From 60270e2849ebd48eaf57b83eb1aa9fbe53281f8b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 24 Oct 2020 02:18:59 +0200 Subject: Fix a bug for nlme with parent only, improve examples --- man/nlme.mmkin.Rd | 37 ++++++++----------------------------- 1 file changed, 8 insertions(+), 29 deletions(-) (limited to 'man') 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", ]) -- cgit v1.2.1