From 1f100167f4f399062fb077ceb983f50384eccaec Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 18 Sep 2018 15:20:30 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/mkinpredict.html | 76 +++++++++++++++++++++++++++++++---------- 1 file changed, 58 insertions(+), 18 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5fad64de..91e9289d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -131,16 +131,18 @@ - 
mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-              use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
-        map_output = TRUE, ...)
+ 
mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
+    solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda",
+    atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)

Arguments

- - + + @@ -204,10 +206,10 @@

Examples

- 
  SFO <- mkinmod(degradinol = list(type = "SFO"))
+    
  SFO <- mkinmod(degradinol = mkinsub("SFO"))
   # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-              solution_type = "analytical")
#>    time  degradinol
+        solution_type = "analytical")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -229,7 +231,7 @@
 #> 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,
-              solution_type = "deSolve")
#>    time  degradinol
+        solution_type = "deSolve")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -251,7 +253,7 @@
 #> 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,
-              solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
+        solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -273,7 +275,7 @@
 #> 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,
-              solution_type = "eigen")
#>    time  degradinol
+        solution_type = "eigen")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
 #> 3     2  54.8811636
@@ -298,21 +300,21 @@
 
   # Compare integration methods to analytical solution
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-              solution_type = "analytical")[21,]
#>    time degradinol
+        solution_type = "analytical")[21,]
#>    time degradinol
 #> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-              method = "lsoda")[21,]
#>    time degradinol
+        method = "lsoda")[21,]
#>    time degradinol
 #> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-              method = "ode45")[21,]
#>    time degradinol
+        method = "ode45")[21,]
#>    time degradinol
 #> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-              method = "rk4")[21,]
#>    time degradinol
+        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),
-              seq(0, 20, by = 0.1))[201,]
#>     time degradinol
+        seq(0, 20, by = 0.1))[201,]
#>     time degradinol
 #> 201   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-              seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
+        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"),
@@ -321,7 +323,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.003       0.000       0.003 
  system.time(
+#>       0.003       0.000       0.004 
  system.time(
     print(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),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
@@ -331,7 +333,45 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.033       0.000       0.034 

+#>       0.034       0.000       0.034 

+  
    # Predict from a fitted model
+    f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call  1 :  552.5739 
+#> Model cost at call  3 :  552.5739 
+#> Model cost at call  4 :  552.5739 
+#> Model cost at call  6 :  279.9345 
+#> Model cost at call  7 :  279.9344 
+#> Model cost at call  8 :  279.9294 
+#> Model cost at call  9 :  279.9294 
+#> Model cost at call  12 :  200.3629 
+#> Model cost at call  13 :  200.3629 
+#> Model cost at call  18 :  197.9039 
+#> Model cost at call  23 :  197.9039 
+#> Model cost at call  25 :  196.6754 
+#> Model cost at call  27 :  196.6754 
+#> Model cost at call  32 :  196.5742 
+#> Model cost at call  33 :  196.5742 
+#> Model cost at call  34 :  196.5742 
+#> Model cost at call  38 :  196.5361 
+#> Model cost at call  40 :  196.5361 
+#> Model cost at call  44 :  196.5336 
+#> Model cost at call  45 :  196.5336 
+#> Model cost at call  50 :  196.5334 
+#> Model cost at call  51 :  196.5334 
+#> Model cost at call  52 :  196.5334 
+#> Model cost at call  56 :  196.5334 
+#> Model cost at call  58 :  196.5334 
+#> Model cost at call  59 :  196.5334 
+#> Model cost at call  65 :  196.5334 
+#> Model cost at call  73 :  196.5334 
+#> Model cost at call  78 :  196.5334 
+#> Model cost at call  80 :  196.5334 
+#> Optimisation by method Port successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
+#> 1  0.0 82.49216 0.000000
+#> 2  0.1 80.00563 1.179955
+#> 3  0.2 77.59404 2.312580
+#> 4  0.3 75.25515 3.399419
+#> 5  0.4 72.98675 4.441969
+#> 6  0.5 70.78673 5.441679
mkinmod

A kinetic model as produced by mkinmod.

x

A kinetic model as produced by mkinmod, or a kinetic + fit as fitted by mkinfit. In the latter case, the fitted + parameters are used for the prediction.
odeparms