Add DTx function, check and testHEAD main

The tolerance of one test had to be increased in test_deSolve.R, and four vdiffr snapshots with negligible differences were updated. Tests run with a maximum of 16 cores when running in the Agroscope Apptainer environment.
author: Ranke Johannes <johannes.ranke@agroscope.admin.ch> 2026-09-07 13:45:39 +0200
committer: Ranke Johannes <johannes.ranke@agroscope.admin.ch> 2026-09-07 13:45:39 +0200
commit: 48d9cad339394c3aa0d730d9a27b1c0680ce13e8 (patch)
tree: 9c0a5766f3d0853c382ba0174f83e2e8ac9b0fbf
parent: 46735d7a6d429bb0c50f951763797f321a0d77ca (diff)
32 files changed, 645 insertions, 458 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 77b53a6d..ded3b27b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 1.2.10
-Date: 2025-09-12
+Version: 1.2.11
+Date: 2026-09-07
 Authors@R: c(
   person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
     email = "johannes.ranke@jrwb.de",
@@ -35,4 +35,4 @@ VignetteBuilder: knitr
 BugReports: https://github.com/jranke/mkin/issues/
 URL: https://pkgdown.jrwb.de/mkin/
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.1.0
diff --git a/NAMESPACE b/NAMESPACE
index 5b9a1c85..445a3649 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -83,6 +83,7 @@ S3method(update,saem.mmkin)
 S3method(which.best,default)
 export(CAKE_export)
 export(DFOP.solution)
+export(DTx)
 export(FOMC.solution)
 export(HS.solution)
 export(IORE.solution)
@@ -155,49 +156,59 @@ import(nlme)
 importFrom(R6,R6Class)
 importFrom(grDevices,dev.cur)
 importFrom(lmtest,lrtest)
-importFrom(methods,is)
-importFrom(methods,signature)
-importFrom(nlme,intervals)
-importFrom(nlme,nlme)
-importFrom(parallel,detectCores)
-importFrom(parallel,mclapply)
-importFrom(parallel,parLapply)
+importFrom(methods,
+  is,
+  signature
+)
+importFrom(nlme,
+  intervals,
+  nlme
+)
+importFrom(parallel,
+  detectCores,
+  mclapply,
+  parLapply
+)
 importFrom(rlang,"!!!")
 importFrom(saemix,saemix)
-importFrom(stats,AIC)
-importFrom(stats,BIC)
-importFrom(stats,aggregate)
-importFrom(stats,anova)
-importFrom(stats,as.formula)
-importFrom(stats,coef)
-importFrom(stats,coefficients)
-importFrom(stats,cov2cor)
-importFrom(stats,dist)
-importFrom(stats,dnorm)
-importFrom(stats,lm)
-importFrom(stats,logLik)
-importFrom(stats,median)
-importFrom(stats,na.fail)
-importFrom(stats,nlminb)
-importFrom(stats,nobs)
-importFrom(stats,optimize)
-importFrom(stats,pchisq)
-importFrom(stats,plogis)
-importFrom(stats,predict)
-importFrom(stats,pt)
-importFrom(stats,qchisq)
-importFrom(stats,qf)
-importFrom(stats,qlogis)
-importFrom(stats,qnorm)
-importFrom(stats,qt)
-importFrom(stats,quantile)
-importFrom(stats,residuals)
-importFrom(stats,rnorm)
-importFrom(stats,shapiro.test)
-importFrom(stats,terms)
-importFrom(stats,update)
-importFrom(stats,vcov)
-importFrom(utils,capture.output)
-importFrom(utils,getFromNamespace)
-importFrom(utils,packageVersion)
-importFrom(utils,write.table)
+importFrom(stats,
+  AIC,
+  BIC,
+  aggregate,
+  anova,
+  as.formula,
+  coef,
+  coefficients,
+  cov2cor,
+  dist,
+  dnorm,
+  lm,
+  logLik,
+  median,
+  na.fail,
+  nlminb,
+  nobs,
+  optimize,
+  pchisq,
+  plogis,
+  predict,
+  pt,
+  qchisq,
+  qf,
+  qlogis,
+  qnorm,
+  qt,
+  quantile,
+  residuals,
+  rnorm,
+  shapiro.test,
+  terms,
+  update,
+  vcov
+)
+importFrom(utils,
+  capture.output,
+  getFromNamespace,
+  packageVersion,
+  write.table
+)
diff --git a/NEWS.md b/NEWS.md
index 82f6aa4d..bbdc1b29 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,10 @@
-# mkin 1.2.10 (unreleased)
+# mkin 1.2.11 (unreleased)
+
+## New features
+
+- 'R/endpoints.R': Introduce the function `DTx` that makes it easy to calculate various types of DTx values such as DT50, DT90 and pseudo-half-lives calculated from DT90 or from the slow phase of biphasic models.
+
+# mkin 1.2.10 (2025-05-13)
 
 ## New features
 
diff --git a/R/endpoints.R b/R/endpoints.R
index 70a9eef3..fd5ecec1 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -158,7 +158,7 @@ endpoints <- function(fit, covariates = NULL, covariate_quantile = 0.5) {
                   silent = TRUE)
       if (inherits(DT50, "try-error")) DT50 = NA
       if (inherits(DT90, "try-error")) DT90 = NA
-      DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011
+      DT50_back = DT90 / (log(10)/log(2))
 
       ep$distimes[obs_var, c("DT50back")] = DT50_back
       ep$distimes[obs_var, c("DT50_k1")] = DT50_k1
@@ -177,7 +177,7 @@ endpoints <- function(fit, covariates = NULL, covariate_quantile = 0.5) {
       }
       DT50 <- DTx(50)
       DT90 <- DTx(90)
-      DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011
+      DT50_back = DT90 / (log(10)/log(2))
       DT50_k1 = log(2)/k1
       DT50_k2 = log(2)/k2
       ep$distimes[obs_var, c("DT50back")] = DT50_back
@@ -254,3 +254,78 @@ endpoints <- function(fit, covariates = NULL, covariate_quantile = 0.5) {
   if (length(ep$SFORB) == 0) ep$SFORB <- NULL
   return(ep)
 }
+
+#' Calculate DTx from parameters of parent degradation models
+#'
+#' @param type Character string specifying the degradation model
+#' @param parms Named numeric vector giving the kinetic parameters
+#' @param exact Should we used log(10)/log(2) instead of the widely used value
+#' of 3.32 for backcalculation of DT50 values from DT90 values?
+#' @export
+#' @examples
+#' # Check what type of DT50 is given in the bixafen EFSA conclusion from 2012 on p. 42
+#' DTx("HS", parms = c(k1 = 0.0081, k2 = 0.00023, tb = 53))
+#' # We get 1200 days for the time the concentration reaches 50%, the value of 1235
+#' # was likely based on more digits for the parameters. The half-life corresponding
+#' # to the slow phase is around 3000 days
+DTx <- function(type = c("SFO", "FOMC", "DFOP", "HS", "SFORB"), parms, exact = FALSE) {
+  type <- match.arg(type)
+  backcalculation_factor <- if (exact) log(10)/log(2) else 3.32
+
+  if (type == "SFO") {
+    DT50 <- log(2)/parms[["k"]]
+    DT90 <- log(10)/parms[["k"]]
+    return(c(DT50 = DT50, DT90 = DT90))
+  }
+  if (type == "FOMC") {
+    alpha = parms[["alpha"]]
+    beta = parms[["beta"]]
+    DT50 = beta * (2^(1/alpha) - 1)
+    DT90 = beta * (10^(1/alpha) - 1)
+    DT50_back = DT90 / backcalculation_factor
+    return(c(DT50 = DT50, DT90 = DT90, DT50back = DT50_back))
+  }
+  if (type == "DFOP") {
+    k1 = parms[["k1"]]
+    k2 = parms[["k2"]]
+    g = parms[["g"]]
+
+    f <- function(log_t, x) {
+      t <- exp(log_t)
+      fraction <- g * exp( - k1 * t) + (1 - g) * exp( - k2 * t)
+      (fraction - (1 - x/100))^2
+    }
+
+    DT50_k1 = log(2)/k1
+    DT50_k2 = log(2)/k2
+    DT90_k1 = log(10)/k1
+    DT90_k2 = log(10)/k2
+
+    DT50 <- try(exp(optimize(f, c(log(DT50_k1), log(DT50_k2)), x=50)$minimum),
+                silent = TRUE)
+    DT90 <- try(exp(optimize(f, c(log(DT90_k1), log(DT90_k2)), x=90)$minimum),
+                silent = TRUE)
+    if (inherits(DT50, "try-error")) DT50 = NA
+    if (inherits(DT90, "try-error")) DT90 = NA
+    DT50_back = DT90 / backcalculation_factor
+    return(c(DT50 = DT50, DT90 = DT90, DT50back = DT50_back, DT50_k1 = DT50_k1, DT50_k2 = DT50_k2))
+  }
+  if (type == "HS") {
+    k1 = parms[["k1"]]
+    k2 = parms[["k2"]]
+    tb = parms[["tb"]]
+    DTx <- function(x) {
+      DTx.a <- (log(100/(100 - x)))/k1
+      DTx.b <- tb + (log(100/(100 - x)) - k1 * tb)/k2
+      if (DTx.a < tb) DTx <- DTx.a
+      else DTx <- DTx.b
+      return(DTx)
+    }
+    DT50 <- DTx(50)
+    DT90 <- DTx(90)
+    DT50_back = DT90 / backcalculation_factor
+    DT50_k1 = log(2)/k1
+    DT50_k2 = log(2)/k2
+    return(c(DT50 = DT50, DT90 = DT90, DT50back = DT50_back, DT50_k1 = DT50_k1, DT50_k2 = DT50_k2))
+  }
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index a88e9cde..ebbe078b 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -94,6 +94,7 @@ reference:
       - plot.nafta
   - title: Utility functions
     contents:
+      - DTx
       - summary_listing
       - f_time_norm_focus
       - set_nd_nq
diff --git a/log/build.log b/log/build.log
index b2206986..0d9a46de 100644
--- a/log/build.log
+++ b/log/build.log
@@ -1,10 +1,10 @@
 * checking for file ‘./DESCRIPTION’ ... OK
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
-* installing the package to build vignettes
+* installing the package (it is needed to build vignettes)
 * 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/vignettes/web_only’
-* building ‘mkin_1.2.10.tar.gz’
+* building ‘mkin_1.2.11.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 7f212453..575e96c3 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,15 +1,16 @@
-* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.5.1 (2025-06-13)
+* using log directory ‘/home/f80868656/projects/mkin/mkin.Rcheck’
+* using R version 4.6.1 (2026-06-24)
 * using platform: x86_64-pc-linux-gnu
 * R was compiled by
-    gcc (Debian 12.2.0-14+deb12u1) 12.2.0
-    GNU Fortran (Debian 12.2.0-14+deb12u1) 12.2.0
-* running under: Debian GNU/Linux 13 (trixie)
+    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
+    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
+* running under: Ubuntu 24.04.4 LTS
 * using session charset: UTF-8
+* current time: 2026-09-07 10:01:19 UTC
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.10’
+* this is package ‘mkin’ version ‘1.2.11’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... OK
 * checking package namespace information ... OK
@@ -43,7 +44,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... [24s/15s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -60,17 +61,23 @@
 * checking sizes of PDF files under ‘inst/doc’ ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [12s/12s] OK
+* checking examples ... [37s/21s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
-* checking re-building of vignette outputs ... [15s/11s] OK
+* checking re-building of vignette outputs ... [30s/19s] OK
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... OK
+* checking HTML version of manual ... NOTE
+Skipping checking HTML validation: no command 'tidy' found.
+Please obtain a recent version of HTML Tidy by downloading a binary
+release or compiling the source code from <https://www.html-tidy.org/>.
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: OK
+Status: 1 NOTE
+See
+  ‘/home/f80868656/projects/mkin/mkin.Rcheck/00check.log’
+for details.
 
