From 4411ea3b88d815232eac3a3c87f7636a0bbf80f1 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Mon, 23 Apr 2012 23:34:57 +0000
Subject: - Fixed the example in the mkinmod documentation - Fixed the vignette
- Did not fix the unit tests for mkinmod yet
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@31 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
TODO | 9 ++++++---
man/mkinpredict.Rd | 16 +++++++++++-----
vignettes/mkin.Rnw | 10 ++++------
3 files changed, 21 insertions(+), 14 deletions(-)
diff --git a/TODO b/TODO
index 13bc6fce..a49957d2 100644
--- a/TODO
+++ b/TODO
@@ -1,9 +1,12 @@
-- Fix transformation and backtransformation of formation fractions
-- Fix problems with the schaefer complex test data (test.R)
+Must have:
+- Fix remaining problem with the schaefer complex test data (test.R)
+- Fix parent only SFORB model (see vignette)
+- Fix unit tests for mkinmod
- Adapt mkinplot function
+
+Nice to have:
- Calculate confidence intervals for parameters assuming normal distribution
- Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved
-- Fix DT50 and DT90 calculation for SFORB_SFO
- Add unit tests for mkinfit
- Document validation against fits documented in chapter 13 of FOCUS (2006)
- Reproduce example anaylses (L1, L2, ...) in FOCUS (2006)
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index af37f7ce..aaa77e6e 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -54,10 +54,16 @@ mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_
}
\examples{
SFO <- mkinmod(degradinol = list(type = "SFO"))
- mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")
- mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "eigen")
- mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20)
- mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20, method = "rk4")
- mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), (1:200)/10)
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical")
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "eigen")
+
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")[20,]
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20)[20,]
+ # The integration method does not make a lot of difference
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "bdf")[20,]
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "rk4")[20,]
+ # The number of output times does make a lot of difference
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.1))[201,]
+ mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.01))[2001,]
}
\keyword{ manip }
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index 1eebd44a..ee472ba5 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -147,14 +147,12 @@ on the fundamental system of the coefficient matrix, as proposed by
<<model_fitting, echo=TRUE>>=
SFO.fit <- mkinfit(SFO, FOCUS_2006_C)
summary(SFO.fit)
-SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)
-summary(SFORB.fit)
+#SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)
+#summary(SFORB.fit)
SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE)
summary(SFO_SFO.fit, data=FALSE)
-#SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D,
-# parms.ini = c(f_parent_to_m1 = 0.5, k_m1 = 0.2),
-# plot=TRUE)
-#summary(SFORB_SFO.fit, data=FALSE)
+SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE)
+summary(SFORB_SFO.fit, data=FALSE)
@
\bibliographystyle{plainnat}
--
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