=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== r-cran-phangorn-2.5.5/inst/doc/Trees.Rnw-271- r-cran-phangorn-2.5.5/inst/doc/Trees.Rnw:272:fitStart = eval(get(mt$Model[which.min(mt$BIC)], env), env) r-cran-phangorn-2.5.5/inst/doc/Trees.Rnw-273- ############################################## r-cran-phangorn-2.5.5/inst/doc/phangorn-specials.Rnw-132-\end{equation} r-cran-phangorn-2.5.5/inst/doc/phangorn-specials.Rnw:133:where we need to assign 6 paramters $\alpha, \dots, \eta$. The elements on the diagonal are chosen so that the rows sum to zero. The Jukes-Cantor (JC) \cite{Jukes1969} model can be derived as special case from the GTR model, for equal equilibrium frequencies $\pi_A = \pi_C = \pi_G = \pi_T = 0.25$ and equal rates set to $\alpha = \beta = \gamma = \delta = \eta$. Table \ref{models} lists all built-in nucleotide models in \phangorn. r-cran-phangorn-2.5.5/inst/doc/phangorn-specials.Rnw-134-The transition probabilities which describe the probabilities of change from character $i$ to $j$ in time $t$, are given by the corresponding entries of the matrix exponential ############################################## r-cran-phangorn-2.5.5/inst/doc/Trees.R-242-## r-cran-phangorn-2.5.5/inst/doc/Trees.R:243:## fitStart = eval(get(mt$Model[which.min(mt$BIC)], env), env) r-cran-phangorn-2.5.5/inst/doc/Trees.R-244-## ############################################## r-cran-phangorn-2.5.5/vignettes/Trees.Rnw-271- r-cran-phangorn-2.5.5/vignettes/Trees.Rnw:272:fitStart = eval(get(mt$Model[which.min(mt$BIC)], env), env) r-cran-phangorn-2.5.5/vignettes/Trees.Rnw-273- ############################################## r-cran-phangorn-2.5.5/vignettes/phangorn-specials.Rnw-132-\end{equation} r-cran-phangorn-2.5.5/vignettes/phangorn-specials.Rnw:133:where we need to assign 6 paramters $\alpha, \dots, \eta$. The elements on the diagonal are chosen so that the rows sum to zero. The Jukes-Cantor (JC) \cite{Jukes1969} model can be derived as special case from the GTR model, for equal equilibrium frequencies $\pi_A = \pi_C = \pi_G = \pi_T = 0.25$ and equal rates set to $\alpha = \beta = \gamma = \delta = \eta$. Table \ref{models} lists all built-in nucleotide models in \phangorn. r-cran-phangorn-2.5.5/vignettes/phangorn-specials.Rnw-134-The transition probabilities which describe the probabilities of change from character $i$ to $j$ in time $t$, are given by the corresponding entries of the matrix exponential ############################################## r-cran-phangorn-2.5.5/debian/tests/run-unit-test-3-oname=phangorn r-cran-phangorn-2.5.5/debian/tests/run-unit-test:4:pkg=r-cran-`echo $oname | tr '[A-Z]' '[a-z]'` r-cran-phangorn-2.5.5/debian/tests/run-unit-test-5- r-cran-phangorn-2.5.5/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then r-cran-phangorn-2.5.5/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` r-cran-phangorn-2.5.5/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM