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authorJohannes Ranke <jranke@uni-bremen.de>2014-11-12 18:15:43 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2014-11-12 18:15:43 +0100
commitff128891aa5075e7ff1b65e5aa107dc2f49aa074 (patch)
tree669b043ecd62771193837a3518bf901fe869570f /vignettes
parentfa1c2009f7c7efc1e61e4e882ca0b0fc6ef27c31 (diff)
Update the FOCUS_Z vignette for default "Port" algorithm
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_Z.Rnw15
-rw-r--r--vignettes/FOCUS_Z.pdfbin398825 -> 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
index a22a3a2e..f215f306 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ

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