diff --git a/log/test.log b/log/test.log
index e1726492..33ee7dfd 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,44 +1,45 @@
 ℹ Testing mkin
 ✔ | F W  S  OK | Context
 ✔ |          5 | AIC calculation
-✔ |          5 | Analytical solutions for coupled models [1.6s]
+✔ |          5 | Analytical solutions for coupled models [2.8s]
 ✔ |          5 | Calculation of Akaike weights
 ✔ |          3 | Export dataset for reading into CAKE
-✔ |          6 | Use of precompiled symbols in mkinpredict [3.7s]
+✔ |          6 | Use of precompiled symbols in mkinpredict [4.7s]
 ✔ |         12 | Confidence intervals and p-values
 ✔ |          1 | Solutions with deSolve
-✔ |      1  12 | Dimethenamid data from 2018 [14.0s]
-✔ |         14 | Error model fitting [2.7s]
+✔ |      1  12 | Dimethenamid data from 2018 [24.3s]
+✔ |          4 | DTx calculations
+✔ |         14 | Error model fitting [4.0s]
 ✔ |          5 | Time step normalisation
 ✔ |          4 | Calculation of FOCUS chi2 error levels
 ✔ |         14 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
 ✔ |          4 | Test fitting the decline of metabolites from their maximum
 ✔ |          1 | Fitting the logistic model
-✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [20.5s]
-✔ |      2  20 | Nonlinear mixed-effects models [142.6s]
+✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [37.9s]
+✔ |      2  20 | Nonlinear mixed-effects models [283.3s]
 ✔ |          3 | Test dataset classes mkinds and mkindsg
 ✔ |         10 | Special cases of mkinfit calls
 ✔ |          3 | mkinfit features
 ✔ |          8 | mkinmod model generation and printing
 ✔ |          4 | Model predictions with mkinpredict
-✔ |         12 | Multistart method for saem.mmkin models [23.8s]
-✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |          9 | Nonlinear mixed-effects models with nlme [4.0s]
-✔ |         15 | Plotting [4.9s]
+✔ |         12 | Multistart method for saem.mmkin models [41.8s]
+✔ |         16 | Evaluations according to 2015 NAFTA guidance [2.6s]
+✔ |          9 | Nonlinear mixed-effects models with nlme [7.6s]
+✔ |         15 | Plotting [9.1s]
 ✔ |          4 | Residuals extracted from mkinfit models
-✔ |      1  38 | saemix parent models [36.1s]
+✔ |      1  38 | saemix parent models [66.6s]
 ✔ |          2 | Complex test case from Schaefer et al. (2007) Piacenza paper
 ✔ |         11 | Processing of residue series
-✔ |         10 | Fitting the SFORB model [1.7s]
+✔ |         10 | Fitting the SFORB model [3.0s]
 ✔ |          1 | Summaries of old mkinfit objects
 ✔ |          5 | Summary
-✔ |          4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
-✔ |          9 | Hypothesis tests [2.8s]
-✔ |          4 | Calculation of maximum time weighted average concentrations (TWAs)
+✔ |          4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.5s]
+✔ |          9 | Hypothesis tests [5.3s]
+✔ |          4 | Calculation of maximum time weighted average concentrations (TWAs) [1.5s]
 ✔ |          2 | water-sediment
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 265.7 s
+Duration: 503.1 s
 
 ── Skipped tests (4) ───────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 5 minutes on my new system
@@ -49,4 +50,4 @@ Duration: 265.7 s
 • This still takes almost 2.5 minutes although we do not solve ODEs (1):
   'test_saemix_parent.R:143:3'
 
-[ FAIL 0 | WARN 0 | SKIP 4 | PASS 291 ]
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 295 ]
diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index d8c4553e..61089081 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -43,12 +43,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/DTx.Rd b/man/DTx.Rd
new file mode 100644
index 00000000..67dba5d6
--- /dev/null
+++ b/man/DTx.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/endpoints.R
+\name{DTx}
+\alias{DTx}
+\title{Calculate DTx from parameters of parent degradation models}
+\usage{
+DTx(type = c("SFO", "FOMC", "DFOP", "HS", "SFORB"), parms, exact = FALSE)
+}
+\arguments{
+\item{type}{Character string specifying the degradation model}
+
+\item{parms}{Named numeric vector giving the kinetic parameters}
+
+\item{exact}{Should we used log(10)/log(2) instead of the widely used value
+of 3.32 for backcalculation of DT50 values from DT90 values?}
+}
+\description{
+Calculate DTx from parameters of parent degradation models
+}
+\examples{
+# Check what type of DT50 is given in the bixafen EFSA conclusion from 2012 on p. 42
+DTx("HS", parms = c(k1 = 0.0081, k2 = 0.00023, tb = 53))
+# We get 1200 days for the time the concentration reaches 50\%, the value of 1235
+# was likely based on more digits for the parameters. The half-life corresponding
+# to the slow phase is around 3000 days
+}
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index d645113c..456b406f 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -56,12 +56,12 @@ A new model based on spatial variability. \emph{Environmental Science and
 Technology} \bold{24}, 1032-1038
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 2940e949..9390a2e9 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -44,12 +44,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index 5d0126a7..9909e87c 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -49,12 +49,12 @@ NAFTA Technical Working Group on Pesticides (not dated) Guidance
 for Evaluating and Calculating Degradation Kinetics in Environmental Media
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
index c0aac237..f76837e8 100644
--- a/man/SFO.solution.Rd
+++ b/man/SFO.solution.Rd
@@ -37,12 +37,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index dc78d1f1..817e9788 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -47,12 +47,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/anova.saem.mmkin.Rd b/man/anova.saem.mmkin.Rd
index 34711c41..59c6754e 100644
--- a/man/anova.saem.mmkin.Rd
+++ b/man/anova.saem.mmkin.Rd
@@ -19,7 +19,7 @@
 
 \item{method}{Method for likelihood calculation: "is" (importance sampling),
 "lin" (linear approximation), or "gq" (Gaussian quadrature). Passed
-to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 
 \item{test}{Should a likelihood ratio test be performed? If TRUE,
 the alternative models are tested against the first model. Should
diff --git a/man/logLik.saem.mmkin.Rd b/man/logLik.saem.mmkin.Rd
index bd0bb72e..e3a29ad2 100644
--- a/man/logLik.saem.mmkin.Rd
+++ b/man/logLik.saem.mmkin.Rd
@@ -9,9 +9,9 @@
 \arguments{
 \item{object}{The fitted \link{saem.mmkin} object}
 
-\item{\dots}{Passed to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+\item{\dots}{Passed to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 
-\item{method}{Passed to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+\item{method}{Passed to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 }
 \description{
 logLik method for saem.mmkin objects
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 22944098..137043d9 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -78,12 +78,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index a2c58300..ce87fb7f 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -27,70 +27,71 @@ print(mds)
 
 }
 \section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{title}}{A full title for the dataset}
+  \if{html}{\out{<div class="r6-fields">}}
+  \describe{
+    \item{\code{title}}{A full title for the dataset}
 
-\item{\code{sampling_times}}{The sampling times}
+    \item{\code{sampling_times}}{The sampling times}
 
-\item{\code{time_unit}}{The time unit}
+    \item{\code{time_unit}}{The time unit}
 
-\item{\code{observed}}{Names of the observed variables}
+    \item{\code{observed}}{Names of the observed variables}
 
-\item{\code{unit}}{The unit of the observations}
+    \item{\code{unit}}{The unit of the observations}
 
-\item{\code{replicates}}{The maximum number of replicates per sampling time}
+    \item{\code{replicates}}{The maximum number of replicates per sampling time}
 
-\item{\code{data}}{A data frame with at least the columns name, time
+    \item{\code{data}}{A data frame with at least the columns name, time
 and value in order to be compatible with mkinfit}
-}
-\if{html}{\out{</div>}}
+  }
+  \if{html}{\out{</div>}}
 }
 \section{Methods}{
 \subsection{Public methods}{
-\itemize{
-\item \href{#method-mkinds-new}{\code{mkinds$new()}}
-\item \href{#method-mkinds-clone}{\code{mkinds$clone()}}
-}
+  \itemize{
+    \item \href{#method-mkinds-initialize}{\code{mkinds$new()}}
+    \item \href{#method-mkinds-clone}{\code{mkinds$clone()}}
+  }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-mkinds-new"></a>}}
-\if{latex}{\out{\hypertarget{method-mkinds-new}{}}}
-\subsection{Method \code{new()}}{
-Create a new mkinds object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}\if{html}{\out{</div>}}
+\if{html}{\out{<a id="method-mkinds-initialize"></a>}}
+\if{latex}{\out{\hypertarget{method-mkinds-initialize}{}}}
+\subsection{\code{mkinds$new()}}{
+  Create a new mkinds object
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{title}}{The dataset title}
+      \item{\code{data}}{The data}
+      \item{\code{time_unit}}{The time unit}
+      \item{\code{unit}}{The unit of the observations}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{title}}{The dataset title}
-
-\item{\code{data}}{The data}
-
-\item{\code{time_unit}}{The time unit}
-
-\item{\code{unit}}{The unit of the observations}
-}
-\if{html}{\out{</div>}}
-}
-}
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-mkinds-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-mkinds-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkinds$clone(deep = FALSE)}\if{html}{\out{</div>}}
+\subsection{\code{mkinds$clone()}}{
+  The objects of this class are cloneable with this method.
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkinds$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>}}
+  }
 }
 
-\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/mkindsg.Rd b/man/mkindsg.Rd
index 3b6a9f61..cb0c9bfd 100644
--- a/man/mkindsg.Rd
+++ b/man/mkindsg.Rd
@@ -37,69 +37,70 @@ print(mdsg, verbose = TRUE, data = TRUE)
 
