diff options
| -rw-r--r-- | TODO | 9 | ||||
| -rw-r--r-- | man/mkinpredict.Rd | 16 | ||||
| -rw-r--r-- | vignettes/mkin.Rnw | 10 |
3 files changed, 21 insertions, 14 deletions
@@ -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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