Reorder endpoints in R/endpoints.R, update vignettes

18 files changed, 3 insertions, 3 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 0bd20ea7..a5bebd71 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -6,11 +6,11 @@ endpoints <- function(fit) {
   ep <- list()

   obs_vars <- fit$obs_vars

   parms.all <- fit$bparms.ode

+  ep$ff <- vector()

+  ep$SFORB <- vector()

   ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), 

 			    DT90 = rep(NA, length(obs_vars)), 

     row.names = obs_vars)

-  ep$ff <- vector()

-  ep$SFORB <- vector()

   for (obs_var in obs_vars) {

     type = names(fit$mkinmod$map[[obs_var]])[1]  

 

diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw
index 62d8729a..40ddfc44 100644
--- a/vignettes/FOCUS_Z.Rnw
+++ b/vignettes/FOCUS_Z.Rnw
@@ -293,7 +293,7 @@ endpoints(m.Z.mkin.5a)
 @
 
 It is clear the degradation rate of Z3 towards the end of the experiment 
-is very low as DT50\_b2 is reported to be infinity.  However, this appears to
+is very low as DT50\_Z3\_b2 is reported to be infinity.  However, this appears to
 be a feature of the data.
 
 <<FOCUS_2006_Z_residuals_11>>=
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index fd1a7cbb..aaa9ce08 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
index 87c42ff5..f38f1f62 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
index 4f4637a4..103f1266 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
index eb3a072f..d4cc8d13 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
index a2a72611..5d3ec2ec 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
index 7ebffab7..d3d7db03 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
index 7ebffab7..7c05df7e 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
index 9a819630..b088005e 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
index 4bbdc189..d51b7298 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
index 3ebd4afa..798fef27 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
index a104dbd2..467b01c5 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
index e646e1ce..fb99e90d 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
index a4f17063..4e092313 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
index 610d10ca..7d9699a9 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
index 3303dac3..1eb94e65 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 13078c45..8aa2795c 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf