102 lines
2.2 KiB
Plaintext
102 lines
2.2 KiB
Plaintext
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<%@include file="includes/setup.md.rsp"%>
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<%@string fcnname="weightedMedian"%>
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<% fcnname <- "<%@string name="fcnname"%>" %>
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<%@meta title="${fcnname}() benchmarks"%>
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<%@meta author="Henrik Bengtsson"%>
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<%@meta date="2014-06-03"%>
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<%@include file="${header}"%>
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<%---
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'ergm' could be hard to install, because it imports
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'Rglpk', which requires GLPK library on the system.
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---%>
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<%@string test_ergm="FALSE"%>
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<%
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use("limma", how = "load")
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limma_weighted.median <- limma::weighted.median
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use("cwhmisc", how = "load")
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cwhmisc_w.median <- cwhmisc::w.median
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use("laeken", how = "load")
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laeken_weightedMedian <- laeken::weightedMedian
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<%@ifeq test_ergm="TRUE"%>
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use("ergm", how = "load")
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ergm_wtd.median <- ergm::wtd.median
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<%@endif%>
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weightedMedian <- matrixStats::weightedMedian
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%>
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# <%@meta name="title"%>
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This report benchmark the performance of <%=fcnname%>() against alternative methods.
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## Alternative methods
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* apply() + limma::weighted.median()
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* apply() + cwhmisc::w.median()
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* apply() + laeken::weightedMedian()
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<%@ifeq test_ergm="TRUE"%>
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* apply() + ergm::wtd.median() --%>
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<%@endif%>
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## Data
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```r
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<%=withCapture({
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<%@include file="R/random-vectors.R"%>
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data <- rvectors(mode = "double")
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data <- data[1:3]
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})%>
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```
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## Results
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<% for (ii in seq_along(data)) { %>
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<%
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dataLabel <- names(data)[ii]
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message(dataLabel)
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x <- data[[dataLabel]]
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gc()
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%>
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### <%=dataLabel%> vector
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```r
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<%=withCapture({
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x <- data[[.dataLabel.]]
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w <- runif(length(x))
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gc()
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stats <- microbenchmark(
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"weightedMedian" = weightedMedian(x, w = w, ties = "mean", na.rm = FALSE),
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"limma::weighted.median" = limma_weighted.median(x, w = w, na.rm = FALSE),
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"cwhmisc::w.median" = cwhmisc_w.median(x, w = w),
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"laeken::weightedMedian" = laeken_weightedMedian(x, w = w),
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<%@ifeq test_ergm="TRUE"%>
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"ergm::wtd.median" = ergm_wtd.median(x, w = w),
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<%@endif%>
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unit = "ms"
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)
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})%>
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```
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<% benchmarkResults(stats, tags=dataLabel) %>
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<% } # for (ii ...) %>
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<%@include file="${footer}"%>
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<%---------------------------------------------------------------------------
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HISTORY:
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2014-12-17
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o Made 'ergm::wtd.median' optional.
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2014-06-03
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o Created using benchmark snippet in incl/weightedMedian.Rex.
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---------------------------------------------------------------------------%>
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