diff options
| -rw-r--r-- | NAMESPACE | 3 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/aw.R | 60 | ||||
| -rw-r--r-- | _pkgdown.yml | 1 | ||||
| -rw-r--r-- | docs/news/index.html | 1 | ||||
| -rw-r--r-- | docs/reference/aw.html | 214 | ||||
| -rw-r--r-- | docs/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/sitemap.xml | 3 | ||||
| -rw-r--r-- | man/aw.Rd | 47 | ||||
| -rw-r--r-- | test.log | 21 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/test_aw.R | 12 |
12 files changed, 361 insertions, 11 deletions
@@ -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) @@ -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' @@ -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 @@ <a href="#mkin-0-9-49-8-unreleased" class="anchor"></a>mkin 0.9.49.8 (unreleased)<small> Unreleased </small> </h1> <ul> +<li><p>‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns</p></li> <li><p>‘loftest’: Add a lack-of-fit test</p></li> <li><p>‘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’</p></li> <li><p>‘lrtest.mkinfit’: Improve naming of the compared fits in the case of fixed parameters</p></li> diff --git a/docs/reference/aw.html b/docs/reference/aw.html new file mode 100644 index 00000000..b6f3ce48 --- /dev/null +++ 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href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate Akaike weights for model averaging</h1> + + <div class="hidden name"><code>aw.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Akaike weights are calculated based on the relative +expected Kullback-Leibler information as specified +by Burnham and Anderson (2004).</p> + </div> + + <pre class="usage"><span class='fu'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mmkin</span> +<span class='fu'>aw</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>An mmkin column object, containing two or more +<code><a href='mkinfit.html'>mkinfit</a></code> 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.</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used in the method for mmkin column objects, +further mkinfit objects in the method for mkinfit objects.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Burnham KP and Anderson DR (2004) Multimodel + Inference: Understanding AIC and BIC in Model Selection + Sociological Methods & Research 33(2) 261-304</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> +<span class='no'>f_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>f_dfop</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>aw_sfo_dfop</span> <span class='kw'><-</span> <span class='fu'>aw</span>(<span class='no'>f_sfo</span>, <span class='no'>f_dfop</span>) +<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>aw_sfo_dfop</span>)</div><div class='output co'>#> [1] 1</div><div class='input'><span class='no'>aw_sfo_dfop</span> <span class='co'># SFO gets more weight as it has less parameters and a similar fit</span></div><div class='output co'>#> [1] 0.5970258 0.4029742</div><div class='input'><span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS D"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_D</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>aw</span>(<span class='no'>f</span>)</div><div class='output co'>#> [1] 0.4808722 0.1945539 0.3245740</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='fu'>aw</span>(<span class='no'>f</span>))</div><div class='output co'>#> [1] 1</div><div class='input'><span class='fu'>aw</span>(<span class='no'>f</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"DFOP"</span>)])</div><div class='output co'>#> [1] 0.5970258 0.4029742</div><div class='input'># } +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + <li><a href="#references">References</a></li> + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + 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 @@ -234,6 +234,12 @@ with mkinfit</p></td> </tr><tr> <td> + <p><code><a href="aw.html">aw()</a></code> </p> + </td> + <td><p>Calculate Akaike weights for model averaging</p></td> + </tr><tr> + + <td> <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p> </td> <td><p>Export a list of datasets format to a CAKE study file</p></td> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 66b776b2..a8d6dfa4 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -55,6 +55,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/aw.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc> </url> <url> 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 +} @@ -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") +}) |