 }
 \section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{title}}{A title for the dataset group}
+  \if{html}{\out{<div class="r6-fields">}}
+  \describe{
+    \item{\code{title}}{A title for the dataset group}
 
-\item{\code{ds}}{A list of mkinds objects}
+    \item{\code{ds}}{A list of mkinds objects}
 
-\item{\code{observed_n}}{Occurrence counts of compounds in datasets}
+    \item{\code{observed_n}}{Occurrence counts of compounds in datasets}
 
-\item{\code{f_time_norm}}{Time normalisation factors}
+    \item{\code{f_time_norm}}{Time normalisation factors}
 
-\item{\code{meta}}{A data frame with a row for each dataset,
+    \item{\code{meta}}{A data frame with a row for each dataset,
 containing additional information in the form
 of categorical data (factors) or numerical data
 (e.g. temperature, moisture,
 or covariates like soil pH).}
-}
-\if{html}{\out{</div>}}
+  }
+  \if{html}{\out{</div>}}
 }
 \section{Methods}{
 \subsection{Public methods}{
-\itemize{
-\item \href{#method-mkindsg-new}{\code{mkindsg$new()}}
-\item \href{#method-mkindsg-clone}{\code{mkindsg$clone()}}
-}
+  \itemize{
+    \item \href{#method-mkindsg-initialize}{\code{mkindsg$new()}}
+    \item \href{#method-mkindsg-clone}{\code{mkindsg$clone()}}
+  }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-mkindsg-new"></a>}}
-\if{latex}{\out{\hypertarget{method-mkindsg-new}{}}}
-\subsection{Method \code{new()}}{
-Create a new mkindsg object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)}\if{html}{\out{</div>}}
+\if{html}{\out{<a id="method-mkindsg-initialize"></a>}}
+\if{latex}{\out{\hypertarget{method-mkindsg-initialize}{}}}
+\subsection{\code{mkindsg$new()}}{
+  Create a new mkindsg object
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{title}}{The title}
+      \item{\code{ds}}{A list of mkinds objects}
+      \item{\code{f_time_norm}}{Time normalisation factors}
+      \item{\code{meta}}{The meta data}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{title}}{The title}
-
-\item{\code{ds}}{A list of mkinds objects}
-
-\item{\code{f_time_norm}}{Time normalisation factors}
-
-\item{\code{meta}}{The meta data}
-}
-\if{html}{\out{</div>}}
-}
-}
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-mkindsg-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-mkindsg-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkindsg$clone(deep = FALSE)}\if{html}{\out{</div>}}
+\subsection{\code{mkindsg$clone()}}{
+  The objects of this class are cloneable with this method.
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkindsg$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>}}
+  }
 }
 
-\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/reexports.Rd b/man/reexports.Rd
index 43d27ac1..4608450f 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -1,5 +1,6 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R, R/nlme.mmkin.R
+% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R,
+%   R/nlme.mmkin.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
@@ -13,8 +14,8 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{lmtest}{\code{\link[lmtest]{lrtest}}}
+  \item{lmtest}{\code{\link[lmtest:lrtest]{lrtest()}}}
 
-  \item{nlme}{\code{\link[nlme]{intervals}}, \code{\link[nlme]{nlme}}}
+  \item{nlme}{\code{\link[nlme:intervals]{intervals()}}, \code{\link[nlme:nlme]{nlme()}}}
 }}
 
diff --git a/man/saem.Rd b/man/saem.Rd
index 5a125ab6..73e42535 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -118,7 +118,7 @@ iterations}
 \item{control}{Passed to \link[saemix:saemix]{saemix::saemix}.}
 
 \item{verbose}{Should we print information about created objects of
-type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?}
+type \link[saemix:SaemixModel]{saemix::SaemixModel} and \link[saemix:SaemixData]{saemix::SaemixData}?}
 
 \item{quiet}{Should we suppress the messages saemix prints at the beginning
 and the end of the optimisation process?}
@@ -129,12 +129,12 @@ and the end of the optimisation process?}
 }
 \value{
 An S3 object of class 'saem.mmkin', containing the fitted
-\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The
+\link[saemix:SaemixObject]{saemix::SaemixObject} as a list component named 'so'. The
 object also inherits from 'mixed.mmkin'.
 
