From 92bd33824bde6b6b21bfc7e30953092a74d3cce5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 7 May 2020 22:13:33 +0200 Subject: Another overhaul of analytical solutions Still in preparation for analytical solutions of coupled models --- docs/reference/mkinpredict.html | 48 ++++++++++++++++++++++++++++++----------- 1 file changed, 35 insertions(+), 13 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 689fb7c7..21c13156 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." /> mkin - 0.9.49.11 + 0.9.50 @@ -268,8 +268,29 @@ solver is used.


 SFO <- mkinmod(degradinol = mkinsub("SFO"))
 # Compare solution types
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-      solution_type = "analytical")
#> Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "analytical")
#>    time  degradinol
+#> 1     0 100.0000000
+#> 2     1  74.0818221
+#> 3     2  54.8811636
+#> 4     3  40.6569660
+#> 5     4  30.1194212
+#> 6     5  22.3130160
+#> 7     6  16.5298888
+#> 8     7  12.2456428
+#> 9     8   9.0717953
+#> 10    9   6.7205513
+#> 11   10   4.9787068
+#> 12   11   3.6883167
+#> 13   12   2.7323722
+#> 14   13   2.0241911
+#> 15   14   1.4995577
+#> 16   15   1.1108997
+#> 17   16   0.8229747
+#> 18   17   0.6096747
+#> 19   18   0.4516581
+#> 20   19   0.3345965
+#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "deSolve")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -291,7 +312,7 @@ solver is used.

 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -313,7 +334,7 @@ solver is used.

 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20   0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "eigen")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -337,25 +358,26 @@ solver is used.

 #> 20   19   0.3345965
 #> 21   20   0.2478752

 # Compare integration methods to analytical solution
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-      solution_type = "analytical")[21,]
#> Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
+      solution_type = "analytical")[21,]
#>    time degradinol
+#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "lsoda")[21,]
#>    time degradinol
-#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "ode45")[21,]
#>    time degradinol
-#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20  0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "rk4")[21,]
#>    time degradinol
 #> 21   20  0.2480043
# rk4 is not as precise here
 
 # The number of output times used to make a lot of difference until the
 # default for atol was adjusted
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
       seq(0, 20, by = 0.1))[201,]
#>     time degradinol
-#> 201   20  0.2478752
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+#> 201   20  0.2478752
mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
       seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
 #> 2001   20  0.2478752

 # Check compiled model versions - they are faster than the eigenvalue based solutions!
 SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
-                  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
if(require(rbenchmark)) {
+                  m1 = list(type = "SFO"), use_of_ff = "min")
#> Successfully compiled differential equation model from auto-generated C code.
if(require(rbenchmark)) {
   benchmark(
     eigen = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
       c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
@@ -371,7 +393,7 @@ solver is used.

 }
#> Lade nötiges Paket: rbenchmark
#>               test replications elapsed relative user.self sys.self user.child
 #> 3          deSolve           10   0.229   28.625     0.229        0          0
 #> 2 deSolve_compiled           10   0.008    1.000     0.008        0          0
-#> 1            eigen           10   0.025    3.125     0.026        0          0
+#> 1            eigen           10   0.026    3.250     0.025        0          0
 #>   sys.child
 #> 3         0
 #> 2         0
-- 
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