From b37e5573c22c3a28014e17699a2ad7c0a958c662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Nov 2014 19:34:56 +0100 Subject: Update date and static docs for release to CRAN --- DESCRIPTION | 2 +- vignettes/FOCUS_L.html | 548 ++++++++++++++++++++++++------------------------- vignettes/FOCUS_Z.pdf | Bin 220799 -> 214460 bytes vignettes/mkin.pdf | Bin 295336 -> 160336 bytes 4 files changed, 272 insertions(+), 278 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b635102b..aa382e66 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-34 -Date: 2014-11-13 +Date: 2014-11-21 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 82bbd2c7..8de60cdd 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -214,13 +214,7 @@ hr { report, p. 284:

library("mkin")
-
- -
## Loading required package: minpack.lm
-## Loading required package: rootSolve
-
- -
FOCUS_2006_L1 = data.frame(
+FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
   parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
@@ -243,16 +237,16 @@ summary(m.L1.SFO)
 
## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:15 2014 
-## Date of summary: Wed Oct 15 00:58:15 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:16:16 2014 
+## Date of summary: Fri Nov 21 19:16:16 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.203 s
+## Fitted with method Port using 37 model solutions performed in 0.216 s
 ## 
 ## Weighting: none
 ## 
@@ -262,66 +256,66 @@ summary(m.L1.SFO)
 ## k_parent_sink  0.10 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                    value lower upper
-## parent_0          89.850  -Inf   Inf
-## log_k_parent_sink -2.303  -Inf   Inf
+##                       value lower upper
+## parent_0          89.850000  -Inf   Inf
+## log_k_parent_sink -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##                   Estimate Std. Error Lower Upper t value Pr(>|t|)
-## parent_0             92.50     1.3700 89.60 95.40    67.6 4.34e-21
-## log_k_parent_sink    -2.35     0.0406 -2.43 -2.26   -57.9 5.15e-20
-##                     Pr(>t)
-## parent_0          2.17e-21
-## log_k_parent_sink 2.58e-20
+##                   Estimate Std. Error  Lower  Upper t value  Pr(>|t|)
+## parent_0            92.470    1.36800 89.570 95.370   67.58 4.339e-21
+## log_k_parent_sink   -2.347    0.04057 -2.433 -2.261  -57.86 5.155e-20
+##                      Pr(>t)
+## parent_0          2.170e-21
+## log_k_parent_sink 2.577e-20
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent_sink
-## parent_0             1.000             0.625
-## log_k_parent_sink    0.625             1.000
+## parent_0            1.0000            0.6248
+## log_k_parent_sink   0.6248            1.0000
 ## 
-## Residual standard error: 2.95 on 16 degrees of freedom
+## Residual standard error: 2.948 on 16 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##               Estimate   Lower  Upper
-## parent_0       92.5000 89.6000 95.400
-## k_parent_sink   0.0956  0.0877  0.104
+##               Estimate    Lower   Upper
+## parent_0      92.47000 89.57000 95.3700
+## k_parent_sink  0.09561  0.08773  0.1042
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    3.42       2  7
-## parent      3.42       2  7
+## All data   3.424       2  7
+## parent     3.424       2  7
 ## 
 ## Resulting formation fractions:
 ##             ff
 ## parent_sink  1
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90
-## parent 7.25 24.1
+##         DT50  DT90
+## parent 7.249 24.08
 ## 
 ## Data:
 ##  time variable observed predicted residual
-##     0   parent     88.3     92.47   -4.171
-##     0   parent     91.4     92.47   -1.071
-##     1   parent     85.6     84.04    1.561
-##     1   parent     84.5     84.04    0.461
-##     2   parent     78.9     76.38    2.524
-##     2   parent     77.6     76.38    1.224
-##     3   parent     72.0     69.41    2.588
-##     3   parent     71.9     69.41    2.488
-##     5   parent     50.3     57.33   -7.030
-##     5   parent     59.4     57.33    2.070
-##     7   parent     47.0     47.35   -0.352
-##     7   parent     45.1     47.35   -2.252
-##    14   parent     27.7     24.25    3.453
-##    14   parent     27.3     24.25    3.053
-##    21   parent     10.0     12.42   -2.416
-##    21   parent     10.4     12.42   -2.016
-##    30   parent      2.9      5.25   -2.351
-##    30   parent      4.0      5.25   -1.251
+##     0   parent     88.3    92.471  -4.1710
+##     0   parent     91.4    92.471  -1.0710
+##     1   parent     85.6    84.039   1.5610
+##     1   parent     84.5    84.039   0.4610
+##     2   parent     78.9    76.376   2.5241
+##     2   parent     77.6    76.376   1.2241
+##     3   parent     72.0    69.412   2.5884
+##     3   parent     71.9    69.412   2.4884
+##     5   parent     50.3    57.330  -7.0301
+##     5   parent     59.4    57.330   2.0699
+##     7   parent     47.0    47.352  -0.3515
+##     7   parent     45.1    47.352  -2.2515
+##    14   parent     27.7    24.247   3.4528
+##    14   parent     27.3    24.247   3.0528
+##    21   parent     10.0    12.416  -2.4163
+##    21   parent     10.4    12.416  -2.0163
+##    30   parent      2.9     5.251  -2.3513
+##    30   parent      4.0     5.251  -1.2513

A plot of the fit is obtained with the plot function for mkinfit objects.

@@ -343,7 +337,7 @@ is checked.

m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
-
## Warning: Optimisation by method Port did not converge.
+
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1
 

 
@@ -351,9 +345,9 @@ is checked.

 
## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:16 2014 
-## Date of summary: Wed Oct 15 00:58:16 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:16:19 2014 
+## Date of summary: Fri Nov 21 19:16:19 2014 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -365,7 +359,7 @@ is checked.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.011 s
+## Fitted with method Port using 188 model solutions performed in 1.083 s
 ## 
 ## Weighting: none
 ## 
@@ -376,42 +370,42 @@ is checked.

 ## beta     10.00 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##            value lower upper
-## parent_0  89.850  -Inf   Inf
-## log_alpha  0.000  -Inf   Inf
-## log_beta   2.303  -Inf   Inf
+##               value lower upper
+## parent_0  89.850000  -Inf   Inf
+## log_alpha  0.000000  -Inf   Inf
+## log_beta   2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##           Estimate Std. Error Lower Upper t value Pr(>|t|)   Pr(>t)
-## parent_0      92.5       1.42  89.4  95.5   65.00 8.32e-20 4.16e-20
-## log_alpha     15.4      15.10 -16.7  47.6    1.02 3.22e-01 1.61e-01
-## log_beta      17.8      15.10 -14.4  49.9    1.18 2.57e-01 1.28e-01
+##           Estimate Std. Error  Lower Upper t value  Pr(>|t|)    Pr(>t)
+## parent_0     92.47      1.422  89.44 95.50  65.030 8.317e-20 4.158e-20
+## log_alpha    15.43     15.080 -16.71 47.58   1.023 3.224e-01 1.612e-01
+## log_beta     17.78     15.090 -14.37 49.93   1.179 2.569e-01 1.284e-01
 ## 
 ## Parameter correlation:
 ##           parent_0 log_alpha log_beta
-## parent_0     1.000     0.113    0.111
-## log_alpha    0.113     1.000    1.000
-## log_beta     0.111     1.000    1.000
+## parent_0    1.0000    0.1129   0.1112
+## log_alpha   0.1129    1.0000   1.0000
+## log_beta    0.1112    1.0000   1.0000
 ## 
-## Residual standard error: 3.05 on 15 degrees of freedom
+## Residual standard error: 3.045 on 15 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##          Estimate    Lower    Upper
-## parent_0 9.25e+01 8.94e+01 9.55e+01
-## alpha    5.04e+06 5.51e-08 4.62e+20
-## beta     5.28e+07 5.73e-07 4.86e+21
+##           Estimate     Lower     Upper
+## parent_0 9.247e+01 8.944e+01 9.550e+01
+## alpha    5.044e+06 5.510e-08 4.618e+20
+## beta     5.276e+07 5.732e-07 4.857e+21
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    3.62       3  6
-## parent      3.62       3  6
+## All data   3.619       3  6
+## parent     3.619       3  6
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90 DT50back
-## parent 7.25 24.1     7.25
+##        DT50  DT90 DT50back
+## parent 7.25 24.08     7.25

