nlme.mmkin {mkin} | R Documentation |
Create an nlme model for an mmkin row object
Description
This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets.
Usage
## S3 method for class 'mmkin'
nlme(
model,
data = "auto",
fixed = lapply(as.list(names(mean_degparms(model))), function(el) eval(parse(text =
paste(el, 1, sep = "~")))),
random = pdDiag(fixed),
groups,
start = mean_degparms(model, random = TRUE, test_log_parms = TRUE),
correlation = NULL,
weights = NULL,
subset,
method = c("ML", "REML"),
na.action = na.fail,
naPattern,
control = list(),
verbose = FALSE
)
## S3 method for class 'nlme.mmkin'
print(x, digits = max(3, getOption("digits") - 3), ...)
## S3 method for class 'nlme.mmkin'
update(object, ...)
Arguments
model |
An mmkin row object. |
data |
Ignored, data are taken from the mmkin model |
fixed |
Ignored, all degradation parameters fitted in the mmkin model are used as fixed parameters |
random |
If not specified, no correlations between random effects are set up for the optimised degradation model parameters. This is achieved by using the nlme::pdDiag method. |
groups |
See the documentation of nlme |
start |
If not specified, mean values of the fitted degradation parameters taken from the mmkin object are used |
correlation |
See the documentation of nlme |
weights |
passed to nlme |
subset |
passed to nlme |
method |
passed to nlme |
na.action |
passed to nlme |
naPattern |
passed to nlme |
control |
passed to nlme |
verbose |
passed to nlme |
x |
An nlme.mmkin object to print |
digits |
Number of digits to use for printing |
... |
Update specifications passed to update.nlme |
object |
An nlme.mmkin object to update |
Details
Note that the convergence of the nlme algorithms depends on the quality of the data. In degradation kinetics, we often only have few datasets (e.g. data for few soils) and complicated degradation models, which may make it impossible to obtain convergence with nlme.
Value
Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.
Note
As the object inherits from nlme::nlme, there is a wealth of
methods that will automatically work on 'nlme.mmkin' objects, such as
nlme::intervals()
, nlme::anova.lme()
and nlme::coef.lme()
.
See Also
nlme_function()
, plot.mixed.mmkin, summary.nlme.mmkin
Examples
ds <- lapply(experimental_data_for_UBA_2019[6:10],
function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
## Not run:
f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
library(nlme)
f_nlme_sfo <- nlme(f["SFO", ])
f_nlme_dfop <- nlme(f["DFOP", ])
anova(f_nlme_sfo, f_nlme_dfop)
print(f_nlme_dfop)
plot(f_nlme_dfop)
endpoints(f_nlme_dfop)
ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
function(x) x$data[c("name", "time", "value")])
m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
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_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,
"DFOP-SFO" = m_dfop_sfo),
ds_2, quiet = TRUE)
f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ])
plot(f_nlme_sfo_sfo)
# With formation fractions this does not coverge with defaults
# f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])
#plot(f_nlme_sfo_sfo_ff)
# For the following, we need to increase pnlsMaxIter and the tolerance
# to get convergence
f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],
control = list(pnlsMaxIter = 120, tolerance = 5e-4))
plot(f_nlme_dfop_sfo)
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 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", ])
f_nlme_dfop_tc <- nlme(f_tc["DFOP", ])
AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc)
print(f_nlme_dfop_tc)
}
f_2_obs <- update(f_2, error_model = "obs")
f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ])
print(f_nlme_sfo_sfo_obs)
f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ],
control = list(pnlsMaxIter = 120, tolerance = 5e-4))
f_2_tc <- update(f_2, error_model = "tc")
# f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations
# f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],
# control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm
anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs)
## End(Not run)