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-rw-r--r--R/dimethenamid_2018.R21
-rw-r--r--R/f_time_norm_focus.R24
-rw-r--r--R/mkinds.R3
-rw-r--r--build.log1
-rw-r--r--data/D24_2014.rdabin5805 -> 5895 bytes
-rw-r--r--data/dimethenamid_2018.rdabin0 -> 8231 bytes
-rw-r--r--inst/dataset_generation/D24_2014.R4
-rw-r--r--inst/dataset_generation/dimethenamid_2018.R153
-rw-r--r--man/dimethenamid_2018.Rd35
-rw-r--r--man/f_time_norm_focus.Rd6
-rw-r--r--test.log16
-rw-r--r--tests/testthat/experimental_data_for_UBA_2019_mkindsg.txt2
-rw-r--r--tests/testthat/test_f_time_norm.R9
-rw-r--r--tests/testthat/test_mixed.R2
14 files changed, 254 insertions, 22 deletions
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R
new file mode 100644
index 00000000..189da618
--- /dev/null
+++ b/R/dimethenamid_2018.R
@@ -0,0 +1,21 @@
+#' Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018
+#'
+#' The datasets were extracted from the active substance evaluation dossier
+#' published by EFSA. Kinetic evaluations shown for these datasets are intended
+#' to illustrate and advance kinetic modelling. The fact that these data and
+#' some results are shown here does not imply a license to use them in the
+#' context of pesticide registrations, as the use of the data may be
+#' constrained by data protection regulations.
+#'
+#' The R code used to create this data object is installed with this package
+#' in the 'dataset_generation' directory. In the code, page numbers are given for
+#' specific pieces of information in the comments.
+#'
+#' @format An [mkindsg] object grouping eight datasets with some meta information
+#' @source Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
+#' Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
+#' Rev. 2 - November 2017
+#' \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211}
+#' @examples
+#' print(dimethenamid_2018)
+"dimethenamid_2018"
diff --git a/R/f_time_norm_focus.R b/R/f_time_norm_focus.R
index 66df527e..e7c6f22e 100644
--- a/R/f_time_norm_focus.R
+++ b/R/f_time_norm_focus.R
@@ -11,7 +11,9 @@ utils::globalVariables("D24_2014")
#' @param field_moisture Numeric vector of moisture contents at field capacity
#' (pF2) in \\% w/w
#' @param study_moisture_ref_source Source for the reference value
-#' used to calculate the study moisture
+#' used to calculate the study moisture. If 'auto', preference is given
+#' to a reference moisture given in the meta information, otherwise
+#' the focus soil moisture for the soil class is used
#' @param Q10 The Q10 value used for temperature normalisation
#' @param walker The Walker exponent used for moisture normalisation
#' @param f_na The factor to use for NA values. If set to NA, only factors
@@ -65,7 +67,7 @@ f_time_norm_focus.numeric <- function(object,