Due to the higher number of parameters, and the lower number of degrees of @@ -450,16 +444,16 @@ summary(m.L2.SFO) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:17 2014 
-## Date of summary: Wed Oct 15 00:58:17 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:44 2014 
+## Date of summary: Fri Nov 21 19:18:44 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.22 s
+## Fitted with method Port using 41 model solutions performed in 0.239 s
 ## 
 ## Weighting: none
 ## 
@@ -469,60 +463,60 @@ summary(m.L2.SFO)
 ## k_parent_sink  0.10 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                    value lower upper
-## parent_0          93.950  -Inf   Inf
-## log_k_parent_sink -2.303  -Inf   Inf
+##                       value lower upper
+## parent_0          93.950000  -Inf   Inf
+## log_k_parent_sink -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##                   Estimate Std. Error  Lower  Upper t value Pr(>|t|)
-## parent_0            91.500      3.810 83.000 99.900   24.00 3.55e-10
-## log_k_parent_sink   -0.411      0.107 -0.651 -0.172   -3.83 3.33e-03
-##                     Pr(>t)
-## parent_0          1.77e-10
-## log_k_parent_sink 1.66e-03
+##                   Estimate Std. Error   Lower   Upper t value  Pr(>|t|)
+## parent_0           91.4700     3.8070 82.9800 99.9500  24.030 3.545e-10
+## log_k_parent_sink  -0.4112     0.1074 -0.6505 -0.1719  -3.828 3.329e-03
+##                      Pr(>t)
+## parent_0          1.773e-10
+## log_k_parent_sink 1.664e-03
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent_sink
-## parent_0              1.00              0.43
-## log_k_parent_sink     0.43              1.00
+## parent_0            1.0000            0.4295
+## log_k_parent_sink   0.4295            1.0000
 ## 
 ## Residual standard error: 5.51 on 10 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##               Estimate  Lower  Upper
-## parent_0        91.500 83.000 99.900
-## k_parent_sink    0.663  0.522  0.842
+##               Estimate   Lower   Upper
+## parent_0       91.4700 82.9800 99.9500
+## k_parent_sink   0.6629  0.5218  0.8421
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    14.4       2  4
-## parent      14.4       2  4
+## All data   14.38       2  4
+## parent     14.38       2  4
 ## 
 ## Resulting formation fractions:
 ##             ff
 ## parent_sink  1
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90
-## parent 1.05 3.47
+##         DT50  DT90
+## parent 1.046 3.474
 ## 
 ## Data:
 ##  time variable observed predicted residual
-##     0   parent     96.1  9.15e+01    4.634
-##     0   parent     91.8  9.15e+01    0.334
-##     1   parent     41.4  4.71e+01   -5.739
-##     1   parent     38.7  4.71e+01   -8.439
-##     3   parent     19.3  1.25e+01    6.779
-##     3   parent     22.3  1.25e+01    9.779
-##     7   parent      4.6  8.83e-01    3.717
-##     7   parent      4.6  8.83e-01    3.717
-##    14   parent      2.6  8.53e-03    2.591
-##    14   parent      1.2  8.53e-03    1.191
-##    28   parent      0.3  7.96e-07    0.300
-##    28   parent      0.6  7.96e-07    0.600
+##     0   parent     96.1 9.147e+01   4.6343
+##     0   parent     91.8 9.147e+01   0.3343
+##     1   parent     41.4 4.714e+01  -5.7394
+##     1   parent     38.7 4.714e+01  -8.4394
+##     3   parent     19.3 1.252e+01   6.7790
+##     3   parent     22.3 1.252e+01   9.7790
+##     7   parent      4.6 8.834e-01   3.7166
+##     7   parent      4.6 8.834e-01   3.7166
+##    14   parent      2.6 8.532e-03   2.5915
+##    14   parent      1.2 8.532e-03   1.1915
+##    28   parent      0.3 7.958e-07   0.3000
+##    28   parent      0.6 7.958e-07   0.6000

The chi2 error level of 14% suggests that the model does not fit very well. @@ -560,16 +554,16 @@ mkinresplot(m.L2.FOMC) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:17 2014 
-## Date of summary: Wed Oct 15 00:58:17 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:45 2014 
+## Date of summary: Fri Nov 21 19:18:45 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.438 s
+## Fitted with method Port using 81 model solutions performed in 0.47 s
 ## 
 ## Weighting: none
 ## 
@@ -580,42 +574,42 @@ mkinresplot(m.L2.FOMC)
 ## beta     10.00 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##            value lower upper
-## parent_0  93.950  -Inf   Inf
-## log_alpha  0.000  -Inf   Inf
-## log_beta   2.303  -Inf   Inf
+##               value lower upper
+## parent_0  93.950000  -Inf   Inf
+## log_alpha  0.000000  -Inf   Inf
+## log_beta   2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##           Estimate Std. Error  Lower  Upper t value Pr(>|t|)   Pr(>t)
-## parent_0    93.800      1.860 89.600 98.000  50.500 2.35e-12 1.17e-12
-## log_alpha    0.318      0.187 -0.104  0.740   1.700 1.23e-01 6.14e-02
-## log_beta     0.210      0.294 -0.456  0.876   0.714 4.93e-01 2.47e-01
+##           Estimate Std. Error   Lower   Upper t value  Pr(>|t|)    Pr(>t)
+## parent_0   93.7700     1.8560 89.5700 97.9700 50.5100 2.345e-12 1.173e-12
+## log_alpha   0.3180     0.1867 -0.1044  0.7405  1.7030 1.227e-01 6.137e-02
+## log_beta    0.2102     0.2943 -0.4555  0.8759  0.7142 4.932e-01 2.466e-01
 ## 
 ## Parameter correlation:
 ##           parent_0 log_alpha log_beta
-## parent_0    1.0000   -0.0955   -0.186
-## log_alpha  -0.0955    1.0000    0.976
-## log_beta   -0.1863    0.9757    1.000
+## parent_0   1.00000  -0.09553  -0.1863
+## log_alpha -0.09553   1.00000   0.9757
+## log_beta  -0.18628   0.97567   1.0000
 ## 
-## Residual standard error: 2.63 on 9 degrees of freedom
+## Residual standard error: 2.628 on 9 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##          Estimate  Lower Upper
-## parent_0    93.80 89.600  98.0
-## alpha        1.37  0.901   2.1
-## beta         1.23  0.634   2.4
+##          Estimate   Lower  Upper
+## parent_0   93.770 89.5700 97.970
+## alpha       1.374  0.9009  2.097
+## beta        1.234  0.6341  2.401
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data     6.2       3  3
-## parent       6.2       3  3
+## All data   6.205       3  3
+## parent     6.205       3  3
 ## 
 ## Estimated disappearance times:
-##         DT50 DT90 DT50back
-## parent 0.809 5.36     1.61
+##          DT50  DT90 DT50back
+## parent 0.8092 5.356    1.612

The error level at which the chi2 test passes is much lower in this case. @@ -646,9 +640,9 @@ plot(m.L2.DFOP) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:21 2014 
-## Date of summary: Wed Oct 15 00:58:21 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:49 2014 
+## Date of summary: Fri Nov 21 19:18:49 2014 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -657,7 +651,7 @@ plot(m.L2.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 1.844 s
+## Fitted with method Port using 336 model solutions performed in 2.026 s
 ## 
 ## Weighting: none
 ## 
@@ -669,33 +663,33 @@ plot(m.L2.DFOP)
 ## g         0.80 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##            value lower upper
-## parent_0 93.9500  -Inf   Inf
-## log_k1    0.0000  -Inf   Inf
-## log_k2   -4.6052  -Inf   Inf
-## g_ilr     0.9803  -Inf   Inf
+##               value lower upper
+## parent_0 93.9500000  -Inf   Inf
+## log_k1    0.0000000  -Inf   Inf
+## log_k2   -4.6051702  -Inf   Inf
+## g_ilr     0.9802581  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
 ##          Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
-## parent_0   93.900         NA    NA    NA      NA       NA     NA
-## log_k1      3.120         NA    NA    NA      NA       NA     NA
-## log_k2     -1.090         NA    NA    NA      NA       NA     NA
-## g_ilr      -0.282         NA    NA    NA      NA       NA     NA
+## parent_0  93.9500         NA    NA    NA      NA       NA     NA
+## log_k1     3.1210         NA    NA    NA      NA       NA     NA
+## log_k2    -1.0880         NA    NA    NA      NA       NA     NA
+## g_ilr     -0.2821         NA    NA    NA      NA       NA     NA
 ## 
 ## Parameter correlation:
 ## Could not estimate covariance matrix; singular system:
 ## 
-## Residual standard error: 1.73 on 8 degrees of freedom
+## Residual standard error: 1.732 on 8 degrees of freedom
 ## 
 ## Backtransformed parameters:
 ##          Estimate Lower Upper
-## parent_0   93.900    NA    NA
-## k1         22.700    NA    NA
-## k2          0.337    NA    NA
-## g           0.402    NA    NA
+## parent_0  93.9500    NA    NA
+## k1        22.6700    NA    NA
+## k2         0.3369    NA    NA
+## g          0.4016    NA    NA
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -704,7 +698,7 @@ plot(m.L2.DFOP)
 ## 
 ## Estimated disappearance times:
 ##        DT50 DT90 DT50_k1 DT50_k2
-## parent   NA   NA  0.0306    2.06
+## parent   NA   NA 0.03058   2.058

Here, the DFOP model is clearly the best-fit model for dataset L2 based on the @@ -735,16 +729,16 @@ plot(m.L3.SFO) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:22 2014 
-## Date of summary: Wed Oct 15 00:58:22 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:50 2014 
+## Date of summary: Fri Nov 21 19:18:50 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.232 s
+## Fitted with method Port using 43 model solutions performed in 0.254 s
 ## 
 ## Weighting: none
 ## 
@@ -754,56 +748,56 @@ plot(m.L3.SFO)
 ## k_parent_sink   0.1 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                    value lower upper
-## parent_0          97.800  -Inf   Inf
-## log_k_parent_sink -2.303  -Inf   Inf
+##                       value lower upper
+## parent_0          97.800000  -Inf   Inf
+## log_k_parent_sink -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##                   Estimate Std. Error Lower Upper t value Pr(>|t|)
-## parent_0             74.90      8.460 54.20 95.60    8.85 0.000116
-## log_k_parent_sink    -3.68      0.326 -4.48 -2.88  -11.30 0.000029
-##                     Pr(>t)
-## parent_0          5.78e-05
-## log_k_parent_sink 1.45e-05
+##                   Estimate Std. Error  Lower Upper t value  Pr(>|t|)
+## parent_0            74.870     8.4570 54.180 95.57   8.853 1.155e-04
+## log_k_parent_sink   -3.678     0.3261 -4.476 -2.88 -11.280 2.903e-05
+##                      Pr(>t)
+## parent_0          5.776e-05
+## log_k_parent_sink 1.451e-05
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent_sink
-## parent_0             1.000             0.548
-## log_k_parent_sink    0.548             1.000
+## parent_0            1.0000            0.5483
+## log_k_parent_sink   0.5483            1.0000
 ## 
-## Residual standard error: 12.9 on 6 degrees of freedom
+## Residual standard error: 12.91 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##               Estimate   Lower   Upper
-## parent_0       74.9000 54.2000 95.6000
-## k_parent_sink   0.0253  0.0114  0.0561
+##               Estimate    Lower    Upper
+## parent_0      74.87000 54.18000 95.57000
+## k_parent_sink  0.02527  0.01138  0.05612
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    21.2       2  6
-## parent      21.2       2  6
+## All data   21.24       2  6
+## parent     21.24       2  6
 ## 
 ## Resulting formation fractions:
 ##             ff
 ## parent_sink  1
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90
-## parent 27.4 91.1
+##         DT50  DT90
+## parent 27.43 91.13
 ## 
 ## Data:
 ##  time variable observed predicted residual
-##     0   parent     97.8     74.87  22.9281
-##     3   parent     60.0     69.41  -9.4061
-##     7   parent     51.0     62.73 -11.7340
-##    14   parent     43.0     52.56  -9.5638
-##    30   parent     35.0     35.08  -0.0839
-##    60   parent     22.0     16.44   5.5602
-##    91   parent     15.0      7.51   7.4887
-##   120   parent     12.0      3.61   8.3903
+##     0   parent     97.8    74.872  22.9281
+##     3   parent     60.0    69.406  -9.4061
+##     7   parent     51.0    62.734 -11.7340
+##    14   parent     43.0    52.564  -9.5638
+##    30   parent     35.0    35.084  -0.0839
+##    60   parent     22.0    16.440   5.5602
+##    91   parent     15.0     7.511   7.4887
+##   120   parent     12.0     3.610   8.3903