-An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object.
+An \link[saemix:SaemixModel]{saemix::SaemixModel} object.
 
-An \link[saemix:SaemixData-class]{saemix::SaemixData} object.
+An \link[saemix:SaemixData]{saemix::SaemixData} object.
 }
 \description{
 This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index 41932547..1c27e941 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -42,7 +42,7 @@ included.}
 \item{digits}{Number of digits to use for printing}
 }
 \value{
-The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject}
+The summary function returns a list based on the \link[saemix:SaemixObject]{saemix::SaemixObject}
 obtained in the fit, with at least the following additional components
 \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used}
 \item{date.fit, date.summary}{The dates where the fit and the summary were
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 3a97ff8d..09723fb8 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -42,7 +42,7 @@ of the estimator. The default (TRUE) is to do transformations.
 The g parameter of the DFOP model is also seen as a fraction.
 If a single fraction is transformed (g parameter of DFOP or only a single
 target variable e.g. a single metabolite plus a pathway to sink), a
-logistic transformation is used \code{\link[stats:Logistic]{stats::qlogis()}}. In other cases, i.e. if
+logistic transformation is used \code{\link[stats:qlogis]{stats::qlogis()}}. In other cases, i.e. if
 two or more formation fractions need to be transformed whose sum cannot
 exceed one, the \link{ilr} transformation is used.}
 
diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
index 3b9d51fb..4c91a43e 100644
--- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
+++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
@@ -27,20 +27,22 @@
 <line x1='471.73' y1='502.56' x2='471.73' y2='509.76' style='stroke-width: 0.75;' />
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 <line x1='666.40' y1='502.56' x2='666.40' y2='509.76' style='stroke-width: 0.75;' />
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+<text x='82.40' y='528.48' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='40.70px' lengthAdjust='spacingAndGlyphs'>-1149.5</text>
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+<text x='374.40' y='528.48' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='40.70px' lengthAdjust='spacingAndGlyphs'>-1149.2</text>
+<text x='471.73' y='528.48' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='40.70px' lengthAdjust='spacingAndGlyphs'>-1149.1</text>
+<text x='569.07' y='528.48' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='40.70px' lengthAdjust='spacingAndGlyphs'>-1149.0</text>
+<text x='666.40' y='528.48' text-anchor='middle' style='font-size: 12.00px; font-family: sans;' textLength='40.70px' lengthAdjust='spacingAndGlyphs'>-1148.9</text>
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 <line x1='59.04' y1='75.47' x2='51.84' y2='75.47' style='stroke-width: 0.75;' />
 <text x='44.64' y='490.26' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>0</text>
-<text x='44.64' y='284.93' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>1</text>
-<text x='44.64' y='79.60' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>2</text>
+<text x='44.64' y='353.37' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>1</text>
+<text x='44.64' y='216.48' text-anchor='end' style='font-size: 12.00px; font-family: sans;' textLength='6.67px' lengthAdjust='spacingAndGlyphs'>2</text>
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 </g>
 <defs>
   <clipPath id='cpNTkuMDR8Njg5Ljc2fDU5LjA0fDUwMi41Ng=='>
@@ -48,13 +50,13 @@
   </clipPath>
 </defs>
 <g clip-path='url(#cpNTkuMDR8Njg5Ljc2fDU5LjA0fDUwMi41Ng==)'>
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diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg
index c94012ce..76fed0dc 100644
--- a/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg
+++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg
@@ -813,7 +813,7 @@
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@@ -921,7 +921,7 @@
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@@ -964,8 +964,8 @@
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@@ -1243,8 +1243,8 @@
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diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt
index 3a1f1667..3d036357 100644
--- a/tests/testthat/print_dfop_saem_1.txt
+++ b/tests/testthat/print_dfop_saem_1.txt
@@ -9,15 +9,15 @@ Data:
 
 Likelihood computed by importance sampling
    AIC  BIC logLik
-  1409 1415   -696
+  1409 1414   -696
 
