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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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              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