The chi2 error level of 21% as well as the plot suggest that the model @@ -821,16 +815,16 @@ plot(m.L3.FOMC) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:22 2014 
-## Date of summary: Wed Oct 15 00:58:22 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:50 2014 
+## Date of summary: Fri Nov 21 19:18:50 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.442 s
+## Fitted with method Port using 83 model solutions performed in 0.496 s
 ## 
 ## Weighting: none
 ## 
@@ -841,33 +835,33 @@ plot(m.L3.FOMC)
 ## beta      10.0 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##            value lower upper
-## parent_0  97.800  -Inf   Inf
-## log_alpha  0.000  -Inf   Inf
-## log_beta   2.303  -Inf   Inf
+##               value lower upper
+## parent_0  97.800000  -Inf   Inf
+## log_alpha  0.000000  -Inf   Inf
+## log_beta   2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##           Estimate Std. Error Lower   Upper t value Pr(>|t|)   Pr(>t)
-## parent_0    97.000      4.550  85.3 109.000   21.30 4.22e-06 2.11e-06
-## log_alpha   -0.862      0.170  -1.3  -0.424   -5.06 3.91e-03 1.96e-03
-## log_beta     0.619      0.474  -0.6   1.840    1.31 2.49e-01 1.24e-01
+##           Estimate Std. Error   Lower    Upper t value  Pr(>|t|)    Pr(>t)
+## parent_0   96.9700     4.5500 85.2800 108.7000  21.310 4.216e-06 2.108e-06
+## log_alpha  -0.8619     0.1704 -1.3000  -0.4238  -5.057 3.911e-03 1.955e-03
+## log_beta    0.6193     0.4744 -0.6003   1.8390   1.305 2.486e-01 1.243e-01
 ## 
 ## Parameter correlation:
 ##           parent_0 log_alpha log_beta
-## parent_0     1.000    -0.151   -0.427
-## log_alpha   -0.151     1.000    0.911
-## log_beta    -0.427     0.911    1.000
+## parent_0    1.0000   -0.1512  -0.4271
+## log_alpha  -0.1512    1.0000   0.9110
+## log_beta   -0.4271    0.9110   1.0000
 ## 
-## Residual standard error: 4.57 on 5 degrees of freedom
+## Residual standard error: 4.572 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##          Estimate  Lower   Upper
-## parent_0   97.000 85.300 109.000
-## alpha       0.422  0.273   0.655
-## beta        1.860  0.549   6.290
+##          Estimate   Lower    Upper
+## parent_0  96.9700 85.2800 108.7000
+## alpha      0.4224  0.2725   0.6546
+## beta       1.8580  0.5487   6.2890
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -875,8 +869,8 @@ plot(m.L3.FOMC)
 ## parent      7.32       3  5
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90 DT50back
-## parent 7.73  431      130
+##         DT50  DT90 DT50back
+## parent 7.729 431.2    129.8

The error level at which the chi2 test passes is 7% in this case.

