From 95178837d3f91e84837628446b5fd468179af2b9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Jun 2019 15:09:28 +0200 Subject: Additional algorithm "d_c", more tests, docs The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets. --- docs/articles/web_only/FOCUS_Z.html | 6 +- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 85592 -> 84962 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 128674 -> 127841 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 127674 -> 127069 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 96502 -> 95832 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22316 -> 22086 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 86198 -> 85657 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 85812 -> 85239 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 101996 -> 101416 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 128979 -> 128185 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 128634 -> 127782 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 108437 -> 107730 bytes docs/articles/web_only/NAFTA_examples.html | 103 +++++++-------- .../NAFTA_examples_files/figure-html/p10-1.png | Bin 53933 -> 53828 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 51316 -> 51210 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 54573 -> 54489 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 47194 -> 47070 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 51486 -> 51343 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 54036 -> 53898 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 51194 -> 51113 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 53096 -> 52979 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 62542 -> 62414 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 55386 -> 55286 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 53549 -> 53505 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 54945 -> 54907 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 66786 -> 66710 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 61538 -> 61400 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 53061 -> 53005 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 50009 -> 49914 bytes docs/articles/web_only/benchmarks.html | 140 +++++++++++---------- docs/articles/web_only/compiled_models.html | 20 +-- 31 files changed, 138 insertions(+), 131 deletions(-) (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 9184fad5..555400df 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -30,7 +30,7 @@ mkin - 0.9.49.4 + 0.9.49.5 @@ -88,7 +88,7 @@

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2019-05-08

+

2019-06-04

@@ -377,7 +377,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

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Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

Johannes Ranke

-

2019-05-08

+

2019-06-04

@@ -308,16 +308,11 @@ Example on page 8

For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.

p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))
-
## Warning in summary.mkinfit(x): Could not calculate correlation; no
-## covariance matrix
-
-## Warning in summary.mkinfit(x): Could not calculate correlation; no
-## covariance matrix
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-
plot(p8)
+
plot(p8)

-
print(p8)
+
print(p8)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 1996.9408  444.9237  547.5616 
@@ -327,11 +322,10 @@
 ## 
 ## Parameters:
 ## $SFO
-##                     Estimate Pr(>t) Lower Upper
-## parent_0            88.16549     NA    NA    NA
-## k__iore_parent_sink  0.00100     NA    NA    NA
-## k_parent_sink        0.00803     NA    NA    NA
-## sigma                7.44786     NA    NA    NA
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      88.16549 6.53e-29 83.37344 92.95754
+## k_parent_sink  0.00803 1.67e-13  0.00674  0.00957
+## sigma          7.44786 4.17e-10  5.66209  9.23363
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
@@ -341,13 +335,12 @@
 ## sigma               3.52e+00 5.36e-10 2.67e+00 4.36e+00
 ## 
 ## $DFOP
-##                     Estimate Pr(>t) Lower Upper
-## parent_0            95.70619     NA    NA    NA
-## k__iore_parent_sink  0.00100     NA    NA    NA
-## k1                   0.02500     NA    NA    NA
-## k2                   0.00273     NA    NA    NA
-## g                    0.58835     NA    NA    NA
-## sigma                3.90001     NA    NA    NA
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 95.70619 8.99e-32 91.87941 99.53298
+## k1        0.02500 5.25e-04  0.01422  0.04394
+## k2        0.00273 6.84e-03  0.00125  0.00597
+## g         0.58835 2.84e-06  0.36595  0.77970
+## sigma     3.90001 6.94e-10  2.96260  4.83741
 ## 
 ## 
 ## DTx values:
@@ -366,12 +359,12 @@
 

 

 Example on page 9, upper panel

-
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])

+
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p9a)

+
plot(p9a)

 

-
print(p9a)

+
print(p9a)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 839.35238  88.57064   9.93363 
@@ -415,7 +408,7 @@
 

 

 Example on page 9, lower panel

-
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])

+
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

@@ -423,9 +416,9 @@
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p9b)

+
plot(p9b)

 

-
print(p9b)

+
print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -469,12 +462,12 @@
 

 

 Example on page 10

-
p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

+
p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p10)

+
plot(p10)

 

-
print(p10)

+
print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -522,12 +515,12 @@
 

 

 Example on page 11

-
p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

+
p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p11)

+
plot(p11)

 

-
print(p11)

+
print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -576,14 +569,14 @@
 

 

 Example on page 12, upper panel

-
p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

+
p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

 
## Warning in summary.mkinfit(x): Could not calculate correlation; no
 ## covariance matrix

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p12a)

+
plot(p12a)

 

-
print(p12a)

+
print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -626,7 +619,7 @@
 

 