#' @rdname f_time_norm_focus
#' @export
f_time_norm_focus.mkindsg <- function(object,
- study_moisture_ref_source = c("meta", "focus"),
+ study_moisture_ref_source = c("auto", "meta", "focus"),
Q10 = 2.58, walker = 0.7, f_na = NA, ...) {
study_moisture_ref_source <- match.arg(study_moisture_ref_source)
@@ -79,11 +81,19 @@ f_time_norm_focus.mkindsg <- function(object,
meta$field_moisture)
}
- if (study_moisture_ref_source == "meta") {
- study_moisture_ref <- meta$study_moisture_ref
+ study_moisture_ref_focus <-
+ focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]
+
+ if (study_moisture_ref_source == "auto") {
+ study_moisture_ref <- ifelse (is.na(meta$study_ref_moisture),
+ study_moisture_ref_focus,
+ meta$study_ref_moisture)
} else {
- study_moisture_ref <-
- focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]
+ if (study_moisture_ref_source == "meta") {
+ study_moisture_ref <- meta$study_moisture_ref
+ } else {
+ study_moisture_ref <- study_moisture_ref_focus
+ }
}
if ("study_moisture" %in% names(meta)) {
@@ -99,5 +109,5 @@ f_time_norm_focus.mkindsg <- function(object,
Q10 = Q10, walker = walker, f_na = f_na)
cat("$time_norm was set to\n")
print(object$f_time_norm)
- return(object$f_time_norm)
+ invisible(object$f_time_norm)
}
diff --git a/R/mkinds.R b/R/mkinds.R
index 0e970694..df66ab0f 100644
--- a/R/mkinds.R
+++ b/R/mkinds.R
@@ -140,6 +140,7 @@ mkindsg <- R6Class("mkindsg",
self$f_time_norm <- f_time_norm
if (!missing(meta)) {
+ rownames(meta) <- lapply(ds, function(x) x$title)
self$meta <- meta
}
}
@@ -157,7 +158,7 @@ mkindsg <- R6Class("mkindsg",
print.mkindsg <- function(x, data = FALSE, verbose = data, ...) {
cat("<mkindsg> holding", length(x$ds), "mkinds objects\n")
cat("Title $title: ", x$title, "\n")
- cat("Occurrene of observed compounds $observed_n:\n")
+ cat("Occurrence of observed compounds $observed_n:\n")
print(x$observed_n)
if (any(x$f_time_norm != 1)) {
cat("Time normalisation factors $f_time_norm:\n")
diff --git a/build.log b/build.log
index 13905abe..d101d06b 100644
--- a/build.log
+++ b/build.log
@@ -5,6 +5,5 @@
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
-Removed empty directory ‘mkin/tests/testthat/_snaps’
* building ‘mkin_0.9.50.4.tar.gz’
diff --git a/data/D24_2014.rda b/data/D24_2014.rda
index ef796e4d..bdfc5a9c 100644
--- a/data/D24_2014.rda
+++ b/data/D24_2014.rda
Binary files differ
diff --git a/data/dimethenamid_2018.rda b/data/dimethenamid_2018.rda
new file mode 100644
index 00000000..dd3d934b
--- /dev/null
+++ b/data/dimethenamid_2018.rda
Binary files differ
diff --git a/inst/dataset_generation/D24_2014.R b/inst/dataset_generation/D24_2014.R
index 435be4a6..46d9c533 100644
--- a/inst/dataset_generation/D24_2014.R
