=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== r-bioc-qvalue-2.22.0/inst/doc/qvalue.Rnw-272- r-bioc-qvalue-2.22.0/inst/doc/qvalue.Rnw:273:The main purpose of the upper-left plot is to gauge the reliability of the $\pi_{0}$ estimate, where the estimated $\pi_{0}$ is plotted versus the tuning parameter $\lambda$. The variable $\lambda$ is called {\tt lambda} in the package; it can be fixed or automatically handled. As $\lambda$ gets larger, the bias of the estimate decreases, yet the variance increases. When {\tt pi0.method = "smoother"} is utilized, the fitted smoother is also shown in this plot. See Storey (2002) \cite{storey:2002} for more on $\lambda$ and its role in estimating $\pi_0$. Comparing your final estimate of $\pi_{0}$ to this plot gives a good sense as to its quality. r-bioc-qvalue-2.22.0/inst/doc/qvalue.Rnw-274- ############################################## r-bioc-qvalue-2.22.0/vignettes/qvalue.Rnw-272- r-bioc-qvalue-2.22.0/vignettes/qvalue.Rnw:273:The main purpose of the upper-left plot is to gauge the reliability of the $\pi_{0}$ estimate, where the estimated $\pi_{0}$ is plotted versus the tuning parameter $\lambda$. The variable $\lambda$ is called {\tt lambda} in the package; it can be fixed or automatically handled. As $\lambda$ gets larger, the bias of the estimate decreases, yet the variance increases. When {\tt pi0.method = "smoother"} is utilized, the fitted smoother is also shown in this plot. See Storey (2002) \cite{storey:2002} for more on $\lambda$ and its role in estimating $\pi_0$. Comparing your final estimate of $\pi_{0}$ to this plot gives a good sense as to its quality. r-bioc-qvalue-2.22.0/vignettes/qvalue.Rnw-274- ############################################## r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-2-oname=qvalue r-bioc-qvalue-2.22.0/debian/tests/run-unit-test:3:pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]` r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-4- r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-5-if [ "$AUTOPKGTEST_TMP" = "" ] ; then r-bioc-qvalue-2.22.0/debian/tests/run-unit-test:6: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-7-fi ############################################## r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-12-for rnw in `ls *.[rRS]nw` ; do r-bioc-qvalue-2.22.0/debian/tests/run-unit-test:13:rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'` r-bioc-qvalue-2.22.0/debian/tests/run-unit-test-14-# Somehow Stangle ends up in error but an R file is created anyway so we ignore this for the moment