 Fitted parameters:
           estimate lower  upper
-parent_0     99.96 98.82 101.11
-log_k1       -2.71 -2.94  -2.49
+parent_0     99.97 98.83 101.12
+log_k1       -2.71 -2.94  -2.48
 log_k2       -4.14 -4.26  -4.01
 g_qlogis     -0.36 -0.54  -0.17
-a.1           0.93  0.69   1.17
+a.1           0.92  0.68   1.17
 b.1           0.05  0.04   0.05
-SD.log_k1     0.37  0.23   0.51
+SD.log_k1     0.37  0.23   0.52
 SD.log_k2     0.23  0.14   0.31
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index b2147fbe..111daa30 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -4,7 +4,12 @@ require(testthat)
 # Per default (on my box where I set NOT_CRAN in .Rprofile) use all cores minus one
 # Otherwise (CRAN check systems) use the allowed maximum of two cores
 if (identical(Sys.getenv("NOT_CRAN"), "true")) {
-  n_cores <- parallel::detectCores() - 1
+  # We cannot use all course if on the Agroscope cluster, if not we use all but one
+  if (grepl("agsad.admin.ch", Sys.getenv("http_proxy"))) {
+    n_cores = 16
+  } else {
+    n_cores <- parallel::detectCores() - 1
+  }
 } else {
   n_cores <- 2
 }
diff --git a/tests/testthat/test_deSolve.R b/tests/testthat/test_deSolve.R
index 3d15de35..c7acdc43 100644
--- a/tests/testthat/test_deSolve.R
+++ b/tests/testthat/test_deSolve.R
@@ -13,7 +13,8 @@ test_that("Solutions with deSolve work if we have no observations at time zero",
     solution_type = "deSolve", quiet = TRUE)
   expect_equal(
     parms(f_sfo_sfo_nozero),
-    parms(f_sfo_sfo_nozero_deSolve)
+    parms(f_sfo_sfo_nozero_deSolve),
+    tolerance = 1e-5
   )
 })
 
diff --git a/tests/testthat/test_endpoints.R b/tests/testthat/test_endpoints.R
new file mode 100644
index 00000000..284e1379
--- /dev/null
+++ b/tests/testthat/test_endpoints.R
@@ -0,0 +1,49 @@
+context("DTx calculations")
+
+test_that("The DTx function gives the same results as the endpoints function", {
+  # We silently assume that the calculations in the endpoint function are correct
+
+  SFO_fit <- fits[["SFO", "FOCUS_C"]]
+  SFO_distimes <- endpoints(SFO_fit)$distimes
+  SFO_DTx <- DTx("SFO", c(k = parms(SFO_fit)[["k_parent"]]))
+
+  expect_equal(
+    as.numeric(SFO_distimes),
+    as.numeric(SFO_DTx)
+  )
+
+  FOMC_fit <- fits[["FOMC", "FOCUS_C"]]
+  FOMC_distimes <- endpoints(FOMC_fit)$distimes
+  FOMC_DTx <- DTx("FOMC", c(
+      alpha = parms(FOMC_fit)[["alpha"]],
+      beta = parms(FOMC_fit)[["beta"]]), exact = TRUE)
+
+  expect_equal(
+    as.numeric(FOMC_distimes),
+    as.numeric(FOMC_DTx)
+  )
+
+  DFOP_fit <- fits[["DFOP", "FOCUS_C"]]
+  DFOP_distimes <- endpoints(DFOP_fit)$distimes
+  DFOP_DTx <- DTx("DFOP", c(
+      k1 = parms(DFOP_fit)[["k1"]],
+      k2 = parms(DFOP_fit)[["k2"]],
+      g = parms(DFOP_fit)[["g"]]), exact = TRUE)
+
+  expect_equal(
+    as.numeric(DFOP_distimes),
+    as.numeric(DFOP_DTx)
+  )
+
+  HS_fit <- fits[["HS", "FOCUS_C"]]
+  HS_distimes <- endpoints(HS_fit)$distimes
+  HS_DTx <- DTx("HS", c(
+      k1 = parms(HS_fit)[["k1"]],
+      k2 = parms(HS_fit)[["k2"]],
+      tb = parms(HS_fit)[["tb"]]), exact = TRUE)
+
+  expect_equal(
+    as.numeric(HS_distimes),
+    as.numeric(HS_DTx)
+  )
+})
author	Ranke Johannes <johannes.ranke@agroscope.admin.ch>	2026-09-07 13:45:39 +0200
committer	Ranke Johannes <johannes.ranke@agroscope.admin.ch>	2026-09-07 13:45:39 +0200
commit	48d9cad339394c3aa0d730d9a27b1c0680ce13e8 (patch)
tree	9c0a5766f3d0853c382ba0174f83e2e8ac9b0fbf
parent	46735d7a6d429bb0c50f951763797f321a0d77ca (diff)