@@ -894,9 +888,9 @@ plot(m.L3.DFOP) 
## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:23 2014 
-## Date of summary: Wed Oct 15 00:58:23 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:51 2014 
+## Date of summary: Fri Nov 21 19:18:51 2014 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -905,7 +899,7 @@ plot(m.L3.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.778 s
+## Fitted with method Port using 137 model solutions performed in 0.835 s
 ## 
 ## Weighting: none
 ## 
@@ -917,46 +911,46 @@ plot(m.L3.DFOP)
 ## g         0.50 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##           value lower upper
-## parent_0 97.800  -Inf   Inf
-## log_k1   -2.303  -Inf   Inf
-## log_k2   -4.605  -Inf   Inf
-## g_ilr     0.000  -Inf   Inf
+##              value lower upper
+## parent_0 97.800000  -Inf   Inf
+## log_k1   -2.302585  -Inf   Inf
+## log_k2   -4.605170  -Inf   Inf
+## g_ilr     0.000000  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##          Estimate Std. Error  Lower    Upper t value Pr(>|t|)   Pr(>t)
-## parent_0   97.700     1.4400 93.800 102.0000   68.00 2.81e-07 1.40e-07
-## log_k1     -0.661     0.1330 -1.030  -0.2910   -4.96 7.72e-03 3.86e-03
-## log_k2     -4.290     0.0590 -4.450  -4.1200  -72.60 2.15e-07 1.08e-07
-## g_ilr      -0.123     0.0512 -0.265   0.0193   -2.40 7.43e-02 3.72e-02
+##          Estimate Std. Error   Lower     Upper t value  Pr(>|t|)    Pr(>t)
+## parent_0  97.7500    1.43800 93.7500 101.70000  67.970 2.808e-07 1.404e-07
+## log_k1    -0.6612    0.13340 -1.0310  -0.29100  -4.958 7.715e-03 3.858e-03
+## log_k2    -4.2860    0.05902 -4.4500  -4.12200 -72.620 2.155e-07 1.077e-07
+## g_ilr     -0.1229    0.05121 -0.2651   0.01925  -2.401 7.431e-02 3.716e-02
 ## 
 ## Parameter correlation:
-##          parent_0 log_k1  log_k2  g_ilr
-## parent_0   1.0000  0.164  0.0131  0.425
-## log_k1     0.1640  1.000  0.4648 -0.553
-## log_k2     0.0131  0.465  1.0000 -0.663
-## g_ilr      0.4253 -0.553 -0.6631  1.000
+##          parent_0  log_k1   log_k2   g_ilr
+## parent_0  1.00000  0.1640  0.01315  0.4253
+## log_k1    0.16400  1.0000  0.46478 -0.5526
+## log_k2    0.01315  0.4648  1.00000 -0.6631
+## g_ilr     0.42526 -0.5526 -0.66310  1.0000
 ## 
-## Residual standard error: 1.44 on 4 degrees of freedom
+## Residual standard error: 1.439 on 4 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##          Estimate   Lower    Upper
-## parent_0  97.7000 93.8000 102.0000
-## k1         0.5160  0.3560   0.7480
-## k2         0.0138  0.0117   0.0162
-## g          0.4570  0.4070   0.5070
+##          Estimate    Lower     Upper
+## parent_0 97.75000 93.75000 101.70000
+## k1        0.51620  0.35650   0.74750
+## k2        0.01376  0.01168   0.01621
+## g         0.45660  0.40730   0.50680
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    2.23       4  4
-## parent      2.23       4  4
+## All data   2.225       4  4
+## parent     2.225       4  4
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90 DT50_k1 DT50_k2
-## parent 7.46  123    1.34    50.4
+##         DT50 DT90 DT50_k1 DT50_k2
+## parent 7.464  123   1.343   50.37

Here, a look to the model plot, the confidence intervals of the parameters @@ -992,16 +986,16 @@ plot(m.L4.SFO) 

## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:24 2014 
-## Date of summary: Wed Oct 15 00:58:24 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:53 2014 
+## Date of summary: Fri Nov 21 19:18:53 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.246 s
+## Fitted with method Port using 46 model solutions performed in 0.268 s
 ## 
 ## Weighting: none
 ## 
@@ -1011,37 +1005,37 @@ plot(m.L4.SFO)
 ## k_parent_sink   0.1 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                    value lower upper
-## parent_0          96.600  -Inf   Inf
-## log_k_parent_sink -2.303  -Inf   Inf
+##                       value lower upper
+## parent_0          96.600000  -Inf   Inf
+## log_k_parent_sink -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##                   Estimate Std. Error Lower  Upper t value Pr(>|t|)
-## parent_0             96.40       1.95 91.70 101.00    49.5 4.57e-09
-## log_k_parent_sink    -5.03       0.08 -5.23  -4.83   -62.9 1.09e-09
-##                     Pr(>t)
-## parent_0          2.28e-09
-## log_k_parent_sink 5.44e-10
+##                   Estimate Std. Error  Lower   Upper t value  Pr(>|t|)
+## parent_0             96.44    1.94900 91.670 101.200   49.49 4.566e-09
+## log_k_parent_sink    -5.03    0.07999 -5.225  -4.834  -62.88 1.088e-09
+##                      Pr(>t)
+## parent_0          2.283e-09
+## log_k_parent_sink 5.438e-10
 ## 
 ## Parameter correlation:
 ##                   parent_0 log_k_parent_sink
-## parent_0             1.000             0.587
-## log_k_parent_sink    0.587             1.000
+## parent_0            1.0000            0.5865
+## log_k_parent_sink   0.5865            1.0000
 ## 
-## Residual standard error: 3.65 on 6 degrees of freedom
+## Residual standard error: 3.651 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##               Estimate    Lower    Upper
-## parent_0      96.40000 91.70000 1.01e+02
-## k_parent_sink  0.00654  0.00538 7.95e-03
+##                Estimate     Lower     Upper
+## parent_0      96.440000 91.670000 1.012e+02
+## k_parent_sink  0.006541  0.005378 7.955e-03
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    3.29       2  6
-## parent      3.29       2  6
+## All data   3.287       2  6
+## parent     3.287       2  6
 ## 
 ## Resulting formation fractions:
 ##             ff
@@ -1067,16 +1061,16 @@ plot(m.L4.FOMC)
 
