diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/aw.Rd | 47 | ||||
| -rw-r--r-- | man/loftest.Rd | 81 | ||||
| -rw-r--r-- | man/lrtest.mkinfit.Rd | 6 | ||||
| -rw-r--r-- | man/plot.mmkin.Rd | 4 | ||||
| -rw-r--r-- | man/sigma_twocomp.Rd | 2 |
5 files changed, 137 insertions, 3 deletions
diff --git a/man/aw.Rd b/man/aw.Rd new file mode 100644 index 00000000..40676716 --- /dev/null +++ b/man/aw.Rd @@ -0,0 +1,47 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/aw.R +\name{aw} +\alias{aw} +\alias{aw.mkinfit} +\alias{aw.mmkin} +\title{Calculate Akaike weights for model averaging} +\usage{ +aw(object, ...) + +\method{aw}{mkinfit}(object, ...) + +\method{aw}{mmkin}(object, ...) +} +\arguments{ +\item{object}{An \link{mmkin} column object, containing two or more +\link{mkinfit} models that have been fitted to the same data, +or an mkinfit object. In the latter case, further mkinfit +objects fitted to the same data should be specified +as dots arguments.} + +\item{\dots}{Not used in the method for \link{mmkin} column objects, +further \link{mkinfit} objects in the method for mkinfit objects.} +} +\description{ +Akaike weights are calculated based on the relative +expected Kullback-Leibler information as specified +by Burnham and Anderson (2004). +} +\examples{ +\dontrun{ +f_sfo <- mkinfit("SFO", FOCUS_2006_D, quiet = TRUE) +f_dfop <- mkinfit("DFOP", FOCUS_2006_D, quiet = TRUE) +aw_sfo_dfop <- aw(f_sfo, f_dfop) +sum(aw_sfo_dfop) +aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit +f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS D" = FOCUS_2006_D), cores = 1, quiet = TRUE) +aw(f) +sum(aw(f)) +aw(f[c("SFO", "DFOP")]) +} +} +\references{ +Burnham KP and Anderson DR (2004) Multimodel +Inference: Understanding AIC and BIC in Model Selection. +\emph{Sociological Methods & Research} \strong{33}(2) 261-304 +} diff --git a/man/loftest.Rd b/man/loftest.Rd new file mode 100644 index 00000000..397b5c08 --- /dev/null +++ b/man/loftest.Rd @@ -0,0 +1,81 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/loftest.R +\name{loftest} +\alias{loftest} +\alias{loftest.mkinfit} +\title{Lack-of-fit test for models fitted to data with replicates} +\usage{ +loftest(object, ...) + +\method{loftest}{mkinfit}(object, ...) +} +\arguments{ +\item{object}{A model object with a defined loftest method} + +\item{\dots}{Not used} +} +\description{ +This is a generic function with a method currently only defined for mkinfit +objects. It fits an anova model to the data contained in the object and +compares the likelihoods using the likelihood ratio test +\code{\link[lmtest]{lrtest.default}} from the lmtest package. +} +\details{ +The anova model is interpreted as the simplest form of an mkinfit model, +assuming only a constant variance about the means, but not enforcing any +structure of the means, so we have one model parameter for every mean +of replicate samples. +} +\examples{ +\dontrun{ +test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent") +sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE) +plot_res(sfo_fit) # We see a clear pattern in the residuals +loftest(sfo_fit) # We have a clear lack of fit +# +# We try a different model (the one that was used to generate the data) +dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE) +plot_res(dfop_fit) # We don't see systematic deviations, but heteroscedastic residuals +# therefore we should consider adapting the error model, although we have +loftest(dfop_fit) # no lack of fit +# +# This is the anova model used internally for the comparison +test_data_anova <- test_data +test_data_anova$time <- as.factor(test_data_anova$time) +anova_fit <- lm(value ~ time, data = test_data_anova) +summary(anova_fit) +logLik(anova_fit) # We get the same likelihood and degrees of freedom +# +test_data_2 <- synthetic_data_for_UBA_2014[[12]]$data +m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") +sfo_lin_fit <- mkinfit(m_synth_SFO_lin, test_data_2, quiet = TRUE) +plot_res(sfo_lin_fit) # not a good model, we try parallel formation +loftest(sfo_lin_fit) +# +m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2")), + M1 = list(type = "SFO"), + M2 = list(type = "SFO"), use_of_ff = "max") +sfo_par_fit <- mkinfit(m_synth_SFO_par, test_data_2, quiet = TRUE) +plot_res(sfo_par_fit) # much better for metabolites +loftest(sfo_par_fit) +# +m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")), + M1 = list(type = "SFO"), + M2 = list(type = "SFO"), use_of_ff = "max") +dfop_par_fit <- mkinfit(m_synth_DFOP_par, test_data_2, quiet = TRUE) +plot_res(dfop_par_fit) # No visual lack of fit +loftest(dfop_par_fit) # no lack of fit found by the test +# +# The anova model used for comparison in the case of transformation products +test_data_anova_2 <- dfop_par_fit$data +test_data_anova_2$variable <- as.factor(test_data_anova_2$variable) +test_data_anova_2$time <- as.factor(test_data_anova_2$time) +anova_fit_2 <- lm(observed ~ time:variable - 1, data = test_data_anova_2) +summary(anova_fit_2) +} +} +\seealso{ +lrtest +} diff --git a/man/lrtest.mkinfit.Rd b/man/lrtest.mkinfit.Rd index bc8ab4dc..84d7bc99 100644 --- a/man/lrtest.mkinfit.Rd +++ b/man/lrtest.mkinfit.Rd @@ -2,12 +2,16 @@ % Please edit documentation in R/lrtest.mkinfit.R \name{lrtest.mkinfit} \alias{lrtest.mkinfit} +\alias{lrtest.mmkin} \title{Likelihood ratio test for mkinfit models} \usage{ \method{lrtest}{mkinfit}(object, object_2 = NULL, ...) + +\method{lrtest}{mmkin}(object, ...) } \arguments{ -\item{object}{An \code{\link{mkinfit}} object} +\item{object}{An \code{\link{mkinfit}} object, or an \code{\link{mmkin}} column +object containing two fits to the same data.} \item{object_2}{Optionally, another mkinfit object fitted to the same data.} diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 333998da..605e458e 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -8,7 +8,7 @@ of an mmkin object} \method{plot}{mmkin}(x, main = "auto", legends = 1, resplot = c("time", "errmod"), show_errmin = TRUE, errmin_var = "All data", errmin_digits = 3, cex = 0.7, - rel.height.middle = 0.9, ...) + rel.height.middle = 0.9, ymax = "auto", ...) } \arguments{ \item{x}{An object of class \code{\link{mmkin}}, with either one row or one @@ -36,6 +36,8 @@ chi2 error percentage.} \item{rel.height.middle}{The relative height of the middle plot, if more than two rows of plots are shown.} +\item{ymax}{Maximum y axis value for \code{\link{plot.mkinfit}}.} + \item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}.} } diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd index 3e7854f1..0004144f 100644 --- a/man/sigma_twocomp.Rd +++ b/man/sigma_twocomp.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/sigma_twocomp.R \name{sigma_twocomp} \alias{sigma_twocomp} -\title{Two component error model} +\title{Two-component error model} \usage{ sigma_twocomp(y, sigma_low, rsd_high) } |