 Example on page 12, lower panel

-
p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

+
p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt

 
## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt

@@ -637,9 +630,9 @@
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p12b)

+
plot(p12b)

 

-
print(p12b)

+
print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -682,16 +675,16 @@
 

 

 Example on page 13

-
p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

+
p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

 
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p13)

+
plot(p13)

 

-
print(p13)

+
print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -735,16 +728,16 @@
 

 

 DT50 not observed in the study and DFOP problems in PestDF

-
p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

+
p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

 
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p14)

+
plot(p14)

 

-
print(p14)

+
print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -788,7 +781,7 @@
 

 

 N is less than 1 and DFOP fraction parameter is below zero

-
p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

+
p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

@@ -796,9 +789,9 @@
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p15a)

+
plot(p15a)

 

-
print(p15a)

+
print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -837,16 +830,16 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33

-
p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

+
p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

 
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p15b)

+
plot(p15b)

 

-
print(p15b)

+
print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -890,14 +883,14 @@
 

 

 The DFOP fraction parameter is greater than 1

-
p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

+
p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The representative half-life of the IORE model is longer than the one corresponding

 
## to the terminal degradation rate found with the DFOP model.

 
## The representative half-life obtained from the DFOP model may be used

-
plot(p16)

+
plot(p16)

 

-
print(p16)

+
print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -1010,7 +1003,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
 

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diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index a53f1927..43f8d238 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     

 
@@ -88,7 +88,7 @@
       
Benchmark timings for mkin on various systems

                         
Johannes Ranke

             
-            
2019-05-08

+            
2019-06-04

       
       
       
@@ -115,32 +115,32 @@
 }

 
# Parent only
 t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
-t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]
-
-# One metabolite
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))

+t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## iteration limit reached without convergence (10)

+
 
## Successfully compiled differential equation model from auto-generated C code.

-
-
## Successfully compiled differential equation model from auto-generated C code.

-
DFOP_SFO <- mkinmod(
+
 
## Successfully compiled differential equation model from auto-generated C code.

-
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]

+
+
## Successfully compiled differential equation model from auto-generated C code.

+
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data

 
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
 
 ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data

-
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]

+
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]

 
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
 
@@ -149,117 +149,131 @@
 
 ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data

-
# Two metabolites, synthetic data
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
-t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
-
-t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
-t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
-
-t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
-t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
-
-mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-mkin_benchmarks

+
# Two metabolites, synthetic data
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                           M1 = mkinsub("SFO"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
+
+DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+
+t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
+
+t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
+t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
+
+t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
+t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
+
+mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+mkin_benchmarks

 
##                                                                                                       CPU
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 AMD Ryzen 7 1700 Eight-Core Processor
 ##                                                                        OS
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 Linux
 ##                                                                         mkin
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 0.9.49.5
 ##                                                                        t1
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.792
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.805
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 17.398
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.748
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.427
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.403
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.104
-##                                                                        t5
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.527
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.613
+##                                                                         t5
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.309
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.541
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.546
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.308
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.214
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.775
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.871
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.116
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.738
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.063
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.763
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.784

-
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.527

+
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

 

   

 
@@ -281,7 +295,7 @@
 

 
 

-  
Site built with pkgdown 1.3.0.9000.

+  
Site built with pkgdown 1.3.0.

 

       
 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index f296c8a4..f3062c66 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -30,7 +30,7 @@
       
       
         mkin
-        0.9.49.4
+        0.9.49.5
       
     
 
@@ -88,7 +88,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2019-05-08

+            
2019-06-04

       
       
       
@@ -163,9 +163,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.131    1.000     3.129        0
-## 1 deSolve, not compiled            3  28.306    9.041    28.290        0
-## 2      Eigenvalue based            3   4.361    1.393     4.358        0
+## 3     deSolve, compiled            3   3.053    1.000     3.052        0
+## 1 deSolve, not compiled            3  28.457    9.321    28.442        0
+## 2      Eigenvalue based            3   4.296    1.407     4.293        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -214,16 +214,16 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   5.023    1.000     5.021        0
-## 1 deSolve, not compiled            3  53.267   10.605    53.235        0
+## 2     deSolve, compiled            3   4.828    1.000     4.825        0
+## 1 deSolve, not compiled            3  53.153   11.009    53.125        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!

-

This vignette was built with mkin 0.9.49.4 on

+

This vignette was built with mkin 0.9.49.5 on

## R version 3.6.0 (2019-04-26)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 9 (stretch)
+## Running under: Debian GNU/Linux 10 (buster) 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor
@@ -247,7 +247,7 @@
-

Site built with pkgdown 1.3.0.9000.

+

Site built with pkgdown 1.3.0.

-- cgit v1.2.1