R
new file mode 100644
index 0000000..d2df1cc
--- /dev/null
+++ b/pkg/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(pfm)
+
+test_check("pfm")
diff --git a/pkg/tests/testthat/H_sw_D4_pond.rds b/pkg/tests/testthat/H_sw_D4_pond.rds
new file mode 100644
index 0000000..9ad8194
--- /dev/null
+++ b/pkg/tests/testthat/H_sw_D4_pond.rds
diff --git a/pkg/tests/testthat/H_sw_R1_stream_events.rds b/pkg/tests/testthat/H_sw_R1_stream_events.rds
new file mode 100644
index 0000000..3e2828e
--- /dev/null
+++ b/pkg/tests/testthat/H_sw_R1_stream_events.rds
diff --git a/pkg/tests/testthat/H_sw_R1_stream_windows.rds b/pkg/tests/testthat/H_sw_R1_stream_windows.rds
new file mode 100644
index 0000000..29e13f2
--- /dev/null
+++ b/pkg/tests/testthat/H_sw_R1_stream_windows.rds
diff --git a/pkg/tests/testthat/test_PEC_soil.R b/pkg/tests/testthat/test_PEC_soil.R
new file mode 100644
index 0000000..27b2eb7
--- /dev/null
+++ b/pkg/tests/testthat/test_PEC_soil.R
@@ -0,0 +1,13 @@
+library(pfm)
+context("Simple PEC soil calculations")
+
+test_that("PEC_soil calculates correctly", {
+  # Application of 100 g/ha gives 0.133 mg/kg under default assumptions
+  expect_equal(PEC_soil(100), 0.1 * 4/3)
+
+  # or 0.1 mg/kg assuming 25% interception
+  expect_equal(PEC_soil(100, interception = 0.25), 0.1) 
+
+  # Mixing depth of 1 cm gives five-fold PEC
+  expect_equal(PEC_soil(100, interception = 0.25, mixing_depth = 1), 0.5)
+})
diff --git a/pkg/tests/testthat/test_TOXSWA_cwa.R b/pkg/tests/testthat/test_TOXSWA_cwa.R
new file mode 100644
index 0000000..d91b79a
--- /dev/null
+++ b/pkg/tests/testthat/test_TOXSWA_cwa.R
@@ -0,0 +1,25 @@
+library(pfm)
+context("Read and analyse TOXSWA cwa files")
+
+test_that("TOXSWA cwa file is correctly read", {
+  H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                   basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                   zipfile = system.file("testdata/SwashProjects.zip",
+                                               package = "pfm"))
+  expect_equal_to_reference(H_sw_D4_pond, file = "H_sw_D4_pond.rds")
+})
+
+test_that("Getting events and moving window analysis works", {
+  H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                   basedir = "SwashProjects/project_H_sw/TOXSWA",
+                                   zipfile = system.file("testdata/SwashProjects.zip",
+                                               package = "pfm"))
+
+  # Event analysis with two different thresholds
+  H_sw_R1_stream$get_events(c(2, 10))
+  expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds")
+
+  # Moving window analysis
+  H_sw_R1_stream$moving_windows(c(7, 21))
+  expect_equal_to_reference(H_sw_R1_stream$windows, file = "H_sw_R1_stream_windows.rds")
+})