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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-24 02:18:59 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-24 02:18:59 +0200
commit60270e2849ebd48eaf57b83eb1aa9fbe53281f8b (patch)
tree644904ea42e6d35d6e43bb88733619b25347fcbb /man
parent6ad4e443b662e8c61b1b350d3e639e821a8ff764 (diff)
Fix a bug for nlme with parent only, improve examples
Diffstat (limited to 'man')
-rw-r--r--man/nlme.mmkin.Rd37
1 files changed, 8 insertions, 29 deletions
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 08ce1ad8..87d84c74 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -83,6 +83,7 @@ f_nlme_sfo <- nlme(f["SFO", ])
f_nlme_dfop <- nlme(f["DFOP", ])
AIC(f_nlme_sfo, f_nlme_dfop)
print(f_nlme_dfop)
+plot(f_nlme_dfop)
endpoints(f_nlme_dfop)
\dontrun{
f_nlme_2 <- nlme(f["SFO", ], start = c(parent_0 = 100, log_k_parent = 0.1))
@@ -93,58 +94,36 @@ endpoints(f_nlme_dfop)
A1 = mkinsub("SFO"), use_of_ff = "min", quiet = TRUE)
m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),
A1 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE)
- m_fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
- A1 = mkinsub("SFO"), quiet = TRUE)
m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
A1 = mkinsub("SFO"), quiet = TRUE)
f_2 <- mmkin(list("SFO-SFO" = m_sfo_sfo,
"SFO-SFO-ff" = m_sfo_sfo_ff,
- "FOMC-SFO" = m_fomc_sfo,
"DFOP-SFO" = m_dfop_sfo),
ds_2, quiet = TRUE)
- plot(f_2["SFO-SFO", 3:4]) # Separate fits for datasets 3 and 4
f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ])
- # plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures
- plot(f_nlme_sfo_sfo, 3:4) # Global mixed model: Fits for datasets 3 and 4
+ plot(f_nlme_sfo_sfo)
# With formation fractions
f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])
- plot(f_nlme_sfo_sfo_ff, 3:4) # chi2 different due to different df attribution
+ plot(f_nlme_sfo_sfo_ff)
- # For more parameters, we need to increase pnlsMaxIter and the tolerance
+ # For the following fit we need to increase pnlsMaxIter and the tolerance
# to get convergence
- f_nlme_fomc_sfo <- nlme(f_2["FOMC-SFO", ],
- control = list(pnlsMaxIter = 100, tolerance = 1e-4), verbose = TRUE)
f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],
control = list(pnlsMaxIter = 120, tolerance = 5e-4), verbose = TRUE)
- plot(f_2["FOMC-SFO", 3:4])
- plot(f_nlme_fomc_sfo, 3:4)
- plot(f_2["DFOP-SFO", 3:4])
- plot(f_nlme_dfop_sfo, 3:4)
+ plot(f_nlme_dfop_sfo)
- anova(f_nlme_dfop_sfo, f_nlme_fomc_sfo, f_nlme_sfo_sfo)
- anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC
+ anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo)
endpoints(f_nlme_sfo_sfo)
endpoints(f_nlme_dfop_sfo)
if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available
- # Attempts to fit metabolite kinetics with the tc error model
- #f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo,
- # "SFO-SFO-ff" = m_sfo_sfo_ff,
- # "FOMC-SFO" = m_fomc_sfo,
- # "DFOP-SFO" = m_dfop_sfo),
- # ds_2, quiet = TRUE,
- # error_model = "tc")
- #f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ], control = list(maxIter = 100))
- #f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ])
- #f_nlme_dfop_sfo_tc <- update(f_nlme_dfop_sfo, weights = varConstProp(),
- # control = list(sigma = 1, msMaxIter = 100, pnlsMaxIter = 15))
- # Fitting metabolite kinetics with nlme.mmkin and the two-component
- # error model currently does not work, at least not with these data.
+ # Attempts to fit metabolite kinetics with the tc error model are possible,
+ # but need tweeking of control values and sometimes do not converge
f_tc <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc")
f_nlme_sfo_tc <- nlme(f_tc["SFO", ])

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