+++ b/inst/dataset_generation/D24_2014.R
@@ -70,4 +70,6 @@ D24_2014 <- mkindsg$new(
temperature = c(25, 20, 20, 20, 20)
)
)
-save(D24_2014, file = "../../data/D24_2014.rda", version = 2)
+f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1)
+
+save(D24_2014, file = "data/D24_2014.rda", version = 2)
diff --git a/inst/dataset_generation/dimethenamid_2018.R b/inst/dataset_generation/dimethenamid_2018.R
new file mode 100644
index 00000000..34a9dad1
--- /dev/null
+++ b/inst/dataset_generation/dimethenamid_2018.R
@@ -0,0 +1,153 @@
+# From the RAR 2018, see the help file for dimethenamid_2018
+# Metabolite residues for time zero were added to the parent value (Wendt 1997)
+library(mkin)
+dimethenamid_2018 <- mkindsg$new(
+ title = "Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018",
+ ds = list(
+ mkinds$new("Calke", # p. 27
+ mkin_wide_to_long(
+ data.frame(
+ t = c(0, 0, 14, 30, 59, 120, 120),
+ DMTAP = c(95.8, 98.7, 60.5, 39.1, 15.2, 4.8, 4.6),
+ M23 = c(NA, NA, 4.1, 5.3, 6.0, 4.3, 4.1),
+ M27 = c(NA, NA, 1.5, 2.4, 3.2, 3.8, 3.7),
+ M31 = c(NA, NA, 2.0, 2.1, 2.2, 1.8, 2.1)
+ )
+ )
+ ),
+ mkinds$new("Borstel 1", # p. 22
+ mkin_wide_to_long(
+ data.frame(
+ t = c(0, 28, 58, 89, 119),
+ DMTAP = c(100.5, 51.4, 26.8, 15.7, 7.9)
+ )
+ )
+ ),
+ mkinds$new("Borstel 2", # p. 19/20
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 2, 7, 14, 28, 58, 89, 119), each = 2),
+ DMTAP = c(100.5, 99.6, 91.9, 91.3, 81.8, 82.1, 69.1, 68.0, 51.4, 51.4,
+ 27.6, 26.8, 15.7, 15.3, 7.9, 8.1),
+ M23 = c(NA, NA, 0.4, 0.5, 1.2, 1.3, 2.8, 2.0, 2.9, 4.9, 12.2, 12.2,
+ 12.2, 12.0, 10.4, 11.6),
+ M27 = c(NA, NA, NA, 0.3, 0.8, 0.9, 1.4, 1.4, 2.7, 2.6, 4.4, 4.7,
+ 5.4, 5.2, 5.4, 5.4),
+ M31 = c(NA, NA, NA, 0.1, 1.0, 0.9, 2.0, 2.5, 4.3, 3.2, 4.3, 4.8,
+ 5.0, 5.1, 4.3, 4.4)
+ )
+ )
+ ),
+ mkinds$new("Elliot 1", # p. 15/16
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 21, 28, 42, 56, 84, 119, 182), each = 2),
+ DMTAP = c(96.2 + 1.3, 100.7, 86.4, 88.5, 69.8, 77.1, 59.0, 54.2, 31.3, 33.5,
+ 19.6, 20.9, 13.3, 15.8, 6.7, 8.7, 8.8, 8.7, 6.0, 4.4, 3.3, 2.8, 1.4, 1.8),
+ M23 = c(rep(NA, 4), 2.8, 1.7, 4.3, 5.8, 8.2, 5.2, 5.1, 6.1,
+ 6.0, 6.0, 5.0, 4.2, 3.9, 2.9, 1.9, 1.5, 2.0, 2.3, 1.2, 1.9),
+ M27 = c(rep(NA, 4), 2.3, 2.1, 4.0, 3.4, 6.6, 6.9, 8.2, 8.8, 9.7, 8.8,
+ 8.3, 9.2, 9.3, 8.5, 8.6, 6.0, 5.6, 4.5, 4.1, 3.9),
+ M31 = c(rep(NA, 3), 1.5, 5.0, 2.4, 4.3, 5.0, 8.0, 7.7, 7.8, 6.5, 8.0,
+ 7.4, 6.9, 9.0, 5.5, 6.1, 6.1, 4.0, 3.1, 2.9, 1.8, 2.6)
+ )
+ )
+ ),
+ mkinds$new("Elliot 2", # p. 16
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 21, 28, 42, 56, 84, 119, 182), each = 2),
+ DMTA = c(93.4, 103.2, 89.2, 86.6, 78.2, 78.1, 55.6, 53.0, 33.7,
+ 33.2, 20.9, 19.9, 18.2, 12.7, 7.8, 9.0, 11.4, 9.0, 3.9, 4.4, 2.6,
+ 3.4, 2.0, 1.7),
