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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd-18-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd:19:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd-20-
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r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd-294-
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd:295:Scree plot of the PCoA used to create Figure 5 from the "Global Patterns" article([Caporaso 2011](http://www.pnas.org/content/early/2010/06/02/1000080107)). The first three axes represent `r round(100*sum(GloPa.pcoa$values$Relative_eig[1:3]))`% of the total variation in the distances. Interestingly, the fourth axis represents another `r round(100*(GloPa.pcoa$values$Relative_eig[4]))`%, and so may warrant exploration as well. A scree plot is an important tool for any ordination method, as the relative importance of axes can vary widely from one dataset to another.
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-analysis.Rmd-296-
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r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-basics.Rmd-16-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-basics.Rmd:17:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-basics.Rmd-18-
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r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-mixture-models.Rmd-16-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-mixture-models.Rmd:17:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/inst/doc/phyloseq-mixture-models.Rmd-18-
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r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd-18-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd:19:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd-20-
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r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd-294-
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd:295:Scree plot of the PCoA used to create Figure 5 from the "Global Patterns" article([Caporaso 2011](http://www.pnas.org/content/early/2010/06/02/1000080107)). The first three axes represent `r round(100*sum(GloPa.pcoa$values$Relative_eig[1:3]))`% of the total variation in the distances. Interestingly, the fourth axis represents another `r round(100*(GloPa.pcoa$values$Relative_eig[4]))`%, and so may warrant exploration as well. A scree plot is an important tool for any ordination method, as the relative importance of axes can vary widely from one dataset to another.
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-analysis.Rmd-296-
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r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-basics.Rmd-16-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-basics.Rmd:17:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-basics.Rmd-18-
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r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-mixture-models.Rmd-16-`r library("knitr")`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-mixture-models.Rmd:17:`r opts_chunk$set(cache=FALSE, fig.width=9, message=FALSE, warning=FALSE)`
r-bioc-phyloseq-1.34.0+dfsg/vignettes/phyloseq-mixture-models.Rmd-18-
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r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test-3-oname=phyloseq
r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test:4:pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test-5-
r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test:7:  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
r-bioc-phyloseq-1.34.0+dfsg/debian/tests/run-unit-test-8-  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM