diff options
| author | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2012-06-26 00:30:43 +0000 |
|---|---|---|
| committer | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2012-06-26 00:30:43 +0000 |
| commit | e7f0ce4dae036912c639f6ac473a9e5ba7345a7b (patch) | |
| tree | 9cc571d553b00945097b567923aecae55a08616f /vignettes | |
| parent | b88dea4b838cd3a1e65b9bc8e6b390f5b47bf144 (diff) | |
- Moved the vignette to the location that is meanwhile recommended
- Update of the vignette
- A bit of cleanup
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@42 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'vignettes')
51 files changed, 4942 insertions, 0 deletions
diff --git a/vignettes/KinGUI/A_DFOP_report.txt b/vignettes/KinGUI/A_DFOP_report.txt new file mode 100644 index 0000000..b887a46 --- /dev/null +++ b/vignettes/KinGUI/A_DFOP_report.txt @@ -0,0 +1,63 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 9.6600 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0373 185.8206 0.4999
+ Parent_k2 0.0372 160.9856 0.4999
+ Parent_g 0.4780 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 109.2019 6.5416
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.6130 NaN
+ DT90: 61.8309 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.2019 -7.9619 NaN 0.0000 NaN
+ 3.0 99.2700 97.6587 1.6113 NaN 11.5432 NaN
+ 7.0 90.1100 84.1431 5.9669 NaN 25.0589 NaN
+ 14.0 72.1900 64.8345 7.3555 NaN 44.3674 NaN
+ 30.0 29.7100 35.7303 -6.0203 NaN 73.4716 NaN
+ 62.0 5.9800 10.8517 -4.8717 NaN 98.3502 NaN
+ 90.0 1.5400 3.8252 -2.2852 NaN 105.3768 NaN
+ 118.0 0.3900 1.3483 -0.9583 NaN 107.8536 NaN
+
diff --git a/vignettes/KinGUI/A_DFOP_report_detailed.txt b/vignettes/KinGUI/A_DFOP_report_detailed.txt new file mode 100644 index 0000000..242c1e7 --- /dev/null +++ b/vignettes/KinGUI/A_DFOP_report_detailed.txt @@ -0,0 +1,86 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 4 0 4
+
+ Parent Sink All
+
+ RMSE: 7.4470 NaN 7.4470
+ Chi2Sigma: 4.8354 NaN 4.8354
+ Chi2Err%: 9.6603 NaN 9.6603
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 4
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.0371<-1000.0000 >1000.0000 799.1761 0.5000
+ Parent_k2 0.0372<-1000.0000 >1000.0000 736.5327 0.5000
+ Parent_g 0.4787<-1000.0000 >1000.0000 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 109.0548 91.3583 126.7513 6.3738
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.6534 NaN
+ DT90: 61.9654 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9845 NaN 0.9845
+ R-square: 0.9857 NaN 0.9857
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_g Parent_M
+ Parent_k1 1.0000 1.0000 1.0000 0.3572
+ Parent_k2 1.0000 1.0000 1.0000 0.3605
+ Parent_g 1.0000 1.0000 1.0000 0.3588
+ Parent_M 0.3572 0.3605 0.3588 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.0548 -7.8148 NaN 0.0000 NaN
+ 3.0 99.2700 97.5507 1.7193 NaN 11.5041 NaN
+ 7.0 90.1100 84.0772 6.0328 NaN 24.9776 NaN
+ 14.0 72.1900 64.8204 7.3696 NaN 44.2344 NaN
+ 30.0 29.7100 35.7686 -6.0586 NaN 73.2862 NaN
+ 62.0 5.9800 10.8915 -4.9115 NaN 98.1634 NaN
+ 90.0 1.5400 3.8479 -2.3079 NaN 105.2069 NaN
+ 118.0 0.3900 1.3594 -0.9694 NaN 107.6954 NaN
+
diff --git a/vignettes/KinGUI/A_FOMC_report.txt b/vignettes/KinGUI/A_FOMC_report.txt new file mode 100644 index 0000000..dbd9182 --- /dev/null +++ b/vignettes/KinGUI/A_FOMC_report.txt @@ -0,0 +1,61 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 9.3116 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 28.4585 227.8602 0.4527
+ Parent_beta 746.2785 >1000.0000 0.4539
+ Parent_FFS 1.0000
+ Parent_M(0) 109.4378 5.5762
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.3999 NaN
+ DT90: 62.8917 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.4378 -8.1978 NaN 0.0000 NaN
+ 3.0 99.2700 97.6300 1.6400 NaN 11.8079 NaN
+ 7.0 90.1100 83.9032 6.2068 NaN 25.5346 NaN
+ 14.0 72.1900 64.4848 7.7052 NaN 44.9531 NaN
+ 30.0 29.7100 35.6496 -5.9396 NaN 73.7882 NaN
+ 62.0 5.9800 11.2926 -5.3126 NaN 98.1452 NaN
+ 90.0 1.5400 4.2845 -2.7445 NaN 105.1534 NaN
+ 118.0 0.3900 1.6783 -1.2883 NaN 107.7596 NaN
+
diff --git a/vignettes/KinGUI/A_FOMC_report_detailed.txt b/vignettes/KinGUI/A_FOMC_report_detailed.txt new file mode 100644 index 0000000..2b14a22 --- /dev/null +++ b/vignettes/KinGUI/A_FOMC_report_detailed.txt @@ -0,0 +1,83 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 3 0 3
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 6.9610 NaN 6.9610
+ Chi2Sigma: 4.6781 NaN 4.6781
+ Chi2Err%: 9.3462 NaN 9.3462
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 5
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_alpha 26.0717 -467.3094 519.4528 191.9336 0.4486
+ Parent_beta 682.1168<-1000.0000 >1000.0000 >1000.0000 0.4500
+ Parent_FFS 1.0000
+ Parent_M(0) 109.4699 95.0742 123.8656 5.6002
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.3781 NaN
+ DT90: 62.9832 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9831 NaN 0.9831
+ R-square: 0.9845 NaN 0.9845
+
+# Correlation matrix of parameters
+ Parent_alpha Parent_beta Parent_M
+ Parent_alpha 1.0000 0.9998 -0.4272
+ Parent_beta 0.9998 1.0000 -0.4364
+ Parent_M -0.4272 -0.4364 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.4699 -8.2299 NaN 0.0000 NaN
+ 3.0 99.2700 97.6350 1.6350 NaN 11.8349 NaN
+ 7.0 90.1100 83.8862 6.2238 NaN 25.5837 NaN
+ 14.0 72.1900 64.4547 7.7353 NaN 45.0152 NaN
+ 30.0 29.7100 35.6410 -5.9310 NaN 73.8288 NaN
+ 62.0 5.9800 11.3304 -5.3504 NaN 98.1395 NaN
+ 90.0 1.5400 4.3252 -2.7852 NaN 105.1447 NaN
+ 118.0 0.3900 1.7087 -1.3187 NaN 107.7612 NaN
+
diff --git a/vignettes/KinGUI/A_HS_report.txt b/vignettes/KinGUI/A_HS_report.txt new file mode 100644 index 0000000..00c5fef --- /dev/null +++ b/vignettes/KinGUI/A_HS_report.txt @@ -0,0 +1,63 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.1106 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0057 0.0149 0.3610
+ Parent_k2 0.0462 0.0037 1.2e-004
+ Parent_tb 5.8616 2.3515 0.0336
+ Parent_FFS 1.0000
+ Parent_M(0) 101.1190 3.1688
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 20.1455 NaN
+ DT90: 54.9884 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 101.1190 0.1210 NaN 0.0000 NaN
+ 3.0 99.2700 99.4072 -0.1372 NaN 1.7118 NaN
+ 7.0 90.1100 92.7915 -2.6815 NaN 8.3275 NaN
+ 14.0 72.1900 67.1559 5.0341 NaN 33.9631 NaN
+ 30.0 29.7100 32.0712 -2.3612 NaN 69.0478 NaN
+ 62.0 5.9800 7.3144 -1.3344 NaN 93.8047 NaN
+ 90.0 1.5400 2.0067 -0.4667 NaN 99.1123 NaN
+ 118.0 0.3900 0.5505 -0.1605 NaN 100.5685 NaN
+
diff --git a/vignettes/KinGUI/A_HS_report_detailed.txt b/vignettes/KinGUI/A_HS_report_detailed.txt new file mode 100644 index 0000000..9cc5aee --- /dev/null +++ b/vignettes/KinGUI/A_HS_report_detailed.txt @@ -0,0 +1,86 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 4 0 4
+
+ Parent Sink All
+
+ RMSE: 3.1728 NaN 3.1728
+ Chi2Sigma: 2.0601 NaN 2.0601
+ Chi2Err%: 4.1158 NaN 4.1158
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 4
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.0049 -0.0365 0.0464 0.0149 0.3785
+ Parent_k2 0.0461 0.0357 0.0565 0.0037 1.2e-004
+ Parent_tb 5.7617 -0.4681 11.9916 2.2438 0.0311
+ Parent_FFS 1.0000
+ Parent_M(0) 100.9820 92.1729 109.7910 3.1728
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 20.1783 NaN
+ DT90: 55.0878 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9972 NaN 0.9972
+ R-square: 0.9973 NaN 0.9973
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_tb Parent_M
+ Parent_k1 1.0000 0.0024 0.8460 0.7018
+ Parent_k2 0.0024 1.0000 0.2691 0.0013
+ Parent_tb 0.8460 0.2691 1.0000 0.3820
+ Parent_M 0.7018 0.0013 0.3820 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 100.9820 0.2580 NaN 0.0000 NaN
+ 3.0 99.2700 99.4947 -0.2247 NaN 1.4873 NaN
+ 7.0 90.1100 92.6989 -2.5889 NaN 8.2831 NaN
+ 14.0 72.1900 67.1302 5.0598 NaN 33.8518 NaN
+ 30.0 29.7100 32.1041 -2.3941 NaN 68.8779 NaN
+ 62.0 5.9800 7.3425 -1.3625 NaN 93.6394 NaN
+ 90.0 1.5400 2.0194 -0.4794 NaN 98.9626 NaN
+ 118.0 0.3900 0.5554 -0.1654 NaN 100.4266 NaN
+
diff --git a/vignettes/KinGUI/A_KinGUI.txt b/vignettes/KinGUI/A_KinGUI.txt new file mode 100644 index 0000000..f42b72c --- /dev/null +++ b/vignettes/KinGUI/A_KinGUI.txt @@ -0,0 +1,13 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 101.24 +3 99.27 +7 90.11 +14 72.19 +30 29.71 +62 5.98 +90 1.54 +118 0.39 diff --git a/vignettes/KinGUI/A_SFO_report.txt b/vignettes/KinGUI/A_SFO_report.txt new file mode 100644 index 0000000..8ee2968 --- /dev/null +++ b/vignettes/KinGUI/A_SFO_report.txt @@ -0,0 +1,59 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 8.3852 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.0372 0.0043 6.5e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 109.1513 4.3906
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.6257 NaN
+ DT90: 61.8733 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.1513 -7.9113 NaN 0.0000 NaN
+ 3.0 99.2700 97.6209 1.6491 NaN 11.5304 NaN
+ 7.0 90.1100 84.1191 5.9909 NaN 25.0322 NaN
+ 14.0 72.1900 64.8276 7.3624 NaN 44.3237 NaN
+ 30.0 29.7100 35.7411 -6.0311 NaN 73.4102 NaN
+ 62.0 5.9800 10.8638 -4.8838 NaN 98.2875 NaN
+ 90.0 1.5400 3.8322 -2.2922 NaN 105.3191 NaN
+ 118.0 0.3900 1.3518 -0.9618 NaN 107.7995 NaN
+
diff --git a/vignettes/KinGUI/A_SFO_report_detailed.txt b/vignettes/KinGUI/A_SFO_report_detailed.txt new file mode 100644 index 0000000..98e5979 --- /dev/null +++ b/vignettes/KinGUI/A_SFO_report_detailed.txt @@ -0,0 +1,80 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\A_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 2 0 2
+ Degrees of Freedom: 6 0 6
+
+ Parent Sink All
+
+ RMSE: 6.0801 NaN 6.0801
+ Chi2Sigma: 4.1971 NaN 4.1971
+ Chi2Err%: 8.3852 NaN 8.3852
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 6
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k 0.0372 0.0267 0.0477 0.0043 6.5e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 109.1513 98.4079 119.8947 4.3906
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 18.6257 NaN
+ DT90: 61.8733 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9845 NaN 0.9845
+ R-square: 0.9856 NaN 0.9856
+
+# Correlation matrix of parameters
+ Parent_k Parent_M
+ Parent_k 1.0000 0.5750
+ Parent_M 0.5750 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 101.2400 109.1513 -7.9113 NaN 0.0000 NaN
+ 3.0 99.2700 97.6209 1.6491 NaN 11.5304 NaN
+ 7.0 90.1100 84.1191 5.9909 NaN 25.0322 NaN
+ 14.0 72.1900 64.8276 7.3624 NaN 44.3237 NaN
+ 30.0 29.7100 35.7411 -6.0311 NaN 73.4102 NaN
+ 62.0 5.9800 10.8638 -4.8838 NaN 98.2875 NaN
+ 90.0 1.5400 3.8322 -2.2922 NaN 105.3191 NaN
+ 118.0 0.3900 1.3518 -0.9618 NaN 107.7995 NaN
+
diff --git a/vignettes/KinGUI/B_DFOP_report.txt b/vignettes/KinGUI/B_DFOP_report.txt new file mode 100644 index 0000000..0ee160b --- /dev/null +++ b/vignettes/KinGUI/B_DFOP_report.txt @@ -0,0 +1,63 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.9562 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.1045 0.2272 0.3347
+ Parent_k2 0.0594 0.1224 0.3266
+ Parent_g 0.5024 3.6431 0.4485
+ Parent_FFS 1.0000
+ Parent_M(0) 99.6663 2.5554
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.6800 NaN
+ DT90: 30.8040 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.6663 -1.0463 NaN 0.0000 NaN
+ 3.0 81.4300 78.0971 3.3329 NaN 21.5692 NaN
+ 7.0 53.1800 56.8198 -3.6398 NaN 42.8465 NaN
+ 14.0 34.8900 33.1902 1.6998 NaN 66.4761 NaN
+ 30.0 10.0900 10.5315 -0.4415 NaN 89.1348 NaN
+ 62.0 1.5000 1.3268 0.1732 NaN 98.3395 NaN
+ 90.0 0.3300 0.2412 0.0888 NaN 99.4251 NaN
+ 118.0 0.0800 0.0452 0.0348 NaN 99.6211 NaN
+
diff --git a/vignettes/KinGUI/B_DFOP_report_detailed.txt b/vignettes/KinGUI/B_DFOP_report_detailed.txt new file mode 100644 index 0000000..e30f7b1 --- /dev/null +++ b/vignettes/KinGUI/B_DFOP_report_detailed.txt @@ -0,0 +1,86 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 4 0 4
+
+ Parent Sink All
+
+ RMSE: 2.6723 NaN 2.6723
+ Chi2Sigma: 1.7351 NaN 1.7351
+ Chi2Err%: 4.9554 NaN 4.9554
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 4
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.1024 -0.4603 0.6650 0.2027 0.3200
+ Parent_k2 0.0580 -0.2942 0.4102 0.1268 0.3355
+ Parent_g 0.5406 -9.3329 10.4141 3.5562 0.4433
+ Parent_FFS 1.0000
+ Parent_M(0) 99.6744 92.5981 106.7508 2.5487
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.6786 NaN
+ DT90: 30.8006 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9973 NaN 0.9973
+ R-square: 0.9973 NaN 0.9973
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_g Parent_M
+ Parent_k1 1.0000 0.9674 -0.9908 0.3017
+ Parent_k2 0.9674 1.0000 -0.9919 0.2094
+ Parent_g -0.9908 -0.9919 1.0000 -0.2409
+ Parent_M 0.3017 0.2094 -0.2409 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.6744 -1.0544 NaN 0.0000 NaN
+ 3.0 81.4300 78.1107 3.3193 NaN 21.5637 NaN
+ 7.0 53.1800 56.8237 -3.6437 NaN 42.8507 NaN
+ 14.0 34.8900 33.1764 1.7136 NaN 66.4981 NaN
+ 30.0 10.0900 10.5286 -0.4386 NaN 89.1458 NaN
+ 62.0 1.5000 1.3480 0.1520 NaN 98.3264 NaN
+ 90.0 0.3300 0.2522 0.0778 NaN 99.4222 NaN
+ 118.0 0.0800 0.0489 0.0311 NaN 99.6255 NaN
+
diff --git a/vignettes/KinGUI/B_FOMC_report.txt b/vignettes/KinGUI/B_FOMC_report.txt new file mode 100644 index 0000000..1a1db57 --- /dev/null +++ b/vignettes/KinGUI/B_FOMC_report.txt @@ -0,0 +1,61 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.6641 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 38.9958 202.8246 0.4276
+ Parent_beta 491.1490 >1000.0000 0.4287
+ Parent_FFS 1.0000
+ Parent_M(0) 99.3410 2.2382
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.8082 NaN
+ DT90: 29.8742 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.3410 -0.7210 NaN 0.0000 NaN
+ 3.0 81.4300 78.3426 3.0874 NaN 20.9984 NaN
+ 7.0 53.1800 57.2085 -4.0285 NaN 42.1325 NaN
+ 14.0 34.8900 33.1999 1.6901 NaN 66.1411 NaN
+ 30.0 10.0900 9.8410 0.2490 NaN 89.5000 NaN
+ 62.0 1.5000 0.9634 0.5366 NaN 98.3776 NaN
+ 90.0 0.3300 0.1405 0.1895 NaN 99.2005 NaN
+ 118.0 0.0800 0.0224 0.0576 NaN 99.3186 NaN
+
diff --git a/vignettes/KinGUI/B_FOMC_report_detailed.txt b/vignettes/KinGUI/B_FOMC_report_detailed.txt new file mode 100644 index 0000000..449ab34 --- /dev/null +++ b/vignettes/KinGUI/B_FOMC_report_detailed.txt @@ -0,0 +1,83 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 3 0 3
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 2.4135 NaN 2.4135
+ Chi2Sigma: 1.6220 NaN 1.6220
+ Chi2Err%: 4.6322 NaN 4.6322
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 5
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_alpha 8.5369 -15.5894 32.6631 9.3855 0.2024
+ Parent_beta 101.4875 -206.6864 409.6614 119.8849 0.2179
+ Parent_FFS 1.0000
+ Parent_M(0) 99.9273 94.1784 105.6762 2.2364
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.5840 NaN
+ DT90: 31.4206 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9973 NaN 0.9973
+ R-square: 0.9973 NaN 0.9973
+
+# Correlation matrix of parameters
+ Parent_alpha Parent_beta Parent_M
+ Parent_alpha 1.0000 0.9989 -0.3574
+ Parent_beta 0.9989 1.0000 -0.3825
+ Parent_M -0.3574 -0.3825 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.9273 -1.3073 NaN 0.0000 NaN
+ 3.0 81.4300 77.9251 3.5049 NaN 22.0022 NaN
+ 7.0 53.1800 56.5452 -3.3652 NaN 43.3822 NaN
+ 14.0 34.8900 33.1569 1.7331 NaN 66.7704 NaN
+ 30.0 10.0900 10.9528 -0.8628 NaN 88.9745 NaN
+ 62.0 1.5000 1.7058 -0.2058 NaN 98.2215 NaN
+ 90.0 0.3300 0.4424 -0.1124 NaN 99.4849 NaN
+ 118.0 0.0800 0.1380 -0.0580 NaN 99.7893 NaN
+
diff --git a/vignettes/KinGUI/B_HS_report.txt b/vignettes/KinGUI/B_HS_report.txt new file mode 100644 index 0000000..18bb818 --- /dev/null +++ b/vignettes/KinGUI/B_HS_report.txt @@ -0,0 +1,63 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.4535 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0840 0.0068 1.3e-004
+ Parent_k2 0.0704 0.0136 0.0033
+ Parent_tb 7.0665 7.2051 0.1911
+ Parent_FFS 1.0000
+ Parent_M(0) 100.2115 2.2443
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.4848 NaN
+ DT90: 31.3565 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 100.2115 -1.5915 NaN 0.0000 NaN
+ 3.0 81.4300 77.8968 3.5332 NaN 22.3146 NaN
+ 7.0 53.1800 55.6745 -2.4945 NaN 44.5370 NaN
+ 14.0 34.8900 33.9891 0.9009 NaN 66.2224 NaN
+ 30.0 10.0900 11.0248 -0.9348 NaN 89.1866 NaN
+ 62.0 1.5000 1.1599 0.3401 NaN 99.0515 NaN
+ 90.0 0.3300 0.1617 0.1683 NaN 100.0497 NaN
+ 118.0 0.0800 0.0225 0.0575 NaN 100.1889 NaN
+
diff --git a/vignettes/KinGUI/B_HS_report_detailed.txt b/vignettes/KinGUI/B_HS_report_detailed.txt new file mode 100644 index 0000000..f723ea4 --- /dev/null +++ b/vignettes/KinGUI/B_HS_report_detailed.txt @@ -0,0 +1,86 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 4 0 4
+
+ Parent Sink All
+
+ RMSE: 2.7291 NaN 2.7291
+ Chi2Sigma: 1.7720 NaN 1.7720
+ Chi2Err%: 5.0608 NaN 5.0608
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 4
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.0747 0.0369 0.1124 0.0136 0.0027
+ Parent_k2 0.0799 0.0614 0.0984 0.0067 1.4e-004
+ Parent_tb 3.0662 NaN NaN NaN NaN
+ Parent_FFS 1.0000
+ Parent_M(0) 99.0235 91.4501 106.5970 2.7277
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.8792 NaN
+ DT90: 29.0329 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9972 NaN 0.9972
+ R-square: 0.9973 NaN 0.9973
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_tb Parent_M
+ Parent_k1 1.0000 -0.4395 NaN 0.6629
+ Parent_k2 -0.4395 1.0000 NaN -0.0336
+ Parent_tb NaN NaN NaN NaN
+ Parent_M 0.6629 -0.0336 NaN 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.0235 -0.4035 NaN 0.0000 NaN
+ 3.0 81.4300 79.1517 2.2783 NaN 19.8719 NaN
+ 7.0 53.1800 57.5283 -4.3483 NaN 41.4952 NaN
+ 14.0 34.8900 32.8934 1.9966 NaN 66.1302 NaN
+ 30.0 10.0900 9.1664 0.9236 NaN 89.8572 NaN
+ 62.0 1.5000 0.7118 0.7882 NaN 98.3117 NaN
+ 90.0 0.3300 0.0761 0.2539 NaN 98.9475 NaN
+ 118.0 0.0800 0.0081 0.0719 NaN 99.0154 NaN
+
diff --git a/vignettes/KinGUI/B_KinGUI.txt b/vignettes/KinGUI/B_KinGUI.txt new file mode 100644 index 0000000..6a589b2 --- /dev/null +++ b/vignettes/KinGUI/B_KinGUI.txt @@ -0,0 +1,13 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 98.62 +3 81.43 +7 53.18 +14 34.89 +30 10.09 +62 1.5 +90 0.33 +118 0.08 diff --git a/vignettes/KinGUI/B_SFO_report.txt b/vignettes/KinGUI/B_SFO_report.txt new file mode 100644 index 0000000..d3856fe --- /dev/null +++ b/vignettes/KinGUI/B_SFO_report.txt @@ -0,0 +1,59 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.4562 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.0782 0.0039 4.7e-007
+ Parent_FFS 1.0000
+ Parent_M(0) 99.1740 1.9239
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.8686 NaN
+ DT90: 29.4608 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.1740 -0.5540 NaN 0.0000 NaN
+ 3.0 81.4300 78.4455 2.9845 NaN 20.7286 NaN
+ 7.0 53.1800 57.3845 -4.2045 NaN 41.7896 NaN
+ 14.0 34.8900 33.2040 1.6860 NaN 65.9700 NaN
+ 30.0 10.0900 9.5082 0.5818 NaN 89.6659 NaN
+ 62.0 1.5000 0.7797 0.7203 NaN 98.3944 NaN
+ 90.0 0.3300 0.0874 0.2426 NaN 99.0866 NaN
+ 118.0 0.0800 0.0098 0.0702 NaN 99.1642 NaN
+
diff --git a/vignettes/KinGUI/B_SFO_report_detailed.txt b/vignettes/KinGUI/B_SFO_report_detailed.txt new file mode 100644 index 0000000..ff6e9c8 --- /dev/null +++ b/vignettes/KinGUI/B_SFO_report_detailed.txt @@ -0,0 +1,80 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\B_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 8 0 8
+ Number of parameters: 2 0 2
+ Degrees of Freedom: 6 0 6
+
+ Parent Sink All
+
+ RMSE: 2.2604 NaN 2.2604
+ Chi2Sigma: 1.5603 NaN 1.5603
+ Chi2Err%: 4.4562 NaN 4.4562
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 6
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k 0.0782 0.0687 0.0876 0.0039 4.7e-007
+ Parent_FFS 1.0000
+ Parent_M(0) 99.1741 94.4666 103.8816 1.9239
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 8.8686 NaN
+ DT90: 29.4608 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9971 NaN 0.9971
+ R-square: 0.9972 NaN 0.9972
+
+# Correlation matrix of parameters
+ Parent_k Parent_M
+ Parent_k 1.0000 0.5804
+ Parent_M 0.5804 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 98.6200 99.1741 -0.5541 NaN 0.0000 NaN
+ 3.0 81.4300 78.4455 2.9845 NaN 20.7286 NaN
+ 7.0 53.1800 57.3844 -4.2044 NaN 41.7897 NaN
+ 14.0 34.8900 33.2040 1.6860 NaN 65.9701 NaN
+ 30.0 10.0900 9.5081 0.5819 NaN 89.6660 NaN
+ 62.0 1.5000 0.7797 0.7203 NaN 98.3944 NaN
+ 90.0 0.3300 0.0874 0.2426 NaN 99.0867 NaN
+ 118.0 0.0800 0.0098 0.0702 NaN 99.1643 NaN
+
diff --git a/vignettes/KinGUI/C_DFOP_report.txt b/vignettes/KinGUI/C_DFOP_report.txt new file mode 100644 index 0000000..65b8f29 --- /dev/null +++ b/vignettes/KinGUI/C_DFOP_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 2.6613 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.4596 0.0204 1.6e-006
+ Parent_k2 0.0179 0.0030 0.0010
+ Parent_g 0.8539 0.0134 9.1e-009
+ Parent_FFS 1.0000
+ Parent_M(0) 85.0044 0.8907
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.8869 NaN
+ DT90: 21.2535 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 85.0044 0.0956 NaN 0.0000 NaN
+ 1.0 57.9000 58.0394 -0.1394 NaN 26.9651 NaN
+ 3.0 29.9000 30.0534 -0.1534 NaN 54.9510 NaN
+ 7.0 14.6000 13.8668 0.7332 NaN 71.1376 NaN
+ 14.0 9.7000 9.7875 -0.0875 NaN 75.2170 NaN
+ 28.0 6.6000 7.5324 -0.9324 NaN 77.4720 NaN
+ 63.0 4.0000 4.0324 -0.0324 NaN 80.9721 NaN
+ 91.0 3.9000 2.4461 1.4539 NaN 82.5583 NaN
+ 119.0 0.6000 1.4838 -0.8838 NaN 83.5206 NaN
+
diff --git a/vignettes/KinGUI/C_DFOP_report_detailed.txt b/vignettes/KinGUI/C_DFOP_report_detailed.txt new file mode 100644 index 0000000..b26c063 --- /dev/null +++ b/vignettes/KinGUI/C_DFOP_report_detailed.txt @@ -0,0 +1,87 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 0.9341 NaN 0.9341
+ Chi2Sigma: 0.6278 NaN 0.6278
+ Chi2Err%: 2.6613 NaN 2.6613
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 5
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.4594 0.4071 0.5117 0.0204 1.6e-006
+ Parent_k2 0.0178 0.0100 0.0256 0.0030 0.0010
+ Parent_g 0.8540 0.8194 0.8885 0.0134 9.1e-009
+ Parent_FFS 1.0000
+ Parent_M(0) 84.9867 82.6972 87.2762 0.8907
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.8876 NaN
+ DT90: 21.2511 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9994 NaN 0.9994
+ R-square: 0.9994 NaN 0.9994
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_g Parent_M
+ Parent_k1 1.0000 0.4657 -0.6601 0.4339
+ Parent_k2 0.4657 1.0000 -0.7418 0.0793
+ Parent_g -0.6601 -0.7418 1.0000 -0.0190
+ Parent_M 0.4339 0.0793 -0.0190 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 84.9867 0.1133 NaN 0.0000 NaN
+ 1.0 57.9000 58.0356 -0.1356 NaN 26.9512 NaN
+ 3.0 29.9000 30.0560 -0.1560 NaN 54.9308 NaN
+ 7.0 14.6000 13.8653 0.7347 NaN 71.1214 NaN
+ 14.0 9.7000 9.7841 -0.0841 NaN 75.2026 NaN
+ 28.0 6.6000 7.5314 -0.9314 NaN 77.4553 NaN
+ 63.0 4.0000 4.0343 -0.0343 NaN 80.9524 NaN
+ 91.0 3.9000 2.4485 1.4515 NaN 82.5382 NaN
+ 119.0 0.6000 1.4860 -0.8860 NaN 83.5007 NaN
+
diff --git a/vignettes/KinGUI/C_FOMC_report.txt b/vignettes/KinGUI/C_FOMC_report.txt new file mode 100644 index 0000000..3d74181 --- /dev/null +++ b/vignettes/KinGUI/C_FOMC_report.txt @@ -0,0 +1,62 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 6.6574 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 1.0564 0.1700 4.0e-004
+ Parent_beta 1.9260 0.5402 0.0059
+ Parent_FFS 1.0000
+ Parent_M(0) 85.8766 2.2459
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.7860 NaN
+ DT90: 15.1052 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 85.8766 -0.7766 NaN 0.0000 NaN
+ 1.0 57.9000 55.2088 2.6912 NaN 30.6678 NaN
+ 3.0 29.9000 31.8437 -1.9437 NaN 54.0329 NaN
+ 7.0 14.6000 16.9940 -2.3940 NaN 68.8827 NaN
+ 14.0 9.7000 9.2184 0.4816 NaN 76.6582 NaN
+ 28.0 6.6000 4.7343 1.8657 NaN 81.1423 NaN
+ 63.0 4.0000 2.0889 1.9111 NaN 83.7877 NaN
+ 91.0 3.9000 1.4302 2.4698 NaN 84.4464 NaN
+ 119.0 0.6000 1.0829 -0.4829 NaN 84.7938 NaN
+
diff --git a/vignettes/KinGUI/C_FOMC_report_detailed.txt b/vignettes/KinGUI/C_FOMC_report_detailed.txt new file mode 100644 index 0000000..f19484c --- /dev/null +++ b/vignettes/KinGUI/C_FOMC_report_detailed.txt @@ -0,0 +1,84 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 3 0 3
+ Degrees of Freedom: 6 0 6
+
+ Parent Sink All
+
+ RMSE: 2.2749 NaN 2.2749
+ Chi2Sigma: 1.5704 NaN 1.5704
+ Chi2Err%: 6.6572 NaN 6.6572
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 6
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_alpha 1.0540 0.6398 1.4681 0.1693 4.0e-004
+ Parent_beta 1.9192 0.6033 3.2352 0.5378 0.0059
+ Parent_FFS 1.0000
+ Parent_M(0) 85.8774 80.3817 91.3731 2.2460
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.7854 NaN
+ DT90: 15.1385 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9955 NaN 0.9955
+ R-square: 0.9959 NaN 0.9959
+
+# Correlation matrix of parameters
+ Parent_alpha Parent_beta Parent_M
+ Parent_alpha 1.0000 0.9547 -0.2034
+ Parent_beta 0.9547 1.0000 -0.3624
+ Parent_M -0.2034 -0.3624 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 85.8774 -0.7774 NaN 0.0000 NaN
+ 1.0 57.9000 55.1960 2.7040 NaN 30.6813 NaN
+ 3.0 29.9000 31.8455 -1.9455 NaN 54.0318 NaN
+ 7.0 14.6000 17.0087 -2.4087 NaN 68.8687 NaN
+ 14.0 9.7000 9.2363 0.4637 NaN 76.6411 NaN
+ 28.0 6.6000 4.7498 1.8502 NaN 81.1275 NaN
+ 63.0 4.0000 2.0994 1.9006 NaN 83.7779 NaN
+ 91.0 3.9000 1.4387 2.4613 NaN 84.4387 NaN
+ 119.0 0.6000 1.0899 -0.4899 NaN 84.7874 NaN
+
diff --git a/vignettes/KinGUI/C_HS_report.txt b/vignettes/KinGUI/C_HS_report.txt new file mode 100644 index 0000000..ca137d4 --- /dev/null +++ b/vignettes/KinGUI/C_HS_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 4.6963 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.3560 0.0185 3.5e-006
+ Parent_k2 0.0227 0.0057 0.0052
+ Parent_tb 5.1551 0.3719 1.8e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 84.4829 1.5377
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.9472 NaN
+ DT90: 25.7931 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 84.4829 0.6171 NaN 0.0000 NaN
+ 1.0 57.9000 59.1796 -1.2796 NaN 25.3034 NaN
+ 3.0 29.9000 29.0387 0.8613 NaN 55.4442 NaN
+ 7.0 14.6000 12.9316 1.6684 NaN 71.5514 NaN
+ 14.0 9.7000 11.0354 -1.3354 NaN 73.4476 NaN
+ 28.0 6.6000 8.0363 -1.4363 NaN 76.4466 NaN
+ 63.0 4.0000 3.6369 0.3631 NaN 80.8460 NaN
+ 91.0 3.9000 1.9287 1.9713 NaN 82.5542 NaN
+ 119.0 0.6000 1.0229 -0.4229 NaN 83.4601 NaN
+
diff --git a/vignettes/KinGUI/C_HS_report_detailed.txt b/vignettes/KinGUI/C_HS_report_detailed.txt new file mode 100644 index 0000000..b8a5753 --- /dev/null +++ b/vignettes/KinGUI/C_HS_report_detailed.txt @@ -0,0 +1,87 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 1.6484 NaN 1.6484
+ Chi2Sigma: 1.1078 NaN 1.1078
+ Chi2Err%: 4.6963 NaN 4.6963
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 5
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.3560 0.3084 0.4036 0.0185 3.5e-006
+ Parent_k2 0.0227 0.0081 0.0372 0.0057 0.0052
+ Parent_tb 5.1547 4.0767 6.2327 0.4193 3.2e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 84.4914 80.5387 88.4441 1.5377
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 1.9470 NaN
+ DT90: 25.7899 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9980 NaN 0.9980
+ R-square: 0.9980 NaN 0.9980
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_tb Parent_M
+ Parent_k1 1.0000 -0.0002 -0.5436 0.5345
+ Parent_k2 -0.0002 1.0000 -0.4781 -0.0001
+ Parent_tb -0.5436 -0.4781 1.0000 -0.1210
+ Parent_M 0.5345 -0.0001 -0.1210 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 84.4914 0.6086 NaN 0.0000 NaN
+ 1.0 57.9000 59.1836 -1.2836 NaN 25.3078 NaN
+ 3.0 29.9000 29.0389 0.8611 NaN 55.4525 NaN
+ 7.0 14.6000 12.9326 1.6674 NaN 71.5588 NaN
+ 14.0 9.7000 11.0360 -1.3360 NaN 73.4553 NaN
+ 28.0 6.6000 8.0365 -1.4365 NaN 76.4548 NaN
+ 63.0 4.0000 3.6367 0.3633 NaN 80.8547 NaN
+ 91.0 3.9000 1.9285 1.9715 NaN 82.5629 NaN
+ 119.0 0.6000 1.0226 -0.4226 NaN 83.4687 NaN
+
diff --git a/vignettes/KinGUI/C_KinGUI.txt b/vignettes/KinGUI/C_KinGUI.txt new file mode 100644 index 0000000..1e0e3d8 --- /dev/null +++ b/vignettes/KinGUI/C_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 85.1 +1 57.9 +3 29.9 +7 14.6 +14 9.7 +28 6.6 +63 4 +91 3.9 +119 0.6 diff --git a/vignettes/KinGUI/C_SFO_report.txt b/vignettes/KinGUI/C_SFO_report.txt new file mode 100644 index 0000000..5e32b0b --- /dev/null +++ b/vignettes/KinGUI/C_SFO_report.txt @@ -0,0 +1,60 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 15.8456 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.3060 0.0459 1.4e-004
+ Parent_FFS 1.0000
+ Parent_M(0) 82.4894 4.7401
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 2.2651 NaN
+ DT90: 7.5245 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 82.4894 2.6106 NaN 0.0000 NaN
+ 1.0 57.9000 60.7434 -2.8434 NaN 21.7460 NaN
+ 3.0 29.9000 32.9383 -3.0383 NaN 49.5511 NaN
+ 7.0 14.6000 9.6851 4.9149 NaN 72.8043 NaN
+ 14.0 9.7000 1.1371 8.5629 NaN 81.3522 NaN
+ 28.0 6.6000 0.0157 6.5843 NaN 82.4737 NaN
+ 63.0 4.0000 0.0000 4.0000 NaN 82.4894 NaN
+ 91.0 3.9000 0.0000 3.9000 NaN 82.4894 NaN
+ 119.0 0.6000 0.0000 0.6000 NaN 82.4894 NaN
+
diff --git a/vignettes/KinGUI/C_SFO_report_detailed.txt b/vignettes/KinGUI/C_SFO_report_detailed.txt new file mode 100644 index 0000000..512e10e --- /dev/null +++ b/vignettes/KinGUI/C_SFO_report_detailed.txt @@ -0,0 +1,81 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\C_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 2 0 2
+ Degrees of Freedom: 7 0 7
+
+ Parent Sink All
+
+ RMSE: 5.2987 NaN 5.2987
+ Chi2Sigma: 3.7378 NaN 3.7378
+ Chi2Err%: 15.8456 NaN 15.8456
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 7
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k 0.3060 0.1975 0.4146 0.0459 1.4e-004
+ Parent_FFS 1.0000
+ Parent_M(0) 82.4905 71.2818 93.6992 4.7402
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 2.2649 NaN
+ DT90: 7.5240 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9714 NaN 0.9714
+ R-square: 0.9869 NaN 0.9869
+
+# Correlation matrix of parameters
+ Parent_k Parent_M
+ Parent_k 1.0000 0.5212
+ Parent_M 0.5212 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 85.1000 82.4905 2.6095 NaN 0.0000 NaN
+ 1.0 57.9000 60.7429 -2.8429 NaN 21.7476 NaN
+ 3.0 29.9000 32.9366 -3.0366 NaN 49.5539 NaN
+ 7.0 14.6000 9.6838 4.9162 NaN 72.8067 NaN
+ 14.0 9.7000 1.1368 8.5632 NaN 81.3537 NaN
+ 28.0 6.6000 0.0157 6.5843 NaN 82.4749 NaN
+ 63.0 4.0000 0.0000 4.0000 NaN 82.4905 NaN
+ 91.0 3.9000 0.0000 3.9000 NaN 82.4905 NaN
+ 119.0 0.6000 0.0000 0.6000 NaN 82.4905 NaN
+
diff --git a/vignettes/KinGUI/D_DFOP_report.txt b/vignettes/KinGUI/D_DFOP_report.txt new file mode 100644 index 0000000..31ab25d --- /dev/null +++ b/vignettes/KinGUI/D_DFOP_report.txt @@ -0,0 +1,77 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 7.2751 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0982 >1000.0000 0.5000
+ Parent_k2 0.0976 >1000.0000 0.5000
+ Parent_g 0.5525 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 99.4468 2.1924
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 7.0773 NaN
+ DT90: 23.5106 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 99.4468 0.0132 NaN 0.0000 NaN
+ 0.0 102.0400 99.4468 2.5932 NaN 0.0000 NaN
+ 1.0 93.5000 90.1688 3.3312 NaN 9.2780 NaN
+ 1.0 92.5000 90.1688 2.3312 NaN 9.2780 NaN
+ 3.0 63.2300 74.1289 -10.8989 NaN 25.3179 NaN
+ 3.0 68.9900 74.1289 -5.1389 NaN 25.3179 NaN
+ 7.0 52.3200 50.1015 2.2185 NaN 49.3454 NaN
+ 7.0 55.1300 50.1015 5.0285 NaN 49.3454 NaN
+ 14.0 27.2700 25.2413 2.0287 NaN 74.2055 NaN
+ 14.0 26.6400 25.2413 1.3987 NaN 74.2055 NaN
+ 21.0 11.5000 12.7167 -1.2167 NaN 86.7301 NaN
+ 21.0 11.6400 12.7167 -1.0767 NaN 86.7301 NaN
+ 35.0 2.8500 3.2278 -0.3778 NaN 96.2190 NaN
+ 35.0 2.9100 3.2278 -0.3178 NaN 96.2190 NaN
+ 50.0 0.6900 0.7429 -0.0529 NaN 98.7040 NaN
+ 50.0 0.6300 0.7429 -0.1129 NaN 98.7040 NaN
+ 75.0 0.0500 0.0642 -0.0142 NaN 99.3826 NaN
+ 75.0 0.0600 0.0642 -0.0042 NaN 99.3826 NaN
+ 100.0 NaN 0.0056 NaN NaN 99.4413 NaN
+ 100.0 NaN 0.0056 NaN NaN 99.4413 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4461 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4461 NaN
+
diff --git a/vignettes/KinGUI/D_DFOP_report_detailed.txt b/vignettes/KinGUI/D_DFOP_report_detailed.txt new file mode 100644 index 0000000..8326b6b --- /dev/null +++ b/vignettes/KinGUI/D_DFOP_report_detailed.txt @@ -0,0 +1,100 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 4.2785 NaN 4.2785
+ Chi2Sigma: 2.8753 NaN 2.8753
+ Chi2Err%: 7.2751 NaN 7.2751
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 14
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.0982<-1000.0000 >1000.0000 696.9952 0.4999
+ Parent_k2 0.0976<-1000.0000 >1000.0000 852.9518 0.5000
+ Parent_g 0.5524<-1000.0000 >1000.0000 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 99.4470 93.8860 105.0081 2.5928
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 7.0773 NaN
+ DT90: 23.5106 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9919 NaN 0.9919
+ R-square: 0.9919 NaN 0.9919
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_g Parent_M
+ Parent_k1 1.0000 1.0000 -1.0000 0.5546
+ Parent_k2 1.0000 1.0000 -1.0000 0.5530
+ Parent_g -1.0000 -1.0000 1.0000 -0.5538
+ Parent_M 0.5546 0.5530 -0.5538 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 99.4470 0.0130 NaN 0.0000 NaN
+ 0.0 102.0400 99.4470 2.5930 NaN 0.0000 NaN
+ 1.0 93.5000 90.1690 3.3310 NaN 9.2780 NaN
+ 1.0 92.5000 90.1690 2.3310 NaN 9.2780 NaN
+ 3.0 63.2300 74.1290 -10.8990 NaN 25.3180 NaN
+ 3.0 68.9900 74.1290 -5.1390 NaN 25.3180 NaN
+ 7.0 52.3200 50.1015 2.2185 NaN 49.3456 NaN
+ 7.0 55.1300 50.1015 5.0285 NaN 49.3456 NaN
+ 14.0 27.2700 25.2413 2.0287 NaN 74.2057 NaN
+ 14.0 26.6400 25.2413 1.3987 NaN 74.2057 NaN
+ 21.0 11.5000 12.7167 -1.2167 NaN 86.7303 NaN
+ 21.0 11.6400 12.7167 -1.0767 NaN 86.7303 NaN
+ 35.0 2.8500 3.2278 -0.3778 NaN 96.2192 NaN
+ 35.0 2.9100 3.2278 -0.3178 NaN 96.2192 NaN
+ 50.0 0.6900 0.7429 -0.0529 NaN 98.7042 NaN
+ 50.0 0.6300 0.7429 -0.1129 NaN 98.7042 NaN
+ 75.0 0.0500 0.0642 -0.0142 NaN 99.3828 NaN
+ 75.0 0.0600 0.0642 -0.0042 NaN 99.3828 NaN
+ 100.0 NaN 0.0056 NaN NaN 99.4415 NaN
+ 100.0 NaN 0.0056 NaN NaN 99.4415 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4463 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4463 NaN
+
diff --git a/vignettes/KinGUI/D_FOMC_report.txt b/vignettes/KinGUI/D_FOMC_report.txt new file mode 100644 index 0000000..a2a60f9 --- /dev/null +++ b/vignettes/KinGUI/D_FOMC_report.txt @@ -0,0 +1,75 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 6.8080 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 10.5446 13.6880 0.2265
+ Parent_beta 100.3104 139.0853 0.2409
+ Parent_FFS 1.0000
+ Parent_M(0) 100.1958 2.1103
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 6.8154 NaN
+ DT90: 24.4801 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 100.1958 -0.7358 NaN 0.0000 NaN
+ 0.0 102.0400 100.1958 1.8442 NaN 0.0000 NaN
+ 1.0 93.5000 90.2449 3.2551 NaN 9.9509 NaN
+ 1.0 92.5000 90.2449 2.2551 NaN 9.9509 NaN
+ 3.0 63.2300 73.4343 -10.2043 NaN 26.7615 NaN
+ 3.0 68.9900 73.4343 -4.4443 NaN 26.7615 NaN
+ 7.0 52.3200 49.1968 3.1232 NaN 50.9990 NaN
+ 7.0 55.1300 49.1968 5.9332 NaN 50.9990 NaN
+ 14.0 27.2700 25.2669 2.0031 NaN 74.9289 NaN
+ 14.0 26.6400 25.2669 1.3731 NaN 74.9289 NaN
+ 21.0 11.5000 13.5012 -2.0012 NaN 86.6946 NaN
+ 21.0 11.6400 13.5012 -1.8612 NaN 86.6946 NaN
+ 35.0 2.8500 4.2679 -1.4179 NaN 95.9279 NaN
+ 35.0 2.9100 4.2679 -1.3579 NaN 95.9279 NaN
+ 50.0 0.6900 1.4085 -0.7185 NaN 98.7872 NaN
+ 50.0 0.6300 1.4085 -0.7785 NaN 98.7872 NaN
+ 75.0 0.0500 0.2781 -0.2281 NaN 99.9177 NaN
+ 75.0 0.0600 0.2781 -0.2181 NaN 99.9177 NaN
+ 100.0 NaN 0.0682 NaN NaN 100.1276 NaN
+ 100.0 NaN 0.0682 NaN NaN 100.1276 NaN
+ 120.0 NaN 0.0250 NaN NaN 100.1708 NaN
+ 120.0 NaN 0.0250 NaN NaN 100.1708 NaN
+
diff --git a/vignettes/KinGUI/D_FOMC_report_detailed.txt b/vignettes/KinGUI/D_FOMC_report_detailed.txt new file mode 100644 index 0000000..a3ff6cc --- /dev/null +++ b/vignettes/KinGUI/D_FOMC_report_detailed.txt @@ -0,0 +1,97 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 3 0 3
+ Degrees of Freedom: 6 0 6
+
+ Parent Sink All
+
+ RMSE: 3.8927 NaN 3.8927
+ Chi2Sigma: 2.6871 NaN 2.6871
+ Chi2Err%: 6.7989 NaN 6.7989
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 15
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_alpha 11.4924 -23.1706 46.1555 16.2627 0.2453
+ Parent_beta 109.9914 -242.4545 462.4373 165.3550 0.2580
+ Parent_FFS 1.0000
+ Parent_M(0) 100.1262 95.6389 104.6136 2.1053
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 6.8381 NaN
+ DT90: 24.4003 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9920 NaN 0.9920
+ R-square: 0.9921 NaN 0.9921
+
+# Correlation matrix of parameters
+ Parent_alpha Parent_beta Parent_M
+ Parent_alpha 1.0000 0.9994 -0.4135
+ Parent_beta 0.9994 1.0000 -0.4306
+ Parent_M -0.4135 -0.4306 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 100.1262 -0.6662 NaN 0.0000 NaN
+ 0.0 102.0400 100.1262 1.9138 NaN 0.0000 NaN
+ 1.0 93.5000 90.2352 3.2648 NaN 9.8911 NaN
+ 1.0 92.5000 90.2352 2.2648 NaN 9.8911 NaN
+ 3.0 63.2300 73.4920 -10.2620 NaN 26.6343 NaN
+ 3.0 68.9900 73.4920 -4.5020 NaN 26.6343 NaN
+ 7.0 52.3200 49.2726 3.0474 NaN 50.8536 NaN
+ 7.0 55.1300 49.2726 5.8574 NaN 50.8536 NaN
+ 14.0 27.2700 25.2676 2.0024 NaN 74.8586 NaN
+ 14.0 26.6400 25.2676 1.3724 NaN 74.8586 NaN
+ 21.0 11.5000 13.4417 -1.9417 NaN 86.6845 NaN
+ 21.0 11.6400 13.4417 -1.8017 NaN 86.6845 NaN
+ 35.0 2.8500 4.1845 -1.3345 NaN 95.9417 NaN
+ 35.0 2.9100 4.1845 -1.2745 NaN 95.9417 NaN
+ 50.0 0.6900 1.3499 -0.6599 NaN 98.7764 NaN
+ 50.0 0.6300 1.3499 -0.7199 NaN 98.7764 NaN
+ 75.0 0.0500 0.2545 -0.2045 NaN 99.8718 NaN
+ 75.0 0.0600 0.2545 -0.1945 NaN 99.8718 NaN
+ 100.0 NaN 0.0593 NaN NaN 100.0670 NaN
+ 100.0 NaN 0.0593 NaN NaN 100.0670 NaN
+ 120.0 NaN 0.0208 NaN NaN 100.1054 NaN
+ 120.0 NaN 0.0208 NaN NaN 100.1054 NaN
+
diff --git a/vignettes/KinGUI/D_HS_report.txt b/vignettes/KinGUI/D_HS_report.txt new file mode 100644 index 0000000..92186cd --- /dev/null +++ b/vignettes/KinGUI/D_HS_report.txt @@ -0,0 +1,77 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 5.8196 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.1213 0.0130 1.1e-007
+ Parent_k2 0.0879 0.0083 2.2e-008
+ Parent_tb 3.0000 5.3734 0.2927
+ Parent_FFS 1.0000
+ Parent_M(0) 100.9303 1.9766
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 6.7461 NaN
+ DT90: 25.0545 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 100.9303 -1.4703 NaN 0.0000 NaN
+ 0.0 102.0400 100.9303 1.1097 NaN 0.0000 NaN
+ 1.0 93.5000 89.4028 4.0972 NaN 11.5275 NaN
+ 1.0 92.5000 89.4028 3.0972 NaN 11.5275 NaN
+ 3.0 63.2300 70.1471 -6.9171 NaN 30.7832 NaN
+ 3.0 68.9900 70.1471 -1.1571 NaN 30.7832 NaN
+ 7.0 52.3200 49.3513 2.9687 NaN 51.5789 NaN
+ 7.0 55.1300 49.3513 5.7787 NaN 51.5789 NaN
+ 14.0 27.2700 26.6720 0.5980 NaN 74.2583 NaN
+ 14.0 26.6400 26.6720 -0.0320 NaN 74.2583 NaN
+ 21.0 11.5000 14.4149 -2.9149 NaN 86.5154 NaN
+ 21.0 11.6400 14.4149 -2.7749 NaN 86.5154 NaN
+ 35.0 2.8500 4.2104 -1.3604 NaN 96.7199 NaN
+ 35.0 2.9100 4.2104 -1.3004 NaN 96.7199 NaN
+ 50.0 0.6900 1.1263 -0.4363 NaN 99.8040 NaN
+ 50.0 0.6300 1.1263 -0.4963 NaN 99.8040 NaN
+ 75.0 0.0500 0.1251 -0.0751 NaN 100.8052 NaN
+ 75.0 0.0600 0.1251 -0.0651 NaN 100.8052 NaN
+ 100.0 NaN 0.0139 NaN NaN 100.9164 NaN
+ 100.0 NaN 0.0139 NaN NaN 100.9164 NaN
+ 120.0 NaN 0.0024 NaN NaN 100.9279 NaN
+ 120.0 NaN 0.0024 NaN NaN 100.9279 NaN
+
diff --git a/vignettes/KinGUI/D_HS_report_detailed.txt b/vignettes/KinGUI/D_HS_report_detailed.txt new file mode 100644 index 0000000..6f9030e --- /dev/null +++ b/vignettes/KinGUI/D_HS_report_detailed.txt @@ -0,0 +1,100 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 4 0 4
+ Degrees of Freedom: 5 0 5
+
+ Parent Sink All
+
+ RMSE: 3.4039 NaN 3.4039
+ Chi2Sigma: 2.2876 NaN 2.2876
+ Chi2Err%: 5.7881 NaN 5.7881
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 14
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k1 0.1219 0.0502 0.1935 0.0334 0.0013
+ Parent_k2 0.0879 0.0757 0.1001 0.0057 1.7e-010
+ Parent_tb 2.9984 1.1617 4.8350 0.8563 0.0018
+ Parent_FFS 1.0000
+ Parent_M(0) 101.1066 96.3031 105.9101 2.2396
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 6.7257 NaN
+ DT90: 25.0308 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9945 NaN 0.9945
+ R-square: 0.9948 NaN 0.9948
+
+# Correlation matrix of parameters
+ Parent_k1 Parent_k2 Parent_tb Parent_M
+ Parent_k1 1.0000 0.0001 0.9101 0.6628
+ Parent_k2 0.0001 1.0000 0.1728 0.0000
+ Parent_tb 0.9101 0.1728 1.0000 0.4166
+ Parent_M 0.6628 0.0000 0.4166 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 101.1066 -1.6466 NaN 0.0000 NaN
+ 0.0 102.0400 101.1066 0.9334 NaN 0.0000 NaN
+ 1.0 93.5000 89.5056 3.9944 NaN 11.6010 NaN
+ 1.0 92.5000 89.5056 2.9944 NaN 11.6010 NaN
+ 3.0 63.2300 70.1481 -6.9181 NaN 30.9585 NaN
+ 3.0 68.9900 70.1481 -1.1581 NaN 30.9585 NaN
+ 7.0 52.3200 49.3489 2.9711 NaN 51.7577 NaN
+ 7.0 55.1300 49.3489 5.7811 NaN 51.7577 NaN
+ 14.0 27.2700 26.6677 0.6023 NaN 74.4389 NaN
+ 14.0 26.6400 26.6677 -0.0277 NaN 74.4389 NaN
+ 21.0 11.5000 14.4109 -2.9109 NaN 86.6956 NaN
+ 21.0 11.6400 14.4109 -2.7709 NaN 86.6956 NaN
+ 35.0 2.8500 4.2083 -1.3583 NaN 96.8983 NaN
+ 35.0 2.9100 4.2083 -1.2983 NaN 96.8983 NaN
+ 50.0 0.6900 1.1255 -0.4355 NaN 99.9811 NaN
+ 50.0 0.6300 1.1255 -0.4955 NaN 99.9811 NaN
+ 75.0 0.0500 0.1249 -0.0749 NaN 100.9816 NaN
+ 75.0 0.0600 0.1249 -0.0649 NaN 100.9816 NaN
+ 100.0 NaN 0.0139 NaN NaN 101.0927 NaN
+ 100.0 NaN 0.0139 NaN NaN 101.0927 NaN
+ 120.0 NaN 0.0024 NaN NaN 101.1042 NaN
+ 120.0 NaN 0.0024 NaN NaN 101.1042 NaN
+
diff --git a/vignettes/KinGUI/D_KinGUI.txt b/vignettes/KinGUI/D_KinGUI.txt new file mode 100644 index 0000000..f1c53e9 --- /dev/null +++ b/vignettes/KinGUI/D_KinGUI.txt @@ -0,0 +1,27 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent m1 +0 99.46 0 +0 102.04 0 +1 93.5 4.84 +1 92.5 5.64 +3 63.23 12.91 +3 68.99 12.96 +7 52.32 22.97 +7 55.13 24.47 +14 27.27 41.69 +14 26.64 33.21 +21 11.5 44.37 +21 11.64 46.44 +35 2.85 41.22 +35 2.91 37.95 +50 0.69 41.19 +50 0.63 40.01 +75 0.05 40.09 +75 0.06 33.85 +100 NaN 31.04 +100 NaN 33.13 +120 NaN 25.15 +120 NaN 33.31 diff --git a/vignettes/KinGUI/D_SFO_report.txt b/vignettes/KinGUI/D_SFO_report.txt new file mode 100644 index 0000000..902decf --- /dev/null +++ b/vignettes/KinGUI/D_SFO_report.txt @@ -0,0 +1,73 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 6.4539 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.0979 0.0048 3.8e-013
+ Parent_FFS 1.0000
+ Parent_M(0) 99.4443 1.8316
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 7.0776 NaN
+ DT90: 23.5111 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 99.4443 0.0157 NaN 0.0000 NaN
+ 0.0 102.0400 99.4443 2.5957 NaN 0.0000 NaN
+ 1.0 93.5000 90.1668 3.3332 NaN 9.2775 NaN
+ 1.0 92.5000 90.1668 2.3332 NaN 9.2775 NaN
+ 3.0 63.2300 74.1277 -10.8977 NaN 25.3165 NaN
+ 3.0 68.9900 74.1277 -5.1377 NaN 25.3165 NaN
+ 7.0 52.3200 50.1013 2.2187 NaN 49.3430 NaN
+ 7.0 55.1300 50.1013 5.0287 NaN 49.3430 NaN
+ 14.0 27.2700 25.2416 2.0284 NaN 74.2026 NaN
+ 14.0 26.6400 25.2416 1.3984 NaN 74.2026 NaN
+ 21.0 11.5000 12.7171 -1.2171 NaN 86.7272 NaN
+ 21.0 11.6400 12.7171 -1.0771 NaN 86.7272 NaN
+ 35.0 2.8500 3.2279 -0.3779 NaN 96.2163 NaN
+ 35.0 2.9100 3.2279 -0.3179 NaN 96.2163 NaN
+ 50.0 0.6900 0.7429 -0.0529 NaN 98.7014 NaN
