diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2014-11-12 18:15:43 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2014-11-12 18:15:43 +0100 |
| commit | ff128891aa5075e7ff1b65e5aa107dc2f49aa074 (patch) | |
| tree | 669b043ecd62771193837a3518bf901fe869570f | |
| parent | fa1c2009f7c7efc1e61e4e882ca0b0fc6ef27c31 (diff) | |
Update the FOCUS_Z vignette for default "Port" algorithm
| -rw-r--r-- | vignettes/FOCUS_Z.Rnw | 15 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 398825 -> 220799 bytes |
2 files changed, 4 insertions, 11 deletions
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw index e2a2473e..5e2e0251 100644 --- a/vignettes/FOCUS_Z.Rnw +++ b/vignettes/FOCUS_Z.Rnw @@ -144,7 +144,6 @@ Z.FOCUS <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE), Z2 = list(type = "SFO", to = "Z3"), Z3 = list(type = "SFO")) m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, - parms.ini = m.Z.5$bparms.ode, quiet = TRUE) plot(m.Z.FOCUS) summary(m.Z.FOCUS, data = FALSE) @@ -192,9 +191,7 @@ Z.mkin.1 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE), Z1 = list(type = "SFO", to = "Z2", sink = FALSE), Z2 = list(type = "SFO", to = "Z3"), Z3 = list(type = "SFORB")) -m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, - parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.3), - quiet = TRUE) +m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) plot(m.Z.mkin.1) summary(m.Z.mkin.1, data = FALSE) @ @@ -235,7 +232,6 @@ Z.mkin.4 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE), Z2 = list(type = "SFO", to = "Z3"), Z3 = list(type = "SFO")) m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, - parms.ini = c(k_Z1_Z2 = 0.05), quiet = TRUE) plot(m.Z.mkin.4) summary(m.Z.mkin.4, data = FALSE) @@ -250,22 +246,19 @@ Z.mkin.5 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE), Z1 = list(type = "SFO", to = "Z2", sink = FALSE), Z2 = list(type = "SFO", to = "Z3"), Z3 = list(type = "SFORB")) -m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, - parms.ini = m.Z.mkin.4$bparms.ode[1:5], - quiet = TRUE) +m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot(m.Z.mkin.5) summary(m.Z.mkin.5, data = FALSE)$bpar @ The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized -\texttt{k\_Z3\_bound\_free} is excessively small, it is reasonable to fix it to +\texttt{k\_Z3\_bound\_free} is excessively small, it seems reasonable to fix it to zero. <<FOCUS_2006_Z_fits_11a, echo=TRUE>>= m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, - parms.ini = c(m.Z.mkin.4$bparms.ode[1:5], - k_Z3_bound_free = 0), + parms.ini = c(k_Z3_bound_free = 0), fixed_parms = "k_Z3_bound_free", quiet = TRUE) summary(m.Z.mkin.5a, data = FALSE)$bpar diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex a22a3a2e..f215f306 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf |