Fast analytical solutions for saemix, update.mmkin

Also, use logit transformation for g and for solitary formation
fractions, addressing #10.

4 files changed, 197 insertions, 162 deletions

diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index b5a83146..88e9ad5c 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -1,4 +1,4 @@
-parent_0   log_k1     log_k2     g_ilr      
+parent_0   log_k1     log_k2     g_qlogis   
   85.10000   -2.30259   -4.60517    0.00000 
 Sum of squared residuals at call 1: 7391.39
   85.10000   -2.30259   -4.60517    0.00000 
@@ -7,159 +7,194 @@ Sum of squared residuals at call 3: 7391.39
   85.10000   -2.30259   -4.60517    0.00000 
 Sum of squared residuals at call 4: 7391.39
  8.51000e+01 -2.30259e+00 -4.60517e+00  1.49012e-08 
- 85.063710  -1.773280  -4.250366   0.769827 
-Sum of squared residuals at call 6: 2000.13
- 85.063752  -1.773280  -4.250366   0.769827 
- 85.063710  -1.773322  -4.250366   0.769827 
- 85.063710  -1.773280  -4.250408   0.769827 
- 85.063710  -1.773280  -4.250366   0.769785 
- 85.035419  -0.960852  -4.115460   1.336361 
-Sum of squared residuals at call 11: 32.978
- 85.035421  -0.960852  -4.115460   1.336361 
- 85.035419  -0.960853  -4.115460   1.336361 
- 85.035419  -0.960852  -4.115460   1.336361 
- 85.035419  -0.960852  -4.115460   1.336361 
- 85.037040  -0.256064  -4.273512   0.644775 
- 85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 17: 5.34813
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-Sum of squared residuals at call 18: 5.34813
- 85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 19: 5.34813
- 85.032855  -0.782283  -4.127513   1.312494 
- 85.032855  -0.782283  -4.127513   1.312494 
-Sum of squared residuals at call 21: 5.34813
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-Sum of squared residuals at call 23: 4.70444
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-Sum of squared residuals at call 24: 4.70444
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- 85.031268  -0.790907  -4.114800   1.268157 
-Sum of squared residuals at call 26: 4.70443
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- 85.030010  -0.780151  -4.069435   1.262797 
-Sum of squared residuals at call 28: 4.42162
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- 85.030010  -0.780151  -4.069435   1.262797 
-Sum of squared residuals at call 30: 4.42162
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-Sum of squared residuals at call 34: 4.41435
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-Sum of squared residuals at call 36: 4.41435
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-Sum of squared residuals at call 39: 4.37246
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- 85.028119  -0.777813  -4.042219   1.253890 
-Sum of squared residuals at call 41: 4.37246
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- 85.028119  -0.777813  -4.042219   1.253890 
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-Sum of squared residuals at call 45: 4.36931
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-Sum of squared residuals at call 47: 4.36931
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-Sum of squared residuals at call 49: 4.36931
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-Sum of squared residuals at call 50: 4.36506
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- 85.022674  -0.778681  -4.029670   1.252015 
-Sum of squared residuals at call 53: 4.36506
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-Sum of squared residuals at call 55: 4.36408
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-Sum of squared residuals at call 56: 4.36408
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-Sum of squared residuals at call 57: 4.36408
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- 85.016327  -0.776316  -4.027611   1.248897 
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-Sum of squared residuals at call 60: 4.36405
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-Sum of squared residuals at call 61: 4.36405
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-Sum of squared residuals at call 62: 4.36405
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-Sum of squared residuals at call 64: 4.36405
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-Sum of squared residuals at call 65: 4.36275
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-Sum of squared residuals at call 67: 4.36275
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-Sum of squared residuals at call 70: 4.36272
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-Sum of squared residuals at call 71: 4.36272
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-Sum of squared residuals at call 75: 4.36271
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-Sum of squared residuals at call 77: 4.36271
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-Sum of squared residuals at call 82: 4.36271
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-Sum of squared residuals at call 83: 4.36271
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-Sum of squared residuals at call 86: 4.36271
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-Sum of squared residuals at call 91: 4.36271
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-Sum of squared residuals at call 93: 4.36271
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-Sum of squared residuals at call 94: 4.36271
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-Sum of squared residuals at call 100: 4.36271
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-Sum of squared residuals at call 109: 4.36271
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+Sum of squared residuals at call 6: 2451.52
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+Sum of squared residuals at call 7: 13.7829
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+Sum of squared residuals at call 8: 13.7829
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+Sum of squared residuals at call 9: 13.7826
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+Sum of squared residuals at call 14: 11.2376
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+Sum of squared residuals at call 19: 10.0865
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+Sum of squared residuals at call 20: 10.0865
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+Sum of squared residuals at call 21: 10.0865
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+Sum of squared residuals at call 24: 9.53394
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+Sum of squared residuals at call 25: 9.53394
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+Sum of squared residuals at call 26: 9.53394
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+Sum of squared residuals at call 29: 7.68535
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+Sum of squared residuals at call 30: 7.68535
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+Sum of squared residuals at call 31: 7.68535
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+Sum of squared residuals at call 33: 7.68534
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+Sum of squared residuals at call 34: 6.54485
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+Sum of squared residuals at call 35: 6.54485
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+Sum of squared residuals at call 39: 5.4816
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+Sum of squared residuals at call 40: 5.4816
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+Sum of squared residuals at call 41: 5.48159
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+Sum of squared residuals at call 45: 4.96084
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+Sum of squared residuals at call 46: 4.96084
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+Sum of squared residuals at call 47: 4.96084
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+Sum of squared residuals at call 50: 4.5314
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+Sum of squared residuals at call 57: 4.51486
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+Sum of squared residuals at call 58: 4.51486
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+Sum of squared residuals at call 59: 4.51486
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+Sum of squared residuals at call 61: 4.51485
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+Sum of squared residuals at call 62: 4.49757
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+Sum of squared residuals at call 63: 4.49757
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+Sum of squared residuals at call 67: 4.46771
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+Sum of squared residuals at call 68: 4.46771
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+Sum of squared residuals at call 69: 4.46771
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+Sum of squared residuals at call 72: 4.42694
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+Sum of squared residuals at call 73: 4.42694
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+Sum of squared residuals at call 76: 4.42694
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+Sum of squared residuals at call 78: 4.41527
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+Sum of squared residuals at call 79: 4.41527
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+Sum of squared residuals at call 81: 4.41527
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+Sum of squared residuals at call 84: 4.39987
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+Sum of squared residuals at call 86: 4.39987
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+Sum of squared residuals at call 89: 4.38752
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+Sum of squared residuals at call 91: 4.38752
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+Sum of squared residuals at call 94: 4.36452
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+Sum of squared residuals at call 98: 4.36452
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+Sum of squared residuals at call 99: 4.36272
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+Sum of squared residuals at call 100: 4.36272
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+Sum of squared residuals at call 101: 4.36272
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+Sum of squared residuals at call 103: 4.36272
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+Sum of squared residuals at call 104: 4.36271
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+Sum of squared residuals at call 106: 4.36271
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+Sum of squared residuals at call 110: 4.36271
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+Sum of squared residuals at call 111: 4.36271
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+Sum of squared residuals at call 114: 4.36271
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+Sum of squared residuals at call 119: 4.36271
+ 85.002737  -0.777491  -4.025819   1.765887 
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+Sum of squared residuals at call 121: 4.36271
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+Sum of squared residuals at call 126: 4.36271
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+Sum of squared residuals at call 128: 4.36271
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+ 85.002736  -0.777491  -4.025819   1.765889 
+ 85.002736  -0.777491  -4.025819   1.765885 
+ 85.002736  -0.777491  -4.025819   1.765887 
+ 85.002736  -0.777491  -4.025819   1.765887   0.696237 
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index c7cb6d41..8da4cd91 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: 2020-11-04
+Date: 2020-11-05
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index b9ba7c17..2b0210c0 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -28,7 +28,7 @@ Starting values for the transformed parameters actually optimised:
 parent_0 85.100000  -Inf   Inf
 log_k1   -2.302585  -Inf   Inf
 log_k2   -4.605170  -Inf   Inf
-g_ilr     0.000000  -Inf   Inf
+g_qlogis  0.000000  -Inf   Inf
 
 Fixed parameter values:
 None
@@ -43,7 +43,7 @@ Optimised, transformed parameters with symmetric confidence intervals:
 parent_0  85.0000    0.66620 83.1500 86.8500
 log_k1    -0.7775    0.03380 -0.8713 -0.6836
 log_k2    -4.0260    0.13100 -4.3890 -3.6620
-g_ilr      1.2490    0.05811  1.0870  1.4100
+g_qlogis   1.7660    0.08218  1.5380  1.9940
 sigma      0.6962    0.16410  0.2406  1.1520
 
 Parameter correlation:
diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R
index 703298d5..60f5d600 100644
--- a/tests/testthat/test_schaefer07_complex_case.R
+++ b/tests/testthat/test_schaefer07_complex_case.R
@@ -1,8 +1,8 @@
 context("Complex test case from Schaefer et al. (2007) Piacenza paper")

 

 test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {

-  

-  skip_on_cran()         

+

+  skip_on_cran()

   schaefer07_complex_model <- mkinmod(

     parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),

     A1 = list(type = "SFO", to = "A2"),