From 20b9c584e7c43ecbb708459e531c24a1a4751e17 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 9 Nov 2019 01:05:51 +0100 Subject: Add a lack-of-fit test - Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat --- NAMESPACE | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index 8ea4c684..f428a612 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ S3method("[",mmkin) S3method(AIC,mmkin) S3method(BIC,mmkin) S3method(confint,mkinfit) +S3method(loftest,mkinfit) S3method(logLik,mkinfit) S3method(lrtest,mkinfit) S3method(mkinpredict,mkinfit) @@ -32,6 +33,7 @@ export(backtransform_odeparms) export(endpoints) export(ilr) export(invilr) +export(loftest) export(logistic.solution) export(lrtest) export(max_twa_dfop) @@ -73,8 +75,11 @@ importFrom(parallel,parLapply) importFrom(stats,AIC) importFrom(stats,BIC) importFrom(stats,aggregate) +importFrom(stats,coef) importFrom(stats,cov2cor) importFrom(stats,dist) +importFrom(stats,dnorm) +importFrom(stats,lm) importFrom(stats,logLik) importFrom(stats,nlminb) importFrom(stats,nobs) -- cgit v1.2.3 From f6385b071cee2c261da28bf98fd1599da1a30ddb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 13 Nov 2019 11:05:39 +0100 Subject: Likelihood ratio test for mmkin columns with two fits --- NAMESPACE | 1 + R/lrtest.mkinfit.R | 5 ++--- docs/reference/index.html | 2 +- docs/reference/lrtest.mkinfit.html | 8 ++++++-- man/lrtest.mkinfit.Rd | 6 +++++- 5 files changed, 15 insertions(+), 7 deletions(-) (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index f428a612..e561621b 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,6 +7,7 @@ S3method(confint,mkinfit) S3method(loftest,mkinfit) S3method(logLik,mkinfit) S3method(lrtest,mkinfit) +S3method(lrtest,mmkin) S3method(mkinpredict,mkinfit) S3method(mkinpredict,mkinmod) S3method(nobs,mkinfit) diff --git a/R/lrtest.mkinfit.R b/R/lrtest.mkinfit.R index 380cf3a5..0054ea88 100644 --- a/R/lrtest.mkinfit.R +++ b/R/lrtest.mkinfit.R @@ -18,10 +18,9 @@ lmtest::lrtest #' parameters (alternative hypothesis) is listed first, then the model with the #' lower number of fitted parameters (null hypothesis). #' -#' The method for mmkin objects only works for column objects with two members. -#' #' @importFrom stats logLik update -#' @param object An \code{\link{mkinfit}} object +#' @param object An \code{\link{mkinfit}} object, or an \code{\link{mmkin}} column +#' object containing two fits to the same data. #' @param object_2 Optionally, another mkinfit object fitted to the same data. #' @param \dots Argument to \code{\link{mkinfit}}, passed to #' \code{\link{update.mkinfit}} for creating the alternative fitted object. diff --git a/docs/reference/index.html b/docs/reference/index.html index 0947ff94..4398469b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -209,7 +209,7 @@ more datasets

-

lrtest(<mkinfit>)

+

lrtest(<mkinfit>) lrtest(<mmkin>)

Likelihood ratio test for mkinfit models

diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 1d82eb74..70157db9 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -145,14 +145,18 @@ and can be expressed by fixing the parameters of the other.

# S3 method for mkinfit
-lrtest(object, object_2 = NULL, ...)
+lrtest(object, object_2 = NULL, ...) + +# S3 method for mmkin +lrtest(object, ...)