+ M23 = c(rep(NA, 4), 2.6, 2.4, 5.5, 5.6, 7.3, 6.5, 5.8, 7.7, 7.8, 7.3, 7.0,
+ 6.3, 4.3, 3.8, 2.6, 2.8, 1.6, 1.1, 1.4, 1.3),
+ M27 = c(rep(NA, 4), 1.0, 2.6, 4.5, 4.6, 7.6, 6.7, 8.7, 7.6, 8.0,
+ 8.6, 7.4, 7.2, 10.3, 9.4, 6.5, 6.9, 4.6, 4.5, 4.3, 4.2),
+ M31 = c(NA, NA, 1.3, NA, 3.1, 2.3, 3.4, 4.3, 7.8, 8.7, 7.7, 6.5,
+ 6.3, 8.7, 5.7, 4.2, 3.2, 4.2, 3.8, 4.0, 4.5, 4.5, 3.8, 2.3)
+ )
+ )
+ ),
+ mkinds$new("Flaach", # p. 13
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 21, 28, 42, 56, 70, 84, 120), each = 3),
+ DMTA = c(96.5, 96.8, 97.0, 82.9, 86.7, 87.4, 72.8, 69.9, 71.9, 51.4,
+ 52.9, 48.6, 28.5, 27.3, 27.5, 14.8, 13.4, 14.4, 7.7, 7.3, 8.1, 2,
+ 1.5, 1.9, 1.3, 1, 1.1, 0.9, 0.7, 0.7, 0.6, 0.4, 0.5, 0.4, 0.3,
+ 0.3),
+ M23 = c(rep(NA, 3), 0.7, 0.7, 0.2, 2.2, 1.8, 1.6, 4.1, 4.2, 4.2, 7.5,
+ 7.1, 7.5, 8.4, 6.8, 8, 7.2, 7.2, 6.9, 4.9, 4.3, 4.5, 3.8, 3.1, 3.1,
+ 2.7, 2.3, 2.1, 1.6, 1.1, 1.3, 0.4, 0.4, 0.3),
+ M27 = c(rep(NA, 3), 1.1, 1.1, 0.3, 2.6, 2.4, 2.3, 5, 5.9, 4.8, 8.5,
+ 8.5, 8.3, 9.3, 8.7, 9.1, 8.6, 8.5, 8.9, 8.1, 7.7, 7.4, 5.9, 6, 5.9,
+ 5.6, 5.2, 5.6, 4.3, 3.7, 3.9, 2.5, 2.4, 2.2),
+ M31 = c(rep(NA, 3), 0.3, 0.3, 0.1, 0.7, 0.6, 0.7, 1.3, 1.2, 1.4,
+ 2.4, 2.1, 2.3, 3.3, 2.4, 2.6, 4, 3.6, 3.3, 2.1, 1.7, 1.8, 1.6, 1.6,
+ 1.4, 1.8, 1.5, 1.3, 1.2, 0.9, 1.1, 0.5, 0.5, 0.3)
+ )
+ )
+ ),
+ mkinds$new("BBA 2.2", # p. 10
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 21, 28, 42, 56, 70, 84, 119), each = 2),
+ DMTA = c(98.09, 98.77, 93.52, 92.03, 88.39, 87.18, 69.38, 71.06,
+ 45.21, 46.81, 30.54, 30.07, 21.60, 20.41, 9.10, 9.70, 6.58, 6.31,
+ 3.47, 3.52, 3.40, 3.67, 1.62, 1.62),
+ M23 = c(NA, NA, 0.36, 0.4, 1.03, 1.07, 3.6, 3.66, 6.97, 7.22, 8.65,
+ 8.38, 9.1, 8.63, 7.63, 8.01, 6.4, 6.35, 5.35, 5.06, 5.14, 5.91,
+ 3.35, 2.87),
+ M27 = c(NA, NA, 0.42, 0.47, 0.71, 0.82, 2.19, 2.28, 5.45, 5.19, 8.81,
+ 7.93,10.25,10.77,10.89,10.85,10.41,10.35, 9.92, 9.42, 9.15, 9.25,
+ 7.14, 7.13),
+ M31 = c(NA, NA, 0.36, 0.33, 0.55, 0.64, 1.94, 1.62, 4.22, 4.37, 6.31,
+ 6.85, 7.05, 6.84, 6.53, 7.11, 6.06, 6.05, 5.5, 5.07, 4.94, 4.39,
+ 3.64, 3.55)
+ )
+ )
+ ),
+ mkinds$new("BBA 2.3", # p. 10
+ mkin_wide_to_long(
+ data.frame(
+ t = rep(c(0, 1, 3, 7, 14, 21, 28, 42, 56, 70, 84, 119), each = 2),
+ DMTA = c(99.33, 97.44, 93.73, 93.77, 87.84, 89.82, 71.61, 71.42,
+ 45.60, 45.42, 31.12, 31.68, 23.20, 24.13, 9.43, 9.82, 7.08, 8.64,
+ 4.41, 4.78, 4.92, 5.08, 2.13, 2.23),
+ M23 = c(NA, NA, 0.18, 0.18, 0.52, 0.43, 1.19, 1.11, 2.26, 1.99, 2.81,
+ 2.83, 3.39, 3.56, 3.49, 3.28, 2.80, 2.97, 2.42, 2.51, 2.22, 1.95,
+ 1.28, 0.99),
+ M27 = c(NA, NA, 0.5, 0.83, 1.25, 1.09, 3.28, 3.24, 7.17, 7.91, 10.15,
+ 9.55, 12.09, 11.89, 13.32, 12.05, 10.04, 10.78, 9.32, 9.62, 8.00,
+ 8.45, 5.71, 3.33),
+ M31 = c(NA, NA, 0.47, 0.34, 1.00, 0.89, 3.58, 3.41, 8.74, 8.28, 9.67,
