mkinfit: Ignore unused components of state.ini

5 files changed, 20 insertions, 6 deletions

diff --git a/NEWS.md b/NEWS.md
index 25fe7f14..8f99b2f9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -16,6 +16,8 @@
 
 - 'mmkin': Do not fail any more if one of the fits fails, but assign the try-error to the respective position in the mmkin object
 
+- 'mkinfit': Ignore components of state.ini that do not correspond to state variables in the model
+
 # mkin 0.9.50.2 (2020-05-12)
 
 - Increase tolerance for a platform specific test results on the Solaris test machine on CRAN
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 12df0325..ee7c0b99 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -424,7 +424,8 @@ mkinfit <- function(mkinmod, observed,
     state.ini_used <- state.ini_auto
   } else {
     state.ini_used <- state.ini_auto
-    state.ini_used[names(state.ini)] <- state.ini
+    state.ini_good <- intersect(names(mkinmod$diffs), names(state.ini))
+    state.ini_used[state.ini_good] <- state.ini[state.ini_good]
   }
   state.ini <- state.ini_used
 
diff --git a/test.log b/test.log
index e96960ef..6e3c2c06 100644
--- a/test.log
+++ b/test.log
@@ -9,10 +9,11 @@ Testing mkin
 ✔ |   5       | Analytical solutions for coupled models [3.2 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  10       | Confidence intervals and p-values [1.1 s]
-✔ |  14       | Error model fitting [3.7 s]
+✔ |  14       | Error model fitting [3.8 s]
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
+✔ |   1       | mkinfit features [0.2 s]
 ✔ |  12       | Special cases of mkinfit calls [0.6 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
@@ -31,7 +32,7 @@ test_plot.R:24: skip: Plotting mkinfit and mmkin objects is reproducible
 Reason: getRversion() < "4.1.0"  is TRUE
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
 ✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
@@ -39,9 +40,9 @@ Reason: getRversion() < "4.1.0"  is TRUE
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 36.8 s
+Duration: 37.1 s
 
-OK:       145
+OK:       146
 Failed:   0
 Warnings: 0
 Skipped:  3
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 232d7dad..a340a0a5 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-07-15
+Date: 2020-07-17
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_mkinfit.R b/tests/testthat/test_mkinfit.R
new file mode 100644
index 00000000..fb81c3d8
--- /dev/null
+++ b/tests/testthat/test_mkinfit.R
@@ -0,0 +1,10 @@
+context("mkinfit features")
+
+test_that("Specifying initial values for state variables works correctly", {
+  f_1 <- mkinfit("SFO", FOCUS_2006_C, state.ini = c(parent = 100), quiet = TRUE)
+  f_2 <- mkinfit("SFO", FOCUS_2006_C, state.ini = c(parrrent = 100), quiet = TRUE)
+
+  # Before mkin 0.9.50.3, these would give different degrees of freedom,
+  # also affecting AIC calculations
+  expect_equal(logLik(f_1), logLik(f_2))
+})