Arguments

- + 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.} -- cgit v1.2.3 From c3700bec3a704660d3ade7a54c56b7084beb02b4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 13 Nov 2019 21:15:35 +0100 Subject: Calculate Akaike weights --- NAMESPACE | 3 + NEWS.md | 2 + R/aw.R | 60 +++++++++++ _pkgdown.yml | 1 + docs/news/index.html | 1 + docs/reference/aw.html | 214 ++++++++++++++++++++++++++++++++++++++++ docs/reference/index.html | 6 ++ docs/sitemap.xml | 3 + man/aw.Rd | 47 +++++++++ test.log | 21 ++-- tests/testthat/FOCUS_2006_D.csf | 2 +- tests/testthat/test_aw.R | 12 +++ 12 files changed, 361 insertions(+), 11 deletions(-) create mode 100644 R/aw.R create mode 100644 docs/reference/aw.html create mode 100644 man/aw.Rd create mode 100644 tests/testthat/test_aw.R (limited to 'NAMESPACE') diff --git a/NAMESPACE b/NAMESPACE index e561621b..26995055 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,6 +3,8 @@ S3method("[",mmkin) S3method(AIC,mmkin) S3method(BIC,mmkin) +S3method(aw,mkinfit) +S3method(aw,mmkin) S3method(confint,mkinfit) S3method(loftest,mkinfit) S3method(logLik,mkinfit) @@ -30,6 +32,7 @@ export(IORE.solution) export(SFO.solution) export(SFORB.solution) export(add_err) +export(aw) export(backtransform_odeparms) export(endpoints) export(ilr) diff --git a/NEWS.md b/NEWS.md index 965105f4..28cf76ad 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # mkin 0.9.49.8 (unreleased) +- 'aw': Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns + - 'loftest': Add a lack-of-fit test - 'plot_res', 'plot_sep' and 'mkinerrplot': Add the possibility to show standardized residuals and make it the default for fits with error models other than 'const' diff --git a/R/aw.R b/R/aw.R new file mode 100644 index 00000000..24078f38 --- /dev/null +++ b/R/aw.R @@ -0,0 +1,60 @@ +#' Calculate Akaike weights for model averaging +#' +#' Akaike weights are calculated based on the relative +#' expected Kullback-Leibler information as specified +#' by Burnham and Anderson (2004). +#' +#' @param object An mmkin column object, containing two or more +#' \code{\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. +#' @param \dots Not used in the method for mmkin column objects, +#' further mkinfit objects in the method for mkinfit objects. +#' @references Burnham KP and Anderson DR (2004) Multimodel +#' Inference: Understanding AIC and BIC in Model Selection +#' Sociological Methods & Research 33(2) 261-304 +#' @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")]) +#' } +#' @export +aw <- function(object, ...) UseMethod("aw") + +#' @export +#' @rdname aw +aw.mkinfit <- function(object, ...) { + oo <- list(...) + data_object <- object$data[c("time", "variable", "observed")] + for (i in seq_along(oo)) { + if (!inherits(oo[[i]], "mkinfit")) stop("Please supply only mkinfit objects") + data_other_object <- oo[[i]]$data[c("time", "variable", "observed")] + if (!identical(data_object, data_other_object)) { + stop("It seems that the mkinfit objects have not all been fitted to the same data") + } + } + all_objects <- list(object, ...) + AIC_all <- sapply(all_objects, AIC) + delta_i <- AIC_all - min(AIC_all) + denom <- sum(exp(-delta_i/2)) + w_i <- exp(-delta_i/2) / denom + return(w_i) +} + +#' @export +#' @rdname aw +aw.mmkin <- function(object, ...) { + if (ncol(object) > 1) stop("Please supply an mmkin column object") + do.call(aw, object) +} + + + diff --git a/_pkgdown.yml b/_pkgdown.yml index c298256f..6bb05b3e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -25,6 +25,7 @@ reference: - loftest - mkinerrmin - endpoints + - aw - CAKE_export - title: Work with mmkin objects desc: Functions working with aggregated results diff --git a/docs/news/index.html b/docs/news/index.html index 9aa2e18b..6b0b89fa 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,6 +134,7 @@ mkin 0.9.49.8 (unreleased) Unreleased
object

An mkinfit object

An mkinfit object, or an mmkin column +object containing two fits to the same data.
object_2
+ + + + + + + + + +
object

An mmkin column object, containing two or more +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.