+ 8.95, 10.34, 10.00, 7.89, 8.13, 5.06, 5.54, 3.79, 4.11, 3.11, 2.98,
+ 1.78, 1.55)
+ )
+ )
+ )
+ ),
+ # Soil data and temperatures from p. 25, p. 18 (Staudenmaier 2013 and 2009)
+ # p. 14 (Wendt 1997), p. 12 (König 1995), p. 9 (König 1995)
+ # Soil classification in the König studies was according to the German scheme,
+ # but the FOCUS generic guidance suggests them to be equivalent to the USDA
+ # classes with the same name
+ meta = data.frame(
+ study = c("Unsworth 2014", "Staudenmaier 2013", "Staudenmaier 2009",
+ rep("Wendt 1997", 2), "König 1996", rep("König 1995", 2)),
+ usda_soil_type = c("Sandy loam", rep("Sand", 2),
+ rep("Clay loam", 2), "Sandy clay loam", "Loamy sand",
+ "Sandy loam"),
+ study_moisture_ref_type = c("pF2", rep("pF1", 2),
+ rep("pF2.5", 2), rep("pF1", 3)),
+ rel_moisture = c(1, rep(0.5, 2),
+ rep(0.75, 2), rep(0.4, 3)),
+ study_ref_moisture = c(NA, rep(23, 2), rep(33.37, 2), rep(NA, 3)),
+ temperature = c(20, rep(20, 2),
+ rep(23, 2), rep(20, 3))
+ )
+)
+f_time_norm_focus(dimethenamid_2018)
+
+save(dimethenamid_2018, file = "data/dimethenamid_2018.rda", version = 2)
diff --git a/man/dimethenamid_2018.Rd b/man/dimethenamid_2018.Rd
new file mode 100644
index 00000000..b6f761e8
--- /dev/null
+++ b/man/dimethenamid_2018.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dimethenamid_2018.R
+\docType{data}
+\name{dimethenamid_2018}
+\alias{dimethenamid_2018}
+\title{Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018}
+\format{
+An \link{mkindsg} object grouping eight datasets with some meta information
+}
+\source{
+Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
+Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
+Rev. 2 - November 2017
+\url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211}
+}
+\usage{
+dimethenamid_2018
+}
+\description{
+The datasets were extracted from the active substance evaluation dossier
+published by EFSA. Kinetic evaluations shown for these datasets are intended
+to illustrate and advance kinetic modelling. The fact that these data and
+some results are shown here does not imply a license to use them in the
+context of pesticide registrations, as the use of the data may be
+constrained by data protection regulations.
+}
+\details{
+The R code used to create this data object is installed with this package
+in the 'dataset_generation' directory. In the code, page numbers are given for
+specific pieces of information in the comments.
+}
+\examples{
+print(dimethenamid_2018)
+}
+\keyword{datasets}
diff --git a/man/f_time_norm_focus.Rd b/man/f_time_norm_focus.Rd
index bc7faa6a..77564799 100644
--- a/man/f_time_norm_focus.Rd
+++ b/man/f_time_norm_focus.Rd
@@ -21,7 +21,7 @@ f_time_norm_focus(object, ...)
