Improvements to CAKE_export()

7 files changed, 45 insertions, 45 deletions

diff --git a/NEWS.md b/NEWS.md
index e675fc72..1524e1cf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,8 @@
 
 - 'dimethenamid_2018': Update example code to use saemix
 
+- 'CAKE_export': Check for validity of the map argument, updates
+
 # mkin 1.1.0 (2022-03-14)
 
 ## Mixed-effects models
diff --git a/R/CAKE_export.R b/R/CAKE_export.R
index 70661b10..b16f186a 100644
--- a/R/CAKE_export.R
+++ b/R/CAKE_export.R
@@ -28,11 +28,11 @@
 CAKE_export <- function(ds, map = c(parent = "Parent"),
   links = NA,
   filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
-  study = "Codlemone aerobic soil degradation",
+  study = "Degradinol aerobic soil degradation",
   description = "",
   time_unit = "days",
   res_unit = "% AR",
-  comment = "Created using mkin::CAKE_export",
+  comment = "",
   date = Sys.Date(),
   optimiser = "IRLS")
 {
@@ -41,11 +41,16 @@ CAKE_export <- function(ds, map = c(parent = "Parent"),
   csf <- file(file, encoding = "latin1", open = "w+")
   on.exit(close(csf))
 
+  CAKE_compartments = c("Parent", "A1", "A2", "A3", "B1", "B2", "C1")
+  if (!all(map %in% CAKE_compartments)) {
+    stop("The elements of map have to be CAKE compartment names")
+  }
+
   add <- function(x) cat(paste0(x, "\r\n"), file = csf, append = TRUE)
   add0 <- function(x) cat(x, file = csf, append = TRUE)
 
   add("[FileInfo]")
-  add("CAKE-Version: 3.3 (Release)")
+  add("CAKE-Version: 3.4 (Release)")
   add(paste("Name:", study))
   add(paste("Description:", description))
   add(paste("MeasurementUnits:", res_unit))
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
index 4bcd8581..fc0aedf5 100644
--- a/man/CAKE_export.Rd
+++ b/man/CAKE_export.Rd
@@ -11,11 +11,11 @@ CAKE_export(
   filename = "CAKE_export.csf",
   path = ".",
   overwrite = FALSE,
-  study = "Codlemone aerobic soil degradation",
+  study = "Degradinol aerobic soil degradation",
   description = "",
   time_unit = "days",
   res_unit = "\% AR",
-  comment = "Created using mkin::CAKE_export",
+  comment = "",
   date = Sys.Date(),
   optimiser = "IRLS"
 )
diff --git a/test.log b/test.log
index cd168e7f..4c273c19 100644
--- a/test.log
+++ b/test.log
@@ -3,65 +3,49 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.3s]
+✔ |         5 | Analytical solutions for coupled models [3.4s]
 ✔ |         5 | Calculation of Akaike weights
-✔ |         2 | Export dataset for reading into CAKE
+✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.2s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.7s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [4.7s]
+✔ |        14 | Error model fitting [5.0s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.2s]
+✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.4s]
+✔ |        10 | Special cases of mkinfit calls [0.5s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.3s]
 ✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.2s]
-✔ |   5    16 | Plotting [10.5s]
-────────────────────────────────────────────────────────────────────────────────
-Warning (test_plot.R:48:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-mmkin-object.svg'
-
-Warning (test_plot.R:51:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-saemix-transformations.svg'
-
-Warning (test_plot.R:56:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-nlme-object.svg'
-
-Warning (test_plot.R:64:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-mkin-transformations.svg'
-
-Warning (test_plot.R:68:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Adding new file snapshot: 'tests/testhat/_snaps/plot-errmod-with-focus-d-obs-eigen.svg'
-────────────────────────────────────────────────────────────────────────────────
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.6s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
+✔ |        16 | Plotting [10.4s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [28.9s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
-✔ |         7 | Fitting the SFORB model [3.8s]
+✔ |        23 | saemix parent models [28.0s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
+✔ |         7 | Fitting the SFORB model [3.7s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
-✔ |         9 | Hypothesis tests [8.2s]
+✔ |         9 | Hypothesis tests [8.1s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 111.6 s
+Duration: 112.8 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 
-[ FAIL 0 | WARN 5 | SKIP 2 | PASS 221 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 222 ]
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 5969712b..180091ab 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -1,11 +1,11 @@
 [FileInfo]
-CAKE-Version: 3.3 (Release)
+CAKE-Version: 3.4 (Release)
 Name: FOCUS 2006 D
 Description: 
 MeasurementUnits: % AR
 TimeUnits: days
-Comments: Created using mkin::CAKE_export
-Date: Dummy date 0000-00-00
+Comments: 
+Date: 1900-01-01
 Optimiser: IRLS
 
 [Data]
@@ -22,7 +22,7 @@ Time	Parent
 119	0.6
 
 NewDataSet: FOCUS D
-Time	Parent	M1
+Time	Parent	A1
 0	99.46	0
 0	102.04	0
 1	93.5	4.84
@@ -49,9 +49,9 @@ Time	Parent	M1
 
 [Model]
 ParentCompartment: Parent	parent	parent
-Compartment: M1	m1	m1
-Link: Parent	M1	0.5	0	1	Free	Explicit
+Compartment: A1	m1	m1
+Link: Parent	A1	0.5	0	1	Free	Explicit
 
 [ComponentNames]
 Parent:parent
-M1:m1
+A1:m1
diff --git a/tests/testthat/FOCUS_2006_D.rds b/tests/testthat/FOCUS_2006_D.rds
index ff3b4f0f..3df805c8 100644
--- a/tests/testthat/FOCUS_2006_D.rds
+++ b/tests/testthat/FOCUS_2006_D.rds
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index b3941f1b..abedc9eb 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -1,13 +1,22 @@
 context("Export dataset for reading into CAKE")
 
 test_that("Exporting is reproducible", {
-  CAKE_export(
+  expect_error(CAKE_export(
     ds = list("FOCUS C" = FOCUS_2006_C,
               "FOCUS D" = FOCUS_2006_D),
     map = c(parent = "Parent", m1 = "M1"),
     links = c(parent = "m1"),
     filename = "FOCUS_2006_D.csf", overwrite = TRUE,
-    study = "FOCUS 2006 D", date = "Dummy date 0000-00-00")
+    study = "FOCUS 2006 D", date = "1900-01-01"),
+    "elements of map have to be CAKE compartment names"
+  )
+  CAKE_export(
+    ds = list("FOCUS C" = FOCUS_2006_C,
+              "FOCUS D" = FOCUS_2006_D),
+    map = c(parent = "Parent", m1 = "A1"),
+    links = c(parent = "m1"),
+    filename = "FOCUS_2006_D.csf", overwrite = TRUE,
+    study = "FOCUS 2006 D", date = "1900-01-01")
   csf <- readLines(con = "FOCUS_2006_D.csf")
   expect_known_value(csf, file = "FOCUS_2006_D.rds")
   expect_error(CAKE_export(ds = list("FOCUS C" = FOCUS_2006_C),