From 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 16:55:20 +0100 Subject: Restore NAMESPACE which was accidentally overwritten by pkgdown -> roxygen --- docs/reference/mkinpredict.html | 165 ++++++++++++++++++++++++++++++++++++---- 1 file changed, 149 insertions(+), 16 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index c126eec9..c34da511 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -208,39 +208,172 @@

Examples

- 
  SFO <- mkinmod(degradinol = mkinsub("SFO"))
#> Error in mkinmod(degradinol = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden
  # Compare solution types
+    
  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 mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, solution_type = "analytical"): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "deSolve")
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, solution_type = "deSolve"): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "deSolve", use_compiled = FALSE)
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, solution_type = "deSolve", use_compiled = FALSE): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        solution_type = "eigen")
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, solution_type = "eigen"): konnte Funktion "mkinpredict" nicht finden

+        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_sink = 0.3), c(degradinol = 100), 0:20,
+        solution_type = "deSolve")
#>    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   1.1108996
+#> 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_sink = 0.3), c(degradinol = 100), 0:20,
+        solution_type = "deSolve", use_compiled = FALSE)
#>    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   1.1108996
+#> 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_sink = 0.3), c(degradinol = 100), 0:20,
+        solution_type = "eigen")
#>    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

 
   # 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 mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, solution_type = "analytical"): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "lsoda")[21,]
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, method = "lsoda"): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "ode45")[21,]
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, method = "ode45"): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
-        method = "rk4")[21,]
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     0:20, method = "rk4"): konnte Funktion "mkinpredict" nicht finden
 # rk4 is not as precise here
+        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
+#> 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,
+        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,]
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     seq(0, 20, by = 0.1)): konnte Funktion "mkinpredict" nicht finden
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-        seq(0, 20, by = 0.01))[2001,]
#> Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),     seq(0, 20, by = 0.01)): konnte Funktion "mkinpredict" nicht finden

+        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
+#> 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"))
#> Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden
  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,]))
#> Error in 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"): konnte Funktion "mkinpredict" nicht finden
#> Timing stopped at: 0 0 0.001
  system.time(
+                solution_type = "eigen")[201,]))
#>     time   parent       m1
+#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
+#>       0.003       0.000       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")[201,]))
#> Error in 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"): konnte Funktion "mkinpredict" nicht finden
#> Timing stopped at: 0 0 0
  system.time(
+                solution_type = "deSolve")[201,]))
#>     time   parent       m1
+#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
+#>       0.002       0.000       0.002 
  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,]))
#> Error in 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): konnte Funktion "mkinpredict" nicht finden
#> Timing stopped at: 0 0 0

+                solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
+#> 201   20 4.978707 27.46227
#>        User      System verstrichen 
+#>       0.042       0.000       0.042 

   
    # Predict from a fitted model
-    f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Error in mkinfit(SFO_SFO, FOCUS_2006_C): konnte Funktion "mkinfit" nicht finden
    head(mkinpredict(f))
#> Error in mkinpredict(f): konnte Funktion "mkinpredict" nicht finden
  

+    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