\method{f_time_norm_focus}{mkindsg}(
object,
- study_moisture_ref_source = c("meta", "focus"),
+ study_moisture_ref_source = c("auto", "meta", "focus"),
Q10 = 2.58,
walker = 0.7,
f_na = NA,
@@ -48,7 +48,9 @@ f_time_norm_focus(object, ...)
for complete cases will be returned.}
\item{study_moisture_ref_source}{Source for the reference value
-used to calculate the study moisture}
+used to calculate the study moisture. If 'auto', preference is given
+to a reference moisture given in the meta information, otherwise
+the focus soil moisture for the soil class is used}
}
\description{
Time step normalisation factors for aerobic soil degradation as described
diff --git a/test.log b/test.log
index 186ec590..7a9c55ed 100644
--- a/test.log
+++ b/test.log
@@ -10,22 +10,22 @@ Testing mkin
✔ | 5 | Analytical solutions for coupled models [3.3 s]
✔ | 5 | Calculation of Akaike weights
✔ | 14 | Confidence intervals and p-values [1.2 s]
-✔ | 14 | Error model fitting [4.7 s]
-✔ | 3 | Time step normalisation
+✔ | 14 | Error model fitting [5.6 s]
+✔ | 5 | Time step normalisation
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
-✔ | 33 1 | Nonlinear mixed effects models [27.8 s]
+✔ | 33 1 | Nonlinear mixed effects models [28.7 s]
────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:137:3): saem results are reproducible for biphasic fits
+Skip (test_mixed.R:143:3): saem results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
✔ | 2 | Test dataset classes mkinds and mkindsg
✔ | 1 | mkinfit features [0.3 s]
-✔ | 12 | Special cases of mkinfit calls [0.8 s]
-✔ | 8 | mkinmod model generation and printing [0.3 s]
+✔ | 10 | Special cases of mkinfit calls [0.3 s]
+✔ | 8 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.4 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s]
-✔ | 9 | Nonlinear mixed-effects models [7.9 s]
+✔ | 9 | Nonlinear mixed-effects models [8.2 s]
✔ | 16 | Plotting [1.9 s]
✔ | 4 | Residuals extracted from mkinfit models
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
@@ -36,7 +36,7 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 69.7 s
+Duration: 71.3 s
── Skipped tests ──────────────────────────────────────────────────────────────
● Fitting with saemix takes around 10 minutes when using deSolve (1)
diff --git a/tests/testthat/experimental_data_for_UBA_2019_mkindsg.txt b/tests/testthat/experimental_data_for_UBA_2019_mkindsg.txt
index f9287b35..7096f26d 100644
--- a/tests/testthat/experimental_data_for_UBA_2019_mkindsg.txt
+++ b/tests/testthat/experimental_data_for_UBA_2019_mkindsg.txt
@@ -1,5 +1,5 @@
<mkindsg> holding 5 mkinds objects
Title $title: Experimental X
-Occurrene of observed compounds $observed_n:
+Occurrence of observed compounds $observed_n:
parent A1
5 5
diff --git a/tests/testthat/test_f_time_norm.R b/tests/testthat/test_f_time_norm.R
index f9aba58a..ca2ebd99 100644
--- a/tests/testthat/test_f_time_norm.R
+++ b/tests/testthat/test_f_time_norm.R
@@ -8,4 +8,13 @@ test_that("Time step normalisation for a dataset works", {
expect_output(f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1),
"was set to")
expect_equal(round(D24_2014$f_time_norm, 3), c(1.606, 0.712, 0.716, 0.716, 0.898))
+ expect_output(f_time_norm_focus(dimethenamid_2018), "was set to")
+
+ # Reference values from Dimethenamid RAR 2018 Vol3 B.8
+ expect_equal(round(dimethenamid_2018$f_time_norm, 3),
+ c(1,
+ rep(0.971, 2), # p. 56
+ rep(round(1.329 * 0.924, 3), 2), # p. 51
+ 0.623, 0.768, 0.673) # p. 45
+ )
})
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 41e8160a..1e96c338 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,4 +1,4 @@
-context("Nonlinear mixed effects models")
+context("Nonlinear mixed-effects models")
test_that("Parent only models can be fitted using nonlinear mixed effects models", {
expect_error(saem(fits), "Only row objects")

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