From 524a8bba89b95840b4e9215c403947a8bb76d7b2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Nov 2020 16:05:10 +0100 Subject: Complete rebuild of static docs of dev version --- docs/dev/reference/mkinmod.html | 91 ++++++++++++++++++++++++++--------------- 1 file changed, 57 insertions(+), 34 deletions(-) (limited to 'docs/dev/reference/mkinmod.html') diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 803be90d..9e37e664 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -162,9 +162,13 @@ components.

mkinmod(
   ...,
   use_of_ff = "max",
+  name = NULL,
   speclist = NULL,
   quiet = FALSE,
-  verbose = FALSE
+  verbose = FALSE,
+  dll_dir = NULL,
+  unload = FALSE,
+  overwrite = FALSE
 )
 
 # S3 method for mkinmod
@@ -200,6 +204,10 @@ formation fractions are always used (default).  If "min", a minimum use of
 formation fractions is made, i.e. each pathway to a metabolite has its
 own rate constant.

     
+    
+      name
+      
A name for the model. Should be a valid R object name.

+    
     
       speclist
       
The specification of the observed variables and their
@@ -214,6 +222,23 @@ argument. Default is NULL.

       verbose
       
If TRUE, passed to inline::cfunction() if
 applicable to give detailed information about the C function being built.

+    
+    
+      dll_dir
+      
Directory where an DLL object, if generated internally by
+inline::cfunction(), should be saved.  The DLL will only be stored in a
+permanent location for use in future sessions, if 'dll_dir' and 'name'
+are specified.

+    
+    
+      unload
+      
If a DLL from the target location in 'dll_dir' is already
+loaded, should that be unloaded first?

+    
+    
+      overwrite
+      
If a file exists at the target DLL location in 'dll_dir',
+should this be overwritten?

     
     
       x
@@ -299,18 +324,37 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
-
#> Successfully compiled differential equation model from auto-generated C code.

+
#> Temporary DLL for differentials generated and loaded
print(SFO_SFO)
+
#> <mkinmod> model generated with
+#> Use of formation fractions $use_of_ff: max 
+#> Specification $spec:
+#> $parent
+#> $type: SFO; $to: m1; $sink: TRUE
+#> $m1
+#> $type: SFO; $sink: TRUE
+#> Coefficient matrix $coefmat available
+#> Compiled model $cf available
+#> Differential equations:
+#> d_parent/dt = - k_parent * parent
+#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1

 # \dontrun{
-# Now supplying full names used for plotting
+ fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
+
#> Warning: Observations with value of zero were removed from the data

+ # Now supplying compound names used for plotting, and write to user defined location
+ # We need to choose a path outside the session tempdir because this gets removed
+ DLL_dir <- "~/.local/share/mkin"
+ if (!dir.exists(DLL_dir)) dir.create(DLL_dir)
  SFO_SFO.2 <- mkinmod(
    parent = mkinsub("SFO", "m1", full_name = "Test compound"),
-   m1 = mkinsub("SFO", full_name = "Metabolite M1"))
-
#> Successfully compiled differential equation model from auto-generated C code.

-# The above model used to be specified like this, before the advent of mkinsub()
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1"),
-  m1 = list(type = "SFO"))
-
#> Successfully compiled differential equation model from auto-generated C code.

+   m1 = mkinsub("SFO", full_name = "Metabolite M1"),
+   name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
+
#> Copied DLL from /tmp/RtmpX9Xf3y/file6d622f3b7e08.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session
+saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
+# Terminate the R session here if you would like to check, and then do
+library(mkin)
+SFO_SFO.3 <- readRDS("~/SFO_SFO.rds")
+fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
+
#> Warning: Observations with value of zero were removed from the data

 # Show details of creating the C function
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
@@ -330,11 +374,11 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

 #>  12: }
 #>  13: 
 #>  14: 
-#>  15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#>  15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
 #>  16: 
 #>  17: f[0] = - k_parent * y[0];
 #>  18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
-#>  19: }
#> Successfully compiled differential equation model from auto-generated C code.

+#>  19: }
#> Temporary DLL for differentials generated and loaded

 # The symbolic solution which is available in this case is not
 # made for human reading but for speed of computation
 SFO_SFO$deg_func
@@ -353,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

 #>     })
 #>     return(predicted)
 #> }
-#> <environment: 0x55555c97f8d8>

+#> <environment: 0x55555c5b8d68>

 # If we have several parallel metabolites
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
 m_synth_DFOP_par <- mkinmod(
@@ -367,27 +411,6 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

   quiet = TRUE)
 # }
 
-
-  m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-                             M1 = list(type = "SFO", to = "M2"),
-                             M2 = list(type = "SFO"), use_of_ff = "max")
-
#> Successfully compiled differential equation model from auto-generated C code.

-  print(m_synth_SFO_lin)
-
#> <mkinmod> model generated with
-#> Use of formation fractions $use_of_ff: max 
-#> Specification $spec:
-#> $parent
-#> $type: SFO; $to: M1; $sink: TRUE
-#> $M1
-#> $type: SFO; $to: M2; $sink: TRUE
-#> $M2
-#> $type: SFO; $sink: TRUE
-#> Coefficient matrix $coefmat available
-#> Compiled model $cf available
-#> Differential equations:
-#> d_parent/dt = - k_parent * parent
-#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
-#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2