## mkin version:    0.9.34 
-## R version:       3.1.1 
-## Date of fit:     Wed Oct 15 00:58:24 2014 
-## Date of summary: Wed Oct 15 00:58:24 2014 
+## R version:       3.1.2 
+## Date of fit:     Fri Nov 21 19:18:54 2014 
+## Date of summary: Fri Nov 21 19:18:54 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.359 s
+## Fitted with method Port using 66 model solutions performed in 0.387 s
 ## 
 ## Weighting: none
 ## 
@@ -1087,42 +1081,42 @@ plot(m.L4.FOMC)
 ## beta      10.0 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##            value lower upper
-## parent_0  96.600  -Inf   Inf
-## log_alpha  0.000  -Inf   Inf
-## log_beta   2.303  -Inf   Inf
+##               value lower upper
+## parent_0  96.600000  -Inf   Inf
+## log_alpha  0.000000  -Inf   Inf
+## log_beta   2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters:
-##           Estimate Std. Error Lower   Upper t value Pr(>|t|)   Pr(>t)
-## parent_0    99.100      1.680 94.80 103.000  59.000 2.64e-08 1.32e-08
-## log_alpha   -0.351      0.372 -1.31   0.607  -0.941 3.90e-01 1.95e-01
-## log_beta     4.170      0.564  2.73   5.620   7.410 7.06e-04 3.53e-04
+##           Estimate Std. Error  Lower    Upper t value  Pr(>|t|)    Pr(>t)
+## parent_0   99.1400     1.6800 94.820 103.5000 59.0200 2.643e-08 1.322e-08
+## log_alpha  -0.3506     0.3725 -1.308   0.6068 -0.9414 3.897e-01 1.949e-01
+## log_beta    4.1740     0.5635  2.726   5.6230  7.4070 7.059e-04 3.530e-04
 ## 
 ## Parameter correlation:
 ##           parent_0 log_alpha log_beta
-## parent_0     1.000    -0.536   -0.608
-## log_alpha   -0.536     1.000    0.991
-## log_beta    -0.608     0.991    1.000
+## parent_0    1.0000   -0.5365  -0.6083
+## log_alpha  -0.5365    1.0000   0.9913
+## log_beta   -0.6083    0.9913   1.0000
 ## 
-## Residual standard error: 2.31 on 5 degrees of freedom
+## Residual standard error: 2.315 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##          Estimate Lower  Upper
-## parent_0   99.100 94.80 103.00
-## alpha       0.704  0.27   1.83
-## beta       65.000 15.30 277.00
+##          Estimate   Lower   Upper
+## parent_0  99.1400 94.8200 103.500
+## alpha      0.7042  0.2703   1.835
+## beta      64.9800 15.2600 276.600
 ## 
 ## Chi2 error levels in percent:
 ##          err.min n.optim df
-## All data    2.03       3  5
-## parent      2.03       3  5
+## All data   2.029       3  5
+## parent     2.029       3  5
 ## 
 ## Estimated disappearance times:
-##        DT50 DT90 DT50back
-## parent  109 1644      495
+##         DT50 DT90 DT50back
+## parent 108.9 1644    494.9

The error level at which the chi2 test passes is slightly lower for the FOMC diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf index f215f306..0e2c5401 100644 Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf index d14b86bf..d151878d 100644 Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ -- cgit v1.2.1