From 54eb679cb599042b33d67e101687dd451c4b53fe Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 15:46:04 +0100 Subject: Correct title for CAKE_export Add NEWS entry. Static documentation rebuilt by pkgdown --- NEWS.md | 4 ++- docs/articles/FOCUS_L.html | 38 ++++++++++++++--------------- docs/articles/web_only/compiled_models.html | 12 ++++----- docs/news/index.html | 7 +++--- docs/reference/CAKE_export.html | 6 ++--- docs/reference/index.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 2 +- man/CAKE_export.Rd | 2 +- 9 files changed, 39 insertions(+), 36 deletions(-) diff --git a/NEWS.md b/NEWS.md index f799a749..8ca0e89c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# mkin 0.9.47.6 (2018-11-26) +# mkin 0.9.47.6 (2019-01-31) - Add the function 'logLik.mkinfit' which makes it possible to calculate an AIC for mkinfit objects @@ -14,6 +14,8 @@ - 'tests/testthat/test_irls.R': Test if the components of the error model used to generate the data can be reproduced with moderate accuracy +- Add the function 'CAKE_export' to facilitate cross-checking of results + # mkin 0.9.47.5 (2018-09-14) - Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index daf887e6..b53ab0d0 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -111,15 +111,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:32 2019 
-## Date of summary: Thu Jan 31 15:37:32 2019 
+## Date of fit:     Thu Jan 31 15:43:40 2019 
+## Date of summary: Thu Jan 31 15:43:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
 ## 
 ## Weighting: none
 ## 
@@ -202,15 +202,15 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:34 2019 
-## Date of summary: Thu Jan 31 15:37:34 2019 
+## Date of fit:     Thu Jan 31 15:43:42 2019 
+## Date of summary: Thu Jan 31 15:43:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.492 s
+## Fitted with method Port using 611 model solutions performed in 1.502 s
 ## 
 ## Weighting: none
 ## 
@@ -297,15 +297,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:35 2019 
-## Date of summary: Thu Jan 31 15:37:35 2019 
+## Date of fit:     Thu Jan 31 15:43:42 2019 
+## Date of summary: Thu Jan 31 15:43:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.196 s
+## Fitted with method Port using 81 model solutions performed in 0.195 s
 ## 
 ## Weighting: none
 ## 
@@ -368,8 +368,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:36 2019 
-## Date of summary: Thu Jan 31 15:37:36 2019 
+## Date of fit:     Thu Jan 31 15:43:43 2019 
+## Date of summary: Thu Jan 31 15:43:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.837 s
+## Fitted with method Port using 336 model solutions performed in 0.836 s
 ## 
 ## Weighting: none
 ## 
@@ -460,8 +460,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:37 2019 
-## Date of summary: Thu Jan 31 15:37:37 2019 
+## Date of fit:     Thu Jan 31 15:43:44 2019 
+## Date of summary: Thu Jan 31 15:43:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.344 s
+## Fitted with method Port using 137 model solutions performed in 0.34 s
 ## 
 ## Weighting: none
 ## 
@@ -561,8 +561,8 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:37 2019 
-## Date of summary: Thu Jan 31 15:37:38 2019 
+## Date of fit:     Thu Jan 31 15:43:45 2019 
+## Date of summary: Thu Jan 31 15:43:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -621,8 +621,8 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Jan 31 15:37:37 2019 
-## Date of summary: Thu Jan 31 15:37:38 2019 
+## Date of fit:     Thu Jan 31 15:43:45 2019 
+## Date of summary: Thu Jan 31 15:43:45 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index a1fa69f5..d7d76b49 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.319    1.000     2.317    0.000
-## 1 deSolve, not compiled            3  17.483    7.539    17.473    0.000
-## 2      Eigenvalue based            3   2.857    1.232     2.852    0.003
+## 3     deSolve, compiled            3   2.331    1.000     2.330        0
+## 1 deSolve, not compiled            3  17.369    7.451    17.360        0
+## 2      Eigenvalue based            3   2.878    1.235     2.876        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
 ## 2          0         0

-
We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

+
We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

 
 

 

