From 7c62da1269e8910a210ba1917d4dc62d186d5606 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 09:40:35 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/articles/FOCUS_D.html | 4 +-- .../figure-html/unnamed-chunk-5-1.png | Bin 74304 -> 0 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 13789 -> 0 bytes docs/articles/FOCUS_L.html | 18 ++++++------- .../figure-html/unnamed-chunk-10-1.png | Bin 28716 -> 0 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 52644 -> 0 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 21438 -> 0 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 36854 -> 0 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 23253 -> 0 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 14728 -> 0 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 23593 -> 0 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 27575 -> 0 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 28058 -> 0 bytes docs/articles/compiled_models.html | 28 ++++++++++----------- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9925 -> 9289 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 11448 -> 12220 bytes docs/articles/mkin.html | 2 +- .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 112161 -> 0 bytes 18 files changed, 26 insertions(+), 26 deletions(-) delete mode 100644 docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png delete mode 100644 docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png delete mode 100644 docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png delete mode 100644 docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index bbfc36b6..02c3aa69 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -103,10 +103,10 @@ 
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

A plot of the fit including a residual plot for both observed variables is obtained using the plot method for mkinfit objects.

plot(fit, show_residuals = TRUE)
-

+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)
-

+

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
## mkin version:    0.9.44.9000 
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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 353f1484..5d586799 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -138,16 +138,16 @@ FOCUS_2006_L1_mkin <- 
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")

-

+

 
The residual plot can be easily obtained by

 
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")

-

+

 
For comparison, the FOMC model is fitted as well, and the \(\chi^2\) error level is checked.

 
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)

 
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1

 
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

-

+

 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -233,7 +233,7 @@ FOCUS_2006_L2_mkin <- 
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, 
      main = "FOCUS L2 - SFO")

-

+

 
The \(\chi^2\) error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

 
In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.

 
We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear a priori why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.

@@ -244,7 +244,7 @@ FOCUS_2006_L2_mkin <- 
m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

-

+

 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -314,7 +314,7 @@ FOCUS_2006_L2_mkin <- 
m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

-

+

 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.1 
@@ -397,7 +397,7 @@ FOCUS_2006_L3_mkin <-  mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
                list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)

-

+

 
The \(\chi^2\) error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the \(\chi^2\) test passes of 7%. Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level considerably.

 
 

@@ -484,7 +484,7 @@ mm.L3 <- 
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

-

+

 
Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the \(\chi^2\) error level criterion for laboratory data L3.

 
This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

 
@@ -502,7 +502,7 @@ mm.L4 <- list("FOCUS L4" = FOCUS_2006_L4_mkin), 
                quiet = TRUE)
 plot(mm.L4)

-

+

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
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diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 1eeb78c6..d2e1d87d 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -73,21 +73,21 @@ mb.1 <- micr
 print(mb.1)

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6407.0333 6420.1971 6434.6510 6433.3609 6448.4598
-##       Eigenvalue based  887.4338  891.8401  906.9270  896.2463  916.6735
-##      deSolve, compiled  720.2433  727.8793  733.2019  735.5152  739.6812
+##  deSolve, not compiled 6365.2773 6407.1609 6467.4083 6449.0446 6518.4738
+##       Eigenvalue based  872.0339  912.6754  926.7178  953.3169  954.0597
+##      deSolve, compiled  730.1252  740.7149  751.8881  751.3045  762.7695
 ##        max neval cld
-##  6463.5587     3   c
-##   937.1007     3  b 
-##   743.8472     3 a

+##  6587.9031     3   b
+##   954.8026     3  a 
+##   774.2345     3  a

 
autoplot(mb.1)

 

-
We see that using the compiled model is by a factor of 8.7 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:

+
We see that using the compiled model is by a factor of 8.6 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:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                         median
-## deSolve, not compiled 8.746741
-## Eigenvalue based      1.218529
+## deSolve, not compiled 8.583796
+## Eigenvalue based      1.268882
 ## deSolve, compiled     1.000000

 
 

@@ -108,12 +108,12 @@ smb.1["median"]/smb
smb.2 <- summary(mb.2)
 print(mb.2)

 
## Unit: seconds
-##                   expr       min       lq      mean    median        uq
-##  deSolve, not compiled 13.501761 13.52142 13.697021 13.541086 13.794651
-##      deSolve, compiled  1.359921  1.35996  1.366796  1.359999  1.370233
+##                   expr       min        lq     mean    median        uq
+##  deSolve, not compiled 13.464194 13.498471 13.52712 13.532748 13.558577
+##      deSolve, compiled  1.328628  1.342168  1.35224  1.355707  1.364046
 ##        max neval cld
-##  14.048217     3   b
-##   1.380468     3  a

+##  13.584407     3   b
+##   1.372385     3  a
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##   median
 ## 1     NA
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
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diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 44c9e9c5..c1b38794 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -66,7 +66,7 @@ d_SFO_SFO_SFO_err <-  mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)
 
 plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))
-

+

Background

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