- Update the TODO list, setting some requirements for version 1.0

- Check that initial values specified using parms.ini are actually needed for the model, stop otherwise
- List all formation fractions in the same place in the summary, also if they were fitted in the model
- Include an FOMC model coupled to two metabolites in the unit tests
- Some updates needed because of the above
- Update of static documentation including the vignettes
- Update of the mkin vignettes in the vignettes directory



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

4 files changed, 5 insertions, 5 deletions

diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw
index fa35c8f..4897f7c 100644
--- a/vignettes/examples.Rnw
+++ b/vignettes/examples.Rnw
@@ -433,7 +433,7 @@ Z.mkin.1 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
                 Z2 = list(type = "SFO", to = "Z3"),

                 Z3 = list(type = "SFORB"))

 m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, 

-                  parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.3, k_Z2_Z3 = 0.2), 

+                  parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.3),

                   quiet = TRUE)

 plot(m.Z.mkin.1)

 summary(m.Z.mkin.1, data = FALSE)

@@ -498,8 +498,8 @@ summary(m.Z.mkin.5, data = FALSE)
 @

 

 Looking at the confidence intervals of the SFORB model parameters of Z3, it is

-clear that nothing can be said about a degradation rate of Z3. However, this

-appears to be a feature of the data.

+clear that nothing can be said about the degradation rate of Z3 towards the end 

+of the experiment. However, this appears to be a feature of the data.

 

 <<FOCUS_2006_Z_residuals_11, fig=TRUE>>=

 par(mfrow = c(2, 2))

diff --git a/vignettes/examples.pdf b/vignettes/examples.pdf
index 8d32159..bd01239 100644
--- a/vignettes/examples.pdf
+++ b/vignettes/examples.pdf
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index 2f79cc5..22c9c15 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -149,9 +149,9 @@ SFO.fit <- mkinfit(SFO, FOCUS_2006_C)
 summary(SFO.fit)

 SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)

 summary(SFORB.fit)

-SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE)

+SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D)

 summary(SFO_SFO.fit, data=FALSE)

-SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE)

+SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D)

 summary(SFORB_SFO.fit, data=FALSE)

 @

 

diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 212feed..3eebf14 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf