From f39815aa87272849f8e0c808099c4cee780c2a81 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Nov 2016 14:33:05 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() Using pkgdown with PR hadley/pkgdown#212 --- docs/reference/mkinpredict.html | 64 ++++++++++++++++------------------------- 1 file changed, 25 insertions(+), 39 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 31556527..57bb747c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,7 +61,12 @@ @@ -154,10 +159,7 @@

A matrix in the same format as the output of ode.

-

- - Examples -

+

Examples

  SFO <- mkinmod(degradinol = list(type = "SFO"))
   # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
@@ -182,8 +184,7 @@
 #> 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_sink = 0.3), c(degradinol = 100), 0:20,
               solution_type = "deSolve")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -205,8 +206,7 @@
 #> 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_sink = 0.3), c(degradinol = 100), 0:20,
               solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -228,8 +228,7 @@
 #> 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_sink = 0.3), c(degradinol = 100), 0:20,
               solution_type = "eigen")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -251,57 +250,44 @@
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
-#> 

+#> 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,]
#>    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_sink = 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_sink = 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_sink = 0.3), c(degradinol = 100), 0:20,
               method = "rk4")[21,]
#>    time degradinol
-#> 21   20  0.2480043
-#> 
 # rk4 is not as precise here
+#> 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
-#> 201   20  0.2478752
-#> 
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+#> 201   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
               seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
-#> 2001   20  0.2478752
-#> 

+#> 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.
  system.time(
+                    m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  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 = "eigen")[201,]))
#>     time   parent       m1
-#> 201   20 4.978707 27.46227
-#> 
#>    user  system elapsed 
-#>   0.028   0.004   0.004 
-#> 
  system.time(
+#> 201   20 4.978707 27.46227
#>    user  system elapsed 
+#>   0.004   0.024   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
-#> 201   20 4.978707 27.46227
-#> 
#>    user  system elapsed 
-#>   0.016   0.004   0.002 
-#> 
  system.time(
+#> 201   20 4.978707 27.46227
#>    user  system elapsed 
+#>   0.004   0.016   0.003 
  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", use_compiled = FALSE)[201,]))
#>     time   parent       m1
-#> 201   20 4.978707 27.46227
-#> 
#>    user  system elapsed 
-#>   0.052   0.000   0.052 
-#>
+#> 201 20 4.978707 27.46227
#> user system elapsed +#> 0.036 0.000 0.033