+ 50.0 0.6300 0.7429 -0.1129 NaN 98.7014 NaN
+ 75.0 0.0500 0.0642 -0.0142 NaN 99.3801 NaN
+ 75.0 0.0600 0.0642 -0.0042 NaN 99.3801 NaN
+ 100.0 NaN 0.0055 NaN NaN 99.4387 NaN
+ 100.0 NaN 0.0055 NaN NaN 99.4387 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4435 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4435 NaN
+
diff --git a/vignettes/KinGUI/D_SFO_report_detailed.txt b/vignettes/KinGUI/D_SFO_report_detailed.txt new file mode 100644 index 0000000..24ace5f --- /dev/null +++ b/vignettes/KinGUI/D_SFO_report_detailed.txt @@ -0,0 +1,94 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\jranke\My Documents\R\mkin.BerliOS\R_packages\kinfit\trunk\inst\doc\KinGUI\D_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink All
+ Number of data sets: 9 0 9
+ Number of parameters: 2 0 2
+ Degrees of Freedom: 7 0 7
+
+ Parent Sink All
+
+ RMSE: 3.6160 NaN 3.6160
+ Chi2Sigma: 2.5508 NaN 2.5508
+ Chi2Err%: 6.4539 NaN 6.4539
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Degrees of Freedom: 16
+ Parameter Estimate Lower CI Upper CI St.Dev Prob > t
+ Parent_k 0.0979 0.0877 0.1082 0.0048 3.8e-013
+ Parent_FFS 1.0000
+ Parent_M(0) 99.4442 95.5614 103.3271 1.8316
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 7.0776 NaN
+ DT90: 23.5112 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Additional Statistics
+# ---------------------------------
+# Correlation and R-square of predicted vs. measured data
+ Parent Sink All
+ EF: 0.9919 NaN 0.9919
+ R-square: 0.9919 NaN 0.9919
+
+# Correlation matrix of parameters
+ Parent_k Parent_M
+ Parent_k 1.0000 0.5360
+ Parent_M 0.5360 1.0000
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 99.4600 99.4442 0.0158 NaN 0.0000 NaN
+ 0.0 102.0400 99.4442 2.5958 NaN 0.0000 NaN
+ 1.0 93.5000 90.1668 3.3332 NaN 9.2774 NaN
+ 1.0 92.5000 90.1668 2.3332 NaN 9.2774 NaN
+ 3.0 63.2300 74.1277 -10.8977 NaN 25.3165 NaN
+ 3.0 68.9900 74.1277 -5.1377 NaN 25.3165 NaN
+ 7.0 52.3200 50.1013 2.2187 NaN 49.3430 NaN
+ 7.0 55.1300 50.1013 5.0287 NaN 49.3430 NaN
+ 14.0 27.2700 25.2417 2.0283 NaN 74.2026 NaN
+ 14.0 26.6400 25.2417 1.3983 NaN 74.2026 NaN
+ 21.0 11.5000 12.7171 -1.2171 NaN 86.7272 NaN
+ 21.0 11.6400 12.7171 -1.0771 NaN 86.7272 NaN
+ 35.0 2.8500 3.2279 -0.3779 NaN 96.2163 NaN
+ 35.0 2.9100 3.2279 -0.3179 NaN 96.2163 NaN
+ 50.0 0.6900 0.7429 -0.0529 NaN 98.7013 NaN
+ 50.0 0.6300 0.7429 -0.1129 NaN 98.7013 NaN
+ 75.0 0.0500 0.0642 -0.0142 NaN 99.3800 NaN
+ 75.0 0.0600 0.0642 -0.0042 NaN 99.3800 NaN
+ 100.0 NaN 0.0055 NaN NaN 99.4387 NaN
+ 100.0 NaN 0.0055 NaN NaN 99.4387 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4435 NaN
+ 120.0 NaN 0.0008 NaN NaN 99.4435 NaN
+
diff --git a/vignettes/KinGUI/F_system_DFOP_report.txt b/vignettes/KinGUI/F_system_DFOP_report.txt new file mode 100644 index 0000000..9ec5931 --- /dev/null +++ b/vignettes/KinGUI/F_system_DFOP_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 14.1524 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0397 547.5131 0.5000
+ Parent_k2 0.0396 >1000.0000 0.5000
+ Parent_g 0.6827 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 103.7338 7.5788
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 17.4895 NaN
+ DT90: 58.0989 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 103.7338 -8.1338 NaN 0.0000 NaN
+ 3.0 91.9000 92.1051 -0.2051 NaN 11.6286 NaN
+ 7.0 86.5000 78.6024 7.8976 NaN 25.1314 NaN
+ 14.0 72.9000 59.5595 13.3405 NaN 44.1742 NaN
+ 28.0 29.6000 34.1966 -4.5966 NaN 69.5372 NaN
+ 43.0 10.0000 18.8713 -8.8713 NaN 84.8624 NaN
+ 56.0 6.8000 11.2732 -4.4732 NaN 92.4606 NaN
+ 70.0 3.5000 6.4726 -2.9726 NaN 97.2612 NaN
+ 100.0 4.2000 1.9711 2.2289 NaN 101.7626 NaN
+
diff --git a/vignettes/KinGUI/F_system_FOMC_report.txt b/vignettes/KinGUI/F_system_FOMC_report.txt new file mode 100644 index 0000000..9eb0651 --- /dev/null +++ b/vignettes/KinGUI/F_system_FOMC_report.txt @@ -0,0 +1,62 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 13.4533 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 53.4222 992.5119 0.4794
+ Parent_beta >1000.0000 >1000.0000 0.4797
+ Parent_FFS 1.0000
+ Parent_M(0) 104.6197 7.0437
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 17.2240 NaN
+ DT90: 58.0894 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 104.6197 -9.0197 NaN 0.0000 NaN
+ 3.0 91.9000 92.6616 -0.7616 NaN 11.9581 NaN
+ 7.0 86.5000 78.8498 7.6502 NaN 25.7699 NaN
+ 14.0 72.9000 59.5161 13.3839 NaN 45.1036 NaN
+ 28.0 29.6000 34.0577 -4.4577 NaN 70.5620 NaN
+ 43.0 10.0000 18.8478 -8.8478 NaN 85.7719 NaN
+ 56.0 6.8000 11.3461 -4.5461 NaN 93.2736 NaN
+ 70.0 3.5000 6.6038 -3.1038 NaN 98.0159 NaN
+ 100.0 4.2000 2.1086 2.0914 NaN 102.5111 NaN
+
diff --git a/vignettes/KinGUI/F_system_HS_report.txt b/vignettes/KinGUI/F_system_HS_report.txt new file mode 100644 index 0000000..81546c7 --- /dev/null +++ b/vignettes/KinGUI/F_system_HS_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 3.2178 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0142 0.0047 0.0151
+ Parent_k2 0.0635 0.0039 8.1e-006
+ Parent_tb 12.4685 1.3021 1.1e-004
+ Parent_FFS 1.0000
+ Parent_M(0) 95.6835 1.9092
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 20.5934 NaN
+ DT90: 45.9498 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 95.6835 -0.0835 NaN 0.0000 NaN
+ 3.0 91.9000 91.6844 0.2156 NaN 3.9991 NaN
+ 7.0 86.5000 86.6111 -0.1111 NaN 9.0724 NaN
+ 14.0 72.9000 72.7042 0.1958 NaN 22.9793 NaN
+ 28.0 29.6000 29.8977 -0.2977 NaN 65.7858 NaN
+ 43.0 10.0000 11.5385 -1.5385 NaN 84.1450 NaN
+ 56.0 6.8000 5.0559 1.7441 NaN 90.6277 NaN
+ 70.0 3.5000 2.0791 1.4209 NaN 93.6044 NaN
+ 100.0 4.2000 0.3097 3.8903 NaN 95.3738 NaN
+
diff --git a/vignettes/KinGUI/F_system_KinGUI.txt b/vignettes/KinGUI/F_system_KinGUI.txt new file mode 100644 index 0000000..92bd722 --- /dev/null +++ b/vignettes/KinGUI/F_system_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 95.6 +3 91.9 +7 86.5 +14 72.9 +28 29.6 +43 10 +56 6.8 +70 3.5 +100 4.2 diff --git a/vignettes/KinGUI/F_system_SFO_report.txt b/vignettes/KinGUI/F_system_SFO_report.txt new file mode 100644 index 0000000..7dffe34 --- /dev/null +++ b/vignettes/KinGUI/F_system_SFO_report.txt @@ -0,0 +1,60 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_system_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 12.5386 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.0400 0.0053 6.4e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 104.4774 5.6578
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 17.3489 NaN
+ DT90: 57.6318 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 104.4774 -8.8774 NaN 0.0000 NaN
+ 3.0 91.9000 92.6761 -0.7761 NaN 11.8013 NaN
+ 7.0 86.5000 78.9881 7.5119 NaN 25.4893 NaN
+ 14.0 72.9000 59.7174 13.1826 NaN 44.7600 NaN
+ 28.0 29.6000 34.1334 -4.5334 NaN 70.3440 NaN
+ 43.0 10.0000 18.7459 -8.7459 NaN 85.7315 NaN
+ 56.0 6.8000 11.1516 -4.3516 NaN 93.3258 NaN
+ 70.0 3.5000 6.3740 -2.8740 NaN 98.1034 NaN
+ 100.0 4.2000 1.9225 2.2775 NaN 102.5549 NaN
+
diff --git a/vignettes/KinGUI/F_water_DFOP_report.txt b/vignettes/KinGUI/F_water_DFOP_report.txt new file mode 100644 index 0000000..c8275d9 --- /dev/null +++ b/vignettes/KinGUI/F_water_DFOP_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_g: 0.5000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 12.1821 NaN
+ Kinetic Model: dfop sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0551 >1000.0000 0.5000
+ Parent_k2 0.0551 >1000.0000 0.5000
+ Parent_g 0.6959 >1000.0000 0.5000
+ Parent_FFS 1.0000
+ Parent_M(0) 100.5778 6.1529
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 12.5797 NaN
+ DT90: 41.7890 NaN
+ Kinetic model: dfop sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 100.5778 -4.9778 NaN 0.0000 NaN
+ 3.0 84.7000 85.2536 -0.5536 NaN 15.3242 NaN
+ 7.0 74.6000 68.3902 6.2098 NaN 32.1876 NaN
+ 14.0 54.1000 46.5035 7.5965 NaN 54.0742 NaN
+ 28.0 13.5000 21.5015 -8.0015 NaN 79.0762 NaN
+ 43.0 4.3000 9.4086 -5.1086 NaN 91.1692 NaN
+ 56.0 2.0000 4.5966 -2.5966 NaN 95.9812 NaN
+ 70.0 0.5000 2.1253 -1.6253 NaN 98.4525 NaN
+ 100.0 0.8000 0.4069 0.3931 NaN 100.1708 NaN
+
diff --git a/vignettes/KinGUI/F_water_FOMC_report.txt b/vignettes/KinGUI/F_water_FOMC_report.txt new file mode 100644 index 0000000..6604e72 --- /dev/null +++ b/vignettes/KinGUI/F_water_FOMC_report.txt @@ -0,0 +1,62 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_alpha: 1.0000 0.0000 Inf
+ Parent_beta: 10.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 11.6682 NaN
+ Kinetic Model: fomc sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_alpha 60.1183 907.7673 0.4747
+ Parent_beta >1000.0000 >1000.0000 0.4750
+ Parent_FFS 1.0000
+ Parent_M(0) 100.6891 5.3413
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 12.4948 NaN
+ DT90: 42.0685 NaN
+ Kinetic model: fomc sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 100.6891 -5.0891 NaN 0.0000 NaN
+ 3.0 84.7000 85.1898 -0.4898 NaN 15.4992 NaN
+ 7.0 74.6000 68.2194 6.3806 NaN 32.4696 NaN
+ 14.0 54.1000 46.3363 7.7637 NaN 54.3527 NaN
+ 28.0 13.5000 21.5356 -8.0356 NaN 79.1535 NaN
+ 43.0 4.3000 9.5778 -5.2778 NaN 91.1112 NaN
+ 56.0 2.0000 4.7873 -2.7873 NaN 95.9018 NaN
+ 70.0 0.5000 2.2886 -1.7886 NaN 98.4004 NaN
+ 100.0 0.8000 0.4850 0.3150 NaN 100.2041 NaN
+
diff --git a/vignettes/KinGUI/F_water_HS_report.txt b/vignettes/KinGUI/F_water_HS_report.txt new file mode 100644 index 0000000..3cda8e3 --- /dev/null +++ b/vignettes/KinGUI/F_water_HS_report.txt @@ -0,0 +1,64 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k1: 0.1000 0.0000 Inf
+ Parent_k2: 0.0100 0.0000 Inf
+ Parent_tb: 3.0000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 1.6558 NaN
+ Kinetic Model: hs sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k1 0.0356 0.0022 8.3e-006
+ Parent_k2 0.0955 0.0041 1.4e-006
+ Parent_tb 12.8509 0.6443 2.9e-006
+ Parent_FFS 1.0000
+ Parent_M(0) 95.1656 0.8209
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 15.3239 NaN
+ DT90: 32.1824 NaN
+ Kinetic model: hs sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 95.1656 0.4344 NaN 0.0000 NaN
+ 3.0 84.7000 85.5346 -0.8346 NaN 9.6310 NaN
+ 7.0 74.6000 74.1920 0.4080 NaN 20.9736 NaN
+ 14.0 54.1000 53.9934 0.1066 NaN 41.1723 NaN
+ 28.0 13.5000 14.1869 -0.6869 NaN 80.9788 NaN
+ 43.0 4.3000 3.3882 0.9118 NaN 91.7774 NaN
+ 56.0 2.0000 0.9794 1.0206 NaN 94.1862 NaN
+ 70.0 0.5000 0.2574 0.2426 NaN 94.9083 NaN
+ 100.0 0.8000 0.0147 0.7853 NaN 95.1510 NaN
+
diff --git a/vignettes/KinGUI/F_water_KinGUI.txt b/vignettes/KinGUI/F_water_KinGUI.txt new file mode 100644 index 0000000..ce3611d --- /dev/null +++ b/vignettes/KinGUI/F_water_KinGUI.txt @@ -0,0 +1,14 @@ +Version: 1.1 +Project: +Testsystem: +Comment: NA +t parent +0 95.6 +3 84.7 +7 74.6 +14 54.1 +28 13.5 +43 4.3 +56 2 +70 0.5 +100 0.8 diff --git a/vignettes/KinGUI/F_water_SFO_report.txt b/vignettes/KinGUI/F_water_SFO_report.txt new file mode 100644 index 0000000..9927133 --- /dev/null +++ b/vignettes/KinGUI/F_water_SFO_report.txt @@ -0,0 +1,60 @@ +Project:
+Testsystem:
+Comment: NA
+
+KinGUI Version: 1.1
+
+Input Data: C:\Documents and Settings\ws_rajo\My Documents\R\kinfit.package\kinfit\inst\doc\KinGUI\F_water_KinGUI.txt
+
+# =================================
+# Results of the kinetic evaluation
+# =================================
+
+# ---------------------------------
+# Initial values
+# ---------------------------------
+ Initial Value Lower Bound Upper Bound
+ Parent_M(0): 100.0000 0.0000 Inf
+ Parent_k: 0.1000 0.0000 Inf
+ Sink_M(0): 0.0000 0.0000 Inf
+
+# ---------------------------------
+# Chi2 error estimation
+# ---------------------------------
+ Parent Sink
+ Chi2Err%: 10.8069 NaN
+ Kinetic Model: sfo sink
+
+# ---------------------------------
+# Parameter estimation
+# ---------------------------------
+
+ Parameter Estimate St.Dev Prob > t
+ Parent_k 0.0551 0.0059 1.7e-005
+ Parent_FFS 1.0000
+ Parent_M(0) 100.5476 4.3549
+ Sink_M(0) 0.0000
+
+# ---------------------------------
+# DT50 and DT90 values
+# ---------------------------------
+ Parent Sink
+ DT50: 12.5846 NaN
+ DT90: 41.8052 NaN
+ Kinetic model: sfo sink
+
+# ---------------------------------
+# Measured vs. predicted values
+# ---------------------------------
+ Time Compartment Parent Compartment Sink
+ measured predicted residual measured predicted residual
+ 0.0 95.6000 100.5476 -4.9476 NaN 0.0000 NaN
+ 3.0 84.7000 85.2335 -0.5335 NaN 15.3141 NaN
+ 7.0 74.6000 68.3799 6.2201 NaN 32.1677 NaN
+ 14.0 54.1000 46.5035 7.5965 NaN 54.0441 NaN
+ 28.0 13.5000 21.5079 -8.0079 NaN 79.0397 NaN
+ 43.0 4.3000 9.4144 -5.1144 NaN 91.1332 NaN
+ 56.0 2.0000 4.6007 -2.6007 NaN 95.9469 NaN
+ 70.0 0.5000 2.1278 -1.6278 NaN 98.4198 NaN
+ 100.0 0.8000 0.4077 0.3923 NaN 100.1399 NaN
+
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+\usepackage{amsfonts}
+\usepackage{latexsym}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{graphicx}
+\usepackage{parskip}
+\usepackage[round]{natbib}
+\usepackage{amstext}
+\usepackage{hyperref}
+\usepackage[latin1]{inputenc}
+
+\newcommand{\Rpackage}[1]{{\normalfont\fontseries{b}\selectfont #1}}
+\newcommand{\Robject}[1]{\texttt{#1}}
+\newcommand{\Rclass}[1]{\textit{#1}}
+\newcommand{\Rcmd}[1]{\texttt{#1}}
+
+\newcommand{\RR}{\textsf{R}}
+
+\RequirePackage[T1]{fontenc}
+\RequirePackage{graphicx,ae,fancyvrb}
+\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
+\usepackage{relsize}
+
+\DefineVerbatimEnvironment{Sinput}{Verbatim}{baselinestretch=1.05}
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+ baselinestretch=1.05,
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+\DefineVerbatimEnvironment{Scode}{Verbatim}{}
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diff --git a/vignettes/kinfit.Rnw b/vignettes/kinfit.Rnw new file mode 100644 index 0000000..7907979 --- /dev/null +++ b/vignettes/kinfit.Rnw @@ -0,0 +1,1019 @@ +% $Id: kinfit.Rnw 125 2011-11-10 07:19:59Z jranke $
+%%\VignetteIndexEntry{Routines for fitting kinetic models to chemical degradation data}
+%%VignetteDepends{nls}
+%%\usepackage{Sweave}
+\documentclass[12pt,a4paper]{article}
+\usepackage{a4wide}
+%%\usepackage[lists,heads]{endfloat}
+\input{header}
+\hypersetup{
+ pdftitle = {kinfit - Routines for fitting kinetic models to chemical degradation data},
+ pdfsubject = {Manuscript},
+ pdfauthor = {Johannes Ranke},
+ colorlinks = {true},
+ linkcolor = {blue},
+ citecolor = {blue},
+ urlcolor = {red},
+ hyperindex = {true},
+ linktocpage = {true},
+}
+\SweaveOpts{engine=R, eps=FALSE, keep.source = TRUE}
+<<setup, echo = FALSE, results = hide>>=
+options(prompt = "R> ")
+options(SweaveHooks = list(
+ cex = function() par(cex.lab = 1.3, cex.axis = 1.3)))
+@
+\begin{document}
+\title{kinfit -\\
+Routines for fitting kinetic models to chemical degradation data}
+\author{\textbf{Johannes Ranke} \\[0.5cm]
+%EndAName
+Eurofins Regulatory AG\\
+Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm]
+and\\[0.5cm]
+University of Bremen\\
+}
+\maketitle
+
+\begin{abstract}
+In the regulatory evaluation of chemical substances like plant protection
+products (pesticides), biocides and other chemicals, degradation data play an
+important role. For the evaluation of pesticide degradation experiments,
+detailed guidance has been developed, based on nonlinear regression.
+The \RR{} add-on package \Rpackage{kinfit} implements fitting the models
+recommended in this guidance from within R and calculates the
+recommended statistical measures for data series within one compartment
+without metabolite data.
+\end{abstract}
+
+
+\thispagestyle{empty} \setcounter{page}{0}
+
+\clearpage
+
+\tableofcontents
+
+\textbf{Key words}: Kinetics, FOCUS, nonlinear fitting
+
+\section{Introduction}
+\label{intro}
+
+Many approaches are possible regarding the evaluation of chemical degradation
+data. The \Rpackage{kinfit} package \citep{pkg:kinfit} in \RR{}
+\citep{rcore2009} implements the approach recommended in the kinetics report
+provided by the FOrum for Co-ordination of pesticide fate models and their
+USe \citep{FOCUS2006} for simple data series for one parent compound in one
+compartment.
+
+\section{Example}
+\label{exam}
+
+In the following, requirements for data formatting are explained. Then the
+procedure for fitting the four kinetic models recommended by the FOCUS group
+to an example dataset given in the FOCUS kinetics report is illustrated.
+The explanations are kept rather verbose in order to lower the barrier for
+\RR{} newcomers.
+
+\subsection{Data format}
+
+The following listing shows example dataset C from the FOCUS kinetics
+report as distributed with the \Rpackage{kinfit} package
+
+<<FOCUS_2006_C_data, echo=TRUE, eval=TRUE>>=
+library("kinfit")
+data("FOCUS_2006_C", package = "kinfit")
+print(FOCUS_2006_C)
+@
+
+Note that the data needs to be in the format of a data frame containing
+a variable \Robject{t} containing sampling times and a variable
+\Robject{parent} containing the measured data. Replicate measurements are
+not recorded in extra columns but simply appended, leading to multiple
+occurrences of the sampling times \Robject{t}.
+
+Small to medium size dataset can be conveniently entered directly as \RR{} code
+as shown in the following listing
+
+<<data_format, echo=TRUE>>=
+kindata_example <- data.frame(
+ t = c(0, 1, 3, 7, 14, 28, 63, 91, 119),
+ parent = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)
+)
+@
+
+
+\subsection{Fitting the kinetic models}
+
+The user can choose for which kinetic models the \Robject{kinfit} function
+will try to find optimised parameters. This is achieved by the argument
+\Robject{kinmodels} to the function, as shown below. The models currently
+implemented are abbreviated \Robject{SFO} (Single First-Order), \Robject{FOMC}
+(First-Order Multi-Compartment), \Robject{DFOP} (Double First-Order in Parallel)
+and \Robject{HS} (Hockey-Stick) as defined by the \cite{FOCUS2006}. From the
+DFOP model, corresponding parameters in the notation of the SFORB model (Single
+First-Order Reversible Binding) are additionally calculated.
+
+<<FOCUS_2006_C_fits, echo=TRUE>>=
+kinfits.C <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP", "HS"))
+@
+
+The results of the fitting procedure are returned by the function, and can
+then be inspected by the function \Robject{kinresults}.
+
+<<FOCUS_2006_C_results, echo = TRUE>>=
+kinresults(kinfits.C)
+@
+
+The higher level functions \Robject{kinplot} and \Robject{kinreport}
+work on lists called \Robject{kinobject}. They contain the fitted models,
+optionally the data used for fitting the models, and the name of the parent
+compound as well as the test system type used for generating the data,
+as well as some more optional entries. The construction of such an
+object is shown below.
+
+<<FOCUS_2006_C_object, echo=TRUE>>=
+kinobject.C <- kinobject <- list(
+ parent = "Compound XY",
+ type = "Degradation in the environment",
+ system = "System 1",
+ source = "Synthetic example data from FOCUS kinetics",
+ data = FOCUS_2006_C,
+ fits = kinfits.C,
+ results = kinresults(kinfits.C))
+@
+
+The plotting and reporting functions then work on this object. The example
+below outputs the report to the console, because no \Robject{file} argument
+is specified. If a filename is specified, the report will be written to
+a text file.
+
+<<FOCUS_2006_C_report, echo = TRUE>>=
+kinreport(kinobject.C)
+@
+
+Plotting is done on an on-screen device. Graphics files in vector based
+formats can be obtained using the \RR{} devices \Robject{pdf}, \Robject{eps},
+or, subject to platform restrictions, \Robject{windows.metafile}.
+
+\setkeys{Gin}{width=0.6\textwidth}
+\begin{figure}[t]
+\begin{center}
+<<FOCUS_2006_C_figure, echo = FALSE, fig = TRUE, width = 7, height = 5, cex = TRUE>>=
+kinfits.C <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP", "HS"))
+kinplot(kinobject.C)
+title("FOCUS dataset C")
+@
+\caption{Fits of standard models to FOCUS dataset C.}
+\label{fig:FOCUS_2006_C}
+\end{center}
+\end{figure}
+
+A residual plot can be obtained with the function \Robject{kinresplot} as
+shown in Figure \ref{fig:FOCUS_2006_C_res}.
+
+\setkeys{Gin}{width=0.6\textwidth}
+\begin{figure}[t]
+\begin{center}
+<<FOCUS_2006_C_res, echo = FALSE, fig = TRUE, width = 7, height = 5, cex = TRUE>>=
+kinresplot(kinobject.C, "SFO")
+@
+\caption{Residual plot for fitting the SFO model to FOCUS dataset C.}
+\label{fig:FOCUS_2006_C_res}
+\end{center}
+\end{figure}
+
+\section{Validation}
+\label{vali}
+
+In the following comparisons, the results for fitting the four recommended
+kinetic models to FOCUS datasets A to F with \Rpackage{kinfit} were
+obtained.
+
+<<kinfits_A_to_F, echo = FALSE>>=
+datasets <- LETTERS[1:4]
+data(list=paste("FOCUS_2006_", datasets, sep=""), package = "kinfit")
+kinobjects <- list()
+for (dataset in datasets)
+{
+ kinobjects[[dataset]] <- list()
+ kinobjects[[dataset]]$data <- get(paste("FOCUS_2006_", dataset, sep=""))
+ kinobjects[[dataset]]$fits <-
+ kinfit(kinobjects[[dataset]]$data,
+ kinmodels = c("SFO", "FOMC", "DFOP", "HS"))
+ kinobjects[[dataset]]$results <-
+ kinresults(kinobjects[[dataset]]$fits)
+}
+
+data(FOCUS_2006_F, package = "kinfit")
+# Set the initial concentration in the sediment to zero
+FOCUS_2006_F[1, "parent.sediment"] <- 0
+# Calculate total system values for the parent compound
+FOCUS_2006_F = transform(FOCUS_2006_F,
+ parent.system = parent.water + parent.sediment)
+
+subsets <- c("system", "water")
+for (subset in subsets)
+{
+ index <- paste("F", subset, sep=" ")
+ kinobjects[[index]] <- list()
+ kinobjects[[index]]$data <- data.frame(
+ t = FOCUS_2006_F$t,
+ parent = FOCUS_2006_F[[paste("parent", subset, sep=".")]])