@@ -157,8 +157,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.102    1.000     4.100        0
-## 1 deSolve, not compiled            3  37.059    9.034    37.041        0
+## 2     deSolve, compiled            3   4.120    1.000     4.116        0
+## 1 deSolve, not compiled            3  37.011    8.983    36.993        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index 1aa9e7a5..7736a28d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -119,9 +119,9 @@
       
     
 
-    

+    

 

-mkin 0.9.47.6 (2018-11-26) Unreleased 
+mkin 0.9.47.6 (2019-01-31) Unreleased 
 

 
    
 
  • Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects
    • 
@@ -131,6 +131,7 @@
 
  • ‘mkinpredict’: Make the function generic and create a method for mkinfit objects
    • 
 
  • ‘mkinfit’: Improve the correctness of the fitted two component error model by fitting the mean absolute deviance at each observation against the observed values, weighting with the current two-component error model
    • 
 
  • ‘tests/testthat/test_irls.R’: Test if the components of the error model used to generate the data can be reproduced with moderate accuracy
    • 
+
  • Add the function ‘CAKE_export’ to facilitate cross-checking of results
    • 
 

 

     

@@ -674,7 +675,7 @@
     

       
Contents

       
    
-        
  • 0.9.47.6
    • 
+        
  • 0.9.47.6
    • 
         
  • 0.9.47.5
    • 
         
  • 0.9.47.3
    • 
         
  • 0.9.47.2
    • 
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index f1768ecc..21dd46a9 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -6,7 +6,7 @@
 
 
 
-Export a list of datasets in wide format to a CAKE study file — CAKE_export • mkin
+Export a list of datasets format to a CAKE study file — CAKE_export • mkin
 
 
 
@@ -30,7 +30,7 @@
 
 
 
-
+
 
 
@@ -119,7 +119,7 @@
 
    
   
    
     
    
-    
    Export a list of datasets in wide format to a CAKE study file
    
+    
    Export a list of datasets format to a CAKE study file
    
     
     
     
    
diff --git a/docs/reference/index.html b/docs/reference/index.html
index fb47d33e..7dd32430 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -374,7 +374,7 @@
         
           
    CAKE_export() 
    
         
-        
    Export a list of datasets in wide format to a CAKE study file
    
+        
    Export a list of datasets format to a CAKE study file
    
       
     
       
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 294a90de..c126eec9 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -232,7 +232,7 @@
                     m1 = list(type = "SFO"))
    #> Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden
      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
      system.time(
+                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(
     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(
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 25f97738..af0b8f6f 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -186,7 +186,7 @@
 models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
    #> Error in eval(expr, envir, enclos): Objekt 'm_synth_SFO_lin' nicht gefunden
    datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
 names(datasets) <- paste("Dataset", 1:3)
 
-time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
    #> Error in mmkin(models, datasets, quiet = TRUE): konnte Funktion "mmkin" nicht finden
    #> Timing stopped at: 0 0 0.001
    time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
    #> Error in mmkin(models, datasets, cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden
    #> Timing stopped at: 0 0 0
    
+time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
    #> Error in mmkin(models, datasets, quiet = TRUE): konnte Funktion "mmkin" nicht finden
    #> Timing stopped at: 0 0 0
    time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
    #> Error in mmkin(models, datasets, cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden
    #> Timing stopped at: 0 0 0
    
 time_default
    #> Error in eval(expr, envir, enclos): Objekt 'time_default' nicht gefunden
    time_1
    #> Error in eval(expr, envir, enclos): Objekt 'time_1' nicht gefunden
    
 endpoints(fits.0[["SFO_lin", 2]])
    #> Error in endpoints(fits.0[["SFO_lin", 2]]): konnte Funktion "endpoints" nicht finden
    
 # plot.mkinfit handles rows or columns of mmkin result objects
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
index 3a3da4d0..c7111bc8 100644
--- a/man/CAKE_export.Rd
+++ b/man/CAKE_export.Rd
@@ -1,7 +1,7 @@
 \name{CAKE_export}
 \alias{CAKE_export}
 \title{
-  Export a list of datasets in wide format to a CAKE study file
+  Export a list of datasets format to a CAKE study file
 }
 \description{
   In addition to the datasets, the pathways in the degradation
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