...

Not used in the method for mmkin column objects, +further mkinfit objects in the method for mkinfit objects.

+ +

References

+ +

Burnham KP and Anderson DR (2004) Multimodel + Inference: Understanding AIC and BIC in Model Selection + Sociological Methods & Research 33(2) 261-304

+ +

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)
#> [1] 1
aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit
#> [1] 0.5970258 0.4029742
f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS D" = FOCUS_2006_D), cores = 1, quiet = TRUE)
+aw(f)
#> [1] 0.4808722 0.1945539 0.3245740
sum(aw(f))
#> [1] 1
aw(f[c("SFO", "DFOP")])
#> [1] 0.5970258 0.4029742
# }
+
+ + + + + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+ + + + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 4398469b..3d417267 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -233,6 +233,12 @@ more datasets

with mkinfit

+ +

aw()

+ +

Calculate Akaike weights for model averaging

+ +

CAKE_export()

diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 66b776b2..a8d6dfa4 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -54,6 +54,9 @@ https://pkgdown.jrwb.de/mkin/reference/add_err.html + + https://pkgdown.jrwb.de/mkin/reference/aw.html + https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html diff --git a/man/aw.Rd b/man/aw.Rd new file mode 100644 index 00000000..f0994b94 --- /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 mmkin column object, containing two or more +\code{\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 mmkin column objects, +further 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 + Sociological Methods & Research 33(2) 261-304 +} diff --git a/test.log b/test.log index bc6d26ae..c51d06b8 100644 --- a/test.log +++ b/test.log @@ -1,11 +1,12 @@ Loading mkin Testing mkin ✔ | OK F W S | Context +✔ | 5 | Calculation of Akaike weights ✔ | 2 | Export dataset for reading into CAKE -✔ | 10 | Confidence intervals and p-values [10.1 s] -✔ | 14 | Error model fitting [40.5 s] +✔ | 10 | Confidence intervals and p-values [9.7 s] +✔ | 14 | Error model fitting [36.9 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s] -✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.4 s] +✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.7 s] ✔ | 1 | Fitting the logistic model [0.9 s] ✔ | 1 | Test dataset class mkinds used in gmkin @@ -18,20 +19,20 @@ Testing mkin ✔ | 11 | Plotting [0.6 s] ✔ | 4 | AIC calculation ✔ | 2 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s] -✔ | 4 | Fitting the SFORB model [1.8 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] +✔ | 4 | Fitting the SFORB model [1.7 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.5 s] -✔ | 7 1 | Hypothesis tests [34.1 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s] +✔ | 7 1 | Hypothesis tests [32.3 s] ──────────────────────────────────────────────────────────────────────────────── -test_tests.R:59: skip: We can do a likelihood ratio test using an update specification +test_tests.R:60: skip: We can do a likelihood ratio test using an update specification Reason: This errors out if called by testthat while it works in a normal R session ──────────────────────────────────────────────────────────────────────────────── ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 116.9 s +Duration: 110.2 s -OK: 133 +OK: 138 Failed: 0 Warnings: 0 Skipped: 1 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 09940aa3..358b50e3 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2019-11-09 +Date: 2019-11-13 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_aw.R b/tests/testthat/test_aw.R new file mode 100644 index 00000000..0a493893 --- /dev/null +++ b/tests/testthat/test_aw.R @@ -0,0 +1,12 @@ +context("Calculation of Akaike weights") + +test_that("Akaike weights sum to one", { + skip_on_cran() + aw_1 <- aw(fit_nw_1, fit_obs_1, fit_tc_1) + expect_error(aw(fit_nw_1, f_2_mkin), "same data") + expect_error(aw(fit_nw_1, 3), "mkinfit objects") + expect_equal(sum(aw_1), 1) + aw_2 <- aw(fits[c("SFO", "DFOP"), "FOCUS_D"]) + expect_equal(sum(aw_2), 1) + expect_error(aw(fits), "mmkin column object") +}) -- cgit v1.2.3