+ kinobjects[[index]]$fits <-
+ kinfit(kinobjects[[index]]$data,
+ kinmodels = c("SFO", "FOMC", "DFOP", "HS"))
+ kinobjects[[index]]$results <-
+ kinresults(kinobjects[[index]]$fits)
+}
+@
+
+\subsection{Single First Order Model}
+
+In Tables \ref{tab:vali.SFO.A} to \ref{tab:vali.SFO.F_water},
+the results from fitting the SFO model to FOCUS example datasets with
+various software packages as given in the report by the \cite{FOCUS2006} are
+compared with the results obtained with \Rpackage{kinfit}.
+
+<<SFO, echo = FALSE>>=
+data("FOCUS_2006_SFO_ref_A_to_F", package = "kinfit")
+kinmodel = "SFO"
+refs <- list()
+for (kinobjectname in names(kinobjects))
+{
+ ref <- subset(FOCUS_2006_SFO_ref_A_to_F, dataset == kinobjectname)
+ ref <- ref[-6]
+ texfile <- paste("FOCUS_2006_", kinmodel, "_",
+ gsub(" ", "_", kinobjectname), "_ref.tex", sep="")
+ write.table(format(ref, nsmall=2),
+ file = texfile,
+ sep=" & ", quote=FALSE,
+ row.names=FALSE, col.names=FALSE, eol = " \\\\ \n")
+ refs[[kinobjectname]] <- ref
+}
+@
+
+\begin{table}
+\caption{Results of fitting the SFO model to the example dataset A
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.A}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_A_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$A$M0), nsmall=2)} &
+\Sexpr{format(median(refs$A$k), nsmall=4)} &
+\Sexpr{format(median(refs$A$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$A$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects$A$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects$A$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{round(kinobjects$A$results$results[["SFO", "DT90"]], 2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the SFO model to the example dataset B
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.B}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_B_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$B$M0), nsmall=2)} &
+\Sexpr{format(median(refs$B$k), nsmall=4)} &
+\Sexpr{format(median(refs$B$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$B$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$B$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects$B$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects$B$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{round(kinobjects$B$results$results[["SFO", "DT90"]], 2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the SFO model to the example dataset C
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.C}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_C_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$C$M0), nsmall=2)} &
+\Sexpr{format(median(refs$C$k), nsmall=4)} &
+\Sexpr{format(median(refs$C$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$C$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$C$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects$C$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects$C$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{round(kinobjects$C$results$results[["SFO", "DT90"]], 2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the SFO model to the example dataset D
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.D}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_D_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$D$M0), nsmall=2)} &
+\Sexpr{format(median(refs$D$k), nsmall=4)} &
+\Sexpr{format(median(refs$D$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$D$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$D$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects$D$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects$D$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{round(kinobjects$D$results$results[["SFO", "DT90"]], 2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the SFO model to the total system data from
+example dataset F \citep{FOCUS2006}, as given in the report, in comparison to
+the results obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.F_system}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_F_system_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs[["F system"]]$M0), nsmall=2)} &
+\Sexpr{format(median(refs[["F system"]]$k), nsmall=4)} &
+\Sexpr{format(median(refs[["F system"]]$DT50), nsmall=2)} &
+\Sexpr{format(median(refs[["F system"]]$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects[["F system"]]$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects[["F system"]]$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects[["F system"]]$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{round(kinobjects[["F system"]]$results$results[["SFO", "DT90"]], 2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the SFO model to the water phase data from
+example dataset F \citep{FOCUS2006}, as given in the report, in comparison to
+the results obtained by \Rpackage{kinfit}. \label{tab:vali.SFO.F_water}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccc}
+\toprule
+Package & $M_0$ & $k$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_SFO_F_water_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs[["F water"]]$M0), nsmall=2)} &
+\Sexpr{format(median(refs[["F water"]]$k), nsmall=4)} &
+\Sexpr{format(median(refs[["F water"]]$DT50), nsmall=2)} &
+\Sexpr{format(median(refs[["F water"]]$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects[["F water"]]$results$parms$SFO$parent.0, 2)} &
+\Sexpr{round(kinobjects[["F water"]]$results$parms$SFO$k, 4)} &
+\Sexpr{round(kinobjects[["F water"]]$results$results[["SFO", "DT50"]], 2)} &
+\Sexpr{format(kinobjects[["F water"]]$results$results[["SFO", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+The comparisons show that all packages evaluated in the FOCUS report give
+very similar results for the SFO model. The results obtained with
+\Rpackage{kinfit} are very close to the median of the results reported for
+the other packages.
+
+\subsection{First Order Multi Compartment Model}
+
+<<FOMC, echo = FALSE>>=
+data("FOCUS_2006_FOMC_ref_A_to_F", package = "kinfit")
+kinmodel = "FOMC"
+refs <- list()
+for (kinobjectname in names(kinobjects)[c(1:3, 5:6)])
+{
+ ref <- subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == kinobjectname)
+ ref$package <- gsub("#", "$^a$", ref$package)
+ ref <- ref[-7]
+ texfile <- paste("FOCUS_2006_", kinmodel, "_",
+ gsub(" ", "_", kinobjectname), "_ref.tex", sep="")
+ write.table(format(ref, nsmall=2),
+ file = texfile,
+ sep=" & ", quote=FALSE,
+ row.names=FALSE, col.names=FALSE, eol = " \\\\ \n")
+ refs[[kinobjectname]] <- ref
+}
+@
+
+\begin{table}
+\caption{Results of fitting the FOMC model to the example dataset A
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.A}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lccccc}
+\toprule
+Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_FOMC_A_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$A$M0), nsmall=2)} &
+\Sexpr{format(median(refs$A$alpha), scientific=TRUE)} &
+\Sexpr{format(median(as.numeric(refs$A$beta)), nsmall=0)} &
+\Sexpr{format(median(refs$A$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+no fit \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the FOMC model to the example dataset B
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.B}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lccccc}
+\toprule
+Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_FOMC_B_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$B$M0), digits=4, nsmall=2)} &
+\Sexpr{format(median(refs$B$alpha), scientific=TRUE)} &
+\Sexpr{format(median(as.numeric(refs$B$beta)), nsmall=0)} &
+\Sexpr{format(median(refs$B$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$B$results$parms$FOMC$parent.0, 2)} &
+\Sexpr{round(kinobjects$B$results$parms$FOMC$alpha, 4)} &
+\Sexpr{round(kinobjects$B$results$parms$FOMC$beta, 4)} &
+\Sexpr{round(kinobjects$B$results$results[["FOMC", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$B$results$results[["FOMC", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+
+\begin{table}
+\caption{Results of fitting the FOMC model to the example dataset C
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.C}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lccccc}
+\toprule
+Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_FOMC_C_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$C$M0), nsmall=2)} &
+\Sexpr{format(median(refs$C$alpha), nsmall=2)} &
+\Sexpr{format(median(as.numeric(refs$C$beta)), nsmall=2)} &
+\Sexpr{format(median(refs$C$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$C$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$C$results$parms$FOMC$parent.0, 2)} &
+\Sexpr{round(kinobjects$C$results$parms$FOMC$alpha, 4)} &
+\Sexpr{round(kinobjects$C$results$parms$FOMC$beta, 4)} &
+\Sexpr{round(kinobjects$C$results$results[["FOMC", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$C$results$results[["FOMC", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the FOMC model to the total system data from
+example dataset F \citep{FOCUS2006}, as given in the report, in comparison to
+the results obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.F_system}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lccccc}
+\toprule
+Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_FOMC_F_system_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs[["F system"]]$M0), nsmall=2)} &
+\Sexpr{format(median(refs[["F system"]]$alpha), nsmall=4)} &
+\Sexpr{format(median(refs[["F system"]]$beta), nsmall=4)} &
+\Sexpr{format(median(refs[["F system"]]$DT50), nsmall=2)} &
+\Sexpr{format(median(refs[["F system"]]$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+no fit \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the FOMC model to the water phase data from
+example dataset F \citep{FOCUS2006}, as given in the report, in comparison to
+the results obtained by \Rpackage{kinfit}. \label{tab:vali.FOMC.F_water}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lccccc}
+\toprule
+Package & $M_0$ & $\alpha$ & $\beta$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_FOMC_F_water_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs[["F water"]]$M0), nsmall=2)} &
+\Sexpr{format(median(refs[["F water"]]$alpha), nsmall=4)} &
+\Sexpr{format(median(refs[["F water"]]$beta), nsmall=4)} &
+\Sexpr{format(median(refs[["F water"]]$DT50), nsmall=2)} &
+\Sexpr{format(median(refs[["F water"]]$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+no fit \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+The comparison of the results obtained for the FOMC model show much more
+variability between software packages. For dataset A, results for the
+\Robject{alpha} and \Robject{beta} parameters differ over several
+orders of magnitude between the different packages. The method used
+by the \Robject{kinfit} routine does not converge for this dataset.
+The same applies to the total system and water phase only data for
+example dataset F and the FOMC model.
+
+For datasets B and C, the \Rpackage{kinfit} function produces results
+which are very close to the median of the results obtained by the
+other packages.
+
+\subsection{Dual First Order in Parallel Model}
+
+<<DFOP, echo = FALSE>>=
+data("FOCUS_2006_DFOP_ref_A_to_B", package = "kinfit")
+kinmodel = "DFOP"
+refs <- list()
+for (kinobjectname in names(kinobjects)[1:2])
+{
+ ref <- subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == kinobjectname)
+ ref <- ref[-8]
+ texfile <- paste("FOCUS_2006_", kinmodel, "_",
+ gsub(" ", "_", kinobjectname), "_ref.tex", sep="")
+ write.table(format(ref, nsmall=2),
+ file = texfile,
+ sep=" & ", quote=FALSE,
+ row.names=FALSE, col.names=FALSE, eol = " \\\\ \n")
+ refs[[kinobjectname]] <- ref
+}
+@
+
+\begin{table}
+\caption{Results of fitting the DFOP model to the example dataset A
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.DFOP.A}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccccc}
+\toprule
+Package & $M_0$ & $f$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_DFOP_A_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$A$M0), nsmall=2)} &
+\Sexpr{format(median(refs$A$f), nsmall=2)} &
+\Sexpr{format(median(refs$A$k1), nsmall=4)} &
+\Sexpr{format(median(refs$A$k2), nsmall=4)} &
+\Sexpr{format(median(refs$A$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$A$DT90), nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+no fit \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the DFOP model to the example dataset B
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.DFOP.B}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccccc}
+\toprule
+Package & $M_0$ & $f$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_DFOP_B_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$B$M0), nsmall=2)} &
+\Sexpr{format(median(refs$B$f), nsmall=2)} &
+\Sexpr{format(median(refs$B$k1), nsmall=4)} &
+\Sexpr{format(median(refs$B$k2), nsmall=4)} &
+\Sexpr{format(median(refs$B$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$B$results$parms$DFOP$parent.0, 2)} &
+\Sexpr{round(kinobjects$B$results$parms$DFOP$g, 2)} &
+\Sexpr{round(kinobjects$B$results$parms$DFOP$k1, 4)} &
+\Sexpr{round(kinobjects$B$results$parms$DFOP$k2, 4)} &
+\Sexpr{round(kinobjects$B$results$results[["DFOP", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$B$results$results[["DFOP", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+Regarding fitting the DFOP model to FOCUS example dataset A, it is already
+indicated in the report that it is not a good example dataset for fitting
+this particular model, as the two kinetic constants postulated by the DFOP
+model are hardly distinguishable. As a consequence, the software packages
+strongly disagree especially on the model parameter $f$ specifying the
+distribution between the kinetic domains that are characterised by the
+two kinetic constants. Again, the \Rpackage{kinfit} routine does not
+show convergence for this model and this dataset (Table \ref{tab:vali.DFOP.A}).
+
+Fitting the DFOP model with \Rpackage{kinfit} to dataset B yields results
+that are very close to the median of the results obtained by other packages,
+as illustrated in Table \ref{tab:vali.DFOP.B}.
+
+\subsection{Hockey Stick Model}
+
+Analysis of dataset A shows basically two different parameter sets
+generated by the 8 packages reported in the FOCUS report \citep{FOCUS2006}.
+The \Rpackage{kinfit} package does not show conversion with the standard
+paramater defaults, but can reproduce the two parameter sets when given
+the respective paramter values as starting values, as shown in the last
+two lines in Table \ref{tab:vali.HS.A}.
+
+<<HS, echo = FALSE>>=
+data("FOCUS_2006_HS_ref_A_to_F", package = "kinfit")
+kinmodel = "HS"
+refs <- list()
+for (kinobjectname in names(kinobjects)[c(1:3, 5:6)])
+{
+ ref <- subset(FOCUS_2006_HS_ref_A_to_F, dataset == kinobjectname)
+ ref$package <- gsub("\\*", "$^a$", ref$package)
+ ref <- ref[-8]
+ texfile <- paste("FOCUS_2006_", kinmodel, "_",
+ gsub(" ", "_", kinobjectname), "_ref.tex", sep="")
+ write.table(format(ref, nsmall=2),
+ file = texfile,
+ sep=" & ", quote=FALSE,
+ row.names=FALSE, col.names=FALSE, eol = " \\\\ \n")
+ refs[[kinobjectname]] <- ref
+}
+@
+
+<<HS2, echo = FALSE>>=
+kinobjects$A$fits.2 <- kinfit(kinobjects$A$data,
+ kinmodels = c("HS"),
+ start.HS = list(parent.0 = 100, tb = 5, k1 = 0.017, k2 = 0.05))
+kinobjects$A$results.2 <- kinresults(kinobjects$A$fits.2)
+
+kinobjects$A$fits.3 <- kinfit(kinobjects$A$data,
+ kinmodels = c("HS"),
+ start.HS = list(parent.0 = 100, tb = 11, k1 = 0.017, k2 = 0.05))
+kinobjects$A$results.3 <- kinresults(kinobjects$A$fits.3)
+@
+
+\begin{table}
+\caption{Results of fitting the HS model to the example dataset A
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.HS.A}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccccc}
+\toprule
+Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_HS_A_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$A$M0), nsmall=2)} &
+\Sexpr{format(median(refs$A$tb), nsmall=2)} &
+\Sexpr{format(median(refs$A$k1), nsmall=4)} &
+\Sexpr{format(median(refs$A$k2), nsmall=4)} &
+\Sexpr{format(median(refs$A$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$A$DT90), digits=4, nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} & no fit \\
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$A$results.2$parms$HS$parent.0, 2)} &
+\Sexpr{round(kinobjects$A$results.2$parms$HS$tb, 2)} &
+\Sexpr{round(kinobjects$A$results.2$parms$HS$k1, 4)} &
+\Sexpr{round(kinobjects$A$results.2$parms$HS$k2, 4)} &
+\Sexpr{round(kinobjects$A$results.2$results[["HS", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$A$results.2$results[["HS", "DT90"]], digits=4, nsmall=2)} \\
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$A$results.3$parms$HS$parent.0, 2)} &
+\Sexpr{round(kinobjects$A$results.3$parms$HS$tb, 2)} &
+\Sexpr{round(kinobjects$A$results.3$parms$HS$k1, 4)} &
+\Sexpr{round(kinobjects$A$results.3$parms$HS$k2, 4)} &
+\Sexpr{round(kinobjects$A$results.3$results[["HS", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$A$results.3$results[["HS", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the HS model to the example dataset B
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.HS.B}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccccc}
+\toprule
+Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_HS_B_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$B$M0), nsmall=2)} &
+\Sexpr{format(median(refs$B$tb), nsmall=2)} &
+\Sexpr{format(median(refs$B$k1), nsmall=4)} &
+\Sexpr{format(median(refs$B$k2), nsmall=4)} &
+\Sexpr{format(median(refs$B$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$B$DT90), digits=4, nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} & no fit \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+\begin{table}
+\caption{Results of fitting the HS model to the example dataset C
+\citep{FOCUS2006}, as given in the report, in comparison to the results
+obtained by \Rpackage{kinfit}. \label{tab:vali.HS.C}}
+\begin{center}
+\vspace{0.5cm}
+\begin{tabular}{lcccccc}
+\toprule
+Package & $M_0$ & $t_b$ & $k_1$ & $k_2$ & DT$_{50}$ & DT$_{90}$ \\
+\midrule
+\input{FOCUS_2006_HS_C_ref}
+\midrule
+Median &
+\Sexpr{format(median(refs$C$M0), nsmall=2)} &
+\Sexpr{format(median(refs$C$tb), nsmall=2)} &
+\Sexpr{format(median(refs$C$k1), nsmall=4)} &
+\Sexpr{format(median(as.numeric(refs$C$k2)), nsmall=4)} &
+\Sexpr{format(median(refs$C$DT50), nsmall=2)} &
+\Sexpr{format(median(refs$C$DT90), digits=4, nsmall=2)} \\
+\midrule
+\Rpackage{kinfit} &
+\Sexpr{round(kinobjects$C$results$parms$HS$parent.0, 2)} &
+\Sexpr{round(kinobjects$C$results$parms$HS$tb, 2)} &
+\Sexpr{round(kinobjects$C$results$parms$HS$k1, 4)} &
+\Sexpr{round(kinobjects$C$results$parms$HS$k2, 4)} &
+\Sexpr{round(kinobjects$C$results$results[["HS", "DT50"]], 2)} &
+\Sexpr{format(kinobjects$C$results$results[["HS", "DT90"]], digits=4, nsmall=2)} \\
+\bottomrule
+\end{tabular}
+\end{center}
+\end{table}
+
+The HS fit did not converge for dataset B with \Rpackage{kinfit}. Again, this
+should be viewed in the light of the vastly differing results produced by
+the other software packages as listed in Table \ref{tab:vali.HS.B}.
+
+The results from fitting the HS model to dataset C with \Rpackage{kinfit}
+agree nicely with the median of the results obtained with the other packages,
+as shown in Table \ref{tab:vali.HS.C}.
+
+\subsection{$\chi^2$ statistics}
+
+As no values for the minimum error rate that has to be assumed for the
+model to agree with the data ($\chi^2$ statistics) are reported for
+the FOCUS datasets A to F, the respective values calculated by
+\Rpackage{kinfit} are compared to the $\chi^2$ values calculated by
+the KinGUI package \citep{schaefer2007} as shown in Table
+\ref{tab:vali.chi2}.
+
+For this, the possibility to write KinGUI input files using the function
+\Robject{kinwrite.KinGUI} from \Rpackage{kinfit} was used.
+
+<<KinGUI_write, echo=FALSE>>=
+chi2.SFO.kinfit <- chi2.FOMC.kinfit <- array(dim = length(kinobjects),
+ dimnames = list(names(kinobjects)))
+chi2.DFOP.kinfit <- chi2.HS.kinfit <- array(dim = length(kinobjects),
+ dimnames = list(names(kinobjects)))
+for (kinobjectname in names(kinobjects))
+{
+ outname <- paste("KinGUI/", gsub(" ", "_", kinobjectname), "_KinGUI.txt",
+ sep="")
+ kinwrite.KinGUI(kinobjects[[kinobjectname]], outname)
+ chi2.SFO.kinfit[[kinobjectname]] <-
+ kinobjects[[kinobjectname]]$results$stats[["SFO", "err.min"]]
+ chi2.FOMC.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$FOMC) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["FOMC", "err.min"]])
+ chi2.DFOP.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$DFOP) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["DFOP", "err.min"]])
+ chi2.HS.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$HS) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["HS", "err.min"]])
+}
+
+chi2.SFO.KinGUI <- c(8.3852, 4.4562, 15.8456, 6.4539, 12.5386, 10.8069)
+chi2.FOMC.KinGUI <- c(9.3116, 4.6641, 6.6574, 6.8080, 13.4533, 11.6682)
+chi2.DFOP.KinGUI <- c(9.6600, 4.9562, 2.6613, 7.2751, 14.1524, 12.1821)
+chi2.HS.KinGUI <- c(4.1106, 4.4535, 4.6963, 5.8196, 3.2178, 1.6558)
+names(chi2.SFO.KinGUI) <- names(chi2.FOMC.KinGUI) <- names(kinobjects)
+names(chi2.DFOP.KinGUI) <- names(chi2.HS.KinGUI) <- names(kinobjects)
+
+chi2 <- data.frame(
+ SFO.KinGUI = chi2.SFO.KinGUI,
+ SFO.kinfit = round(100 * chi2.SFO.kinfit, 4),
+ FOMC.KinGUI = chi2.FOMC.KinGUI,
+ FOMC.kinfit = round(100 * chi2.FOMC.kinfit, 4),
+ DFOP.KinGUI = chi2.DFOP.KinGUI,
+ DFOP.kinfit = round(100 * chi2.DFOP.kinfit, 4),
+ HS.KinGUI = chi2.HS.KinGUI,
+ HS.kinfit = round(100 * chi2.HS.kinfit, 4)
+)
+write.table(chi2,
+ file = "chi2_comparison.tex",
+ sep=" & ", quote=FALSE, na="",
+ row.names=TRUE, col.names=FALSE, eol = " \\\\ \n")
+@
+
+\begin{table}
+\caption{Comparison of $\chi^2$ error levels in percent calculated for model
+fits by the KinGUI and \Rpackage{kinfit} packages. \label{tab:vali.chi2}}
+\vspace{0.5cm}
+\begin{tabular}{lcccccccc}
+\toprule
+ & \multicolumn{2}{c}{SFO} &
+\multicolumn{2}{c}{FOMC} &
+\multicolumn{2}{c}{DFOP} &
+\multicolumn{2}{c}{HS} \\
+Dataset & KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} &
+KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} \\
+\midrule
+\input{chi2_comparison}
+\bottomrule
+\end{tabular}
+\end{table}
+
+The comparison shows that whenever a minimum error level $\chi^2$ was
+calculated using the \Rpackage{kinfit} package, it was very close to
+the value generated by KinGUI.
+
+\subsection{$R^2$ value}
+
+In a similar manner, the coefficient of determination calculated by kinfit
+according to the formula
+
+\begin{equation}
+R^2 = 1 - RSS / TSS
+\end{equation}
+
+where RSS is the sum of squares of the residuals and TSS is the sum of squares
+of the deviations from the mean value is compared to the model efficiency EF
+calculated by KinGUI based on the same formula (FOCUS 2006, p. 99) as shown
+in Table \ref{tab:vali.R2}. This exercise was done for FOCUS datasets A to D
+only.
+
+<<KinGUI_write, echo=FALSE>>=
+R2.SFO.kinfit <- R2.FOMC.kinfit <- array(dim = 4,
+ dimnames = list(names(kinobjects[1:4])))
+R2.DFOP.kinfit <- R2.HS.kinfit <- array(dim = 4,
+ dimnames = list(names(kinobjects[1:4])))
+for (kinobjectname in names(kinobjects[1:4]))
+{
+ R2.SFO.kinfit[[kinobjectname]] <-
+ kinobjects[[kinobjectname]]$results$stats[["SFO", "R2"]]
+ R2.FOMC.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$FOMC) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["FOMC", "R2"]])
+ R2.DFOP.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$DFOP) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["DFOP", "R2"]])
+ R2.HS.kinfit[[kinobjectname]] <-
+ ifelse(class(kinobjects[[kinobjectname]]$fits$HS) == "try-error",
+ NA, kinobjects[[kinobjectname]]$results$stats[["HS", "R2"]])
+}
+
+EF.SFO.KinGUI <- c(0.9845, 0.9971, 0.9714, 0.9919)
+EF.FOMC.KinGUI <- c(0.9831, 0.9973, 0.9955, 0.9920)
+EF.HS.KinGUI <- c(0.9972, 0.9972, 0.9980, 0.9945)
+EF.DFOP.KinGUI <- c(0.9845, 0.9973, 0.9994, 0.9919)
+names(EF.SFO.KinGUI) <- names(EF.FOMC.KinGUI) <- names(kinobjects[1:4])
+names(EF.DFOP.KinGUI) <- names(EF.HS.KinGUI) <- names(kinobjects[1:4])
+
+R2 <- data.frame(
+ SFO.KinGUI = EF.SFO.KinGUI,
+ SFO.kinfit = round(R2.SFO.kinfit, 4),
+ FOMC.KinGUI = EF.FOMC.KinGUI,
+ FOMC.kinfit = round(R2.FOMC.kinfit, 4),
+ DFOP.KinGUI = EF.DFOP.KinGUI,
+ DFOP.kinfit = round(R2.DFOP.kinfit, 4),
+ HS.KinGUI = EF.HS.KinGUI,
+ HS.kinfit = round(R2.HS.kinfit, 4)
+)
+write.table(R2,
+ file = "R2_comparison.tex",
+ sep=" & ", quote=FALSE, na="",
+ row.names=TRUE, col.names=FALSE, eol = " \\\\ \n")
+@
+
+\begin{table}
+\caption{Comparison of model efficiency (EF) values calculated
+by KinGUI and $R^2$ values calculated by \Rpackage{kinfit}. \label{tab:vali.R2}}
+\vspace{0.5cm}
+\begin{tabular}{lcccccccc}
+\toprule
+ & \multicolumn{2}{c}{SFO} &
+\multicolumn{2}{c}{FOMC} &
+\multicolumn{2}{c}{DFOP} &
+\multicolumn{2}{c}{HS} \\
+Dataset & KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} &
+KinGUI & \Rpackage{kinfit} & KinGUI & \Rpackage{kinfit} \\
+\midrule
+\input{R2_comparison}
+\bottomrule
+\end{tabular}
+\end{table}
+
+The comparison shows that whenever the comparison was possible, the $R^2$
+value calculated by the \Rpackage{kinfit} package was equal to the model
+efficiency calculated by KinGUI, both rounded to four digits.
+
+\section{Conclusion}
+
+The \Rpackage{kinfit} package for \RR{} gives access to the possibility to
+fit the kinetic models recommended by the FOCUS group \citep{FOCUS2006}
+from within \RR. Comparison with the results obtained with other
+software packages shows that \Rpackage{kinfit} produces kinetic endpoints that
+are within the variability and even very close to the median of results obtained
+with other packages, except for some cases where \Rpackage{kinfit} does not
+produce results and the results obtained with other software packages are
+strongly divergent.
+
+\section{Acknowledgements}
+
+This package would not have been written without me being introduced to regulatory
+fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd
+(formerly RCC Ltd). Parts of the package were written during my employment at Harlan.
+
+\bibliographystyle{plainnat}
+\bibliography{references}
+
+\end{document}
+% vim: set foldmethod=marker:
diff --git a/vignettes/kinfit.pdf b/vignettes/kinfit.pdf Binary files differnew file mode 100644 index 0000000..1128f91 --- /dev/null +++ b/vignettes/kinfit.pdf diff --git a/vignettes/references.bib b/vignettes/references.bib new file mode 100644 index 0000000..8cde4bd --- /dev/null +++ b/vignettes/references.bib @@ -0,0 +1,38 @@ +@Manual{pkg:kinfit,
+ title = {kinfit: {R}outines for fitting kinetic models to chemical degradation data},
+ author = {kinfit},
+ year = {2009},
+ note = {R package version 1.0-0},
+ url = {http://CRAN.R-project.org}
+}
+
+@Manual{ rcore2009,
+ title = {\textsf{R}: A Language and Environment for Statistical
+ Computing},
+ author = {{R Development Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = 2009,
+ note = {{ISBN} 3-900051-07-0},
+ url = {http://www.R-project.org}
+}
+
+@Manual{ FOCUS2006,
+ title = {Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration. Report of the FOCUS Work Group on Degradation Kinetics},
+ note = {EC Document Reference Sanco/10058/2005 version 2.0},
+ author = {{FOCUS Work Group on Degradation Kinetics}},
+ year = {2006},
+ url = {http://focus.jrc.ec.europa.eu/dk}
+}
+
+@Inproceedings{ schaefer2007,
+ title = {{KinGUI}: a new kinetic software tool for evaluations according to {FOCUS} degradation kinetics},
+ author = {D. Sch\"{a}fer and M. Mikolasch and P. Rainbird and B. Harvey},
+ booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry},
+ editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.},
+ year = {2007},
+ address = {Piacenza},
+ pages = {916--923}
+}
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