=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== r-cran-epiestim-2.2-3+dfsg/man/sample_posterior_R.Rd-42-R_median <- res$R$`Median(R)`[win] r-cran-epiestim-2.2-3+dfsg/man/sample_posterior_R.Rd:43:R_CrI <- c(res$R$`Quantile.0.025(R)`[win], res$R$`Quantile.0.975(R)`[win]) r-cran-epiestim-2.2-3+dfsg/man/sample_posterior_R.Rd-44- ############################################## r-cran-epiestim-2.2-3+dfsg/man/estimate_R.Rd-257-## sample (either internally to EpiEstim or externally) r-cran-epiestim-2.2-3+dfsg/man/estimate_R.Rd:258:all(R_si_from_sample$R$`Mean(R)` == R_si_from_data$R$`Mean(R)`) r-cran-epiestim-2.2-3+dfsg/man/estimate_R.Rd-259-} ############################################## r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-76-For i), the default behavior is to estimate R over weekly sliding windows. r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:77:This can be changed through the `config$t_start` and `config$t_end` arguments r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-78-(see below, "Changing the time windows for estimation"). ############################################## r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-135-Note that you can obtain such a full distribution of the serial interval using r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:136:`discr_si` function (this is how `Flu2009$si_distr` was obtained, with r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-137-additional rounding): ############################################## r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-167-compute. You can adjust the parameters governing the sample sizes by altering r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:168:the default values of `config$n1` and `config$n2` (`n1` is the number of pairs r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-169-of mean and sd of the SI that are drawn and `n2` is the size of the posterior ############################################## r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-263-## sample (either internally to EpiEstim or externally) r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:264:all(res_si_from_sample$R$`Mean(R)` == res_si_from_data$R$`Mean(R)`) r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-265-``` ############################################## r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-268- r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:269:The time window can be specified through arguments `config$t_start` and r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd:270:`config$t_end`. For instance, the default weekly sliding windows can also be r-cran-epiestim-2.2-3+dfsg/vignettes/demo.Rmd-271-obtained by specifying: ############################################## r-cran-epiestim-2.2-3+dfsg/R/sample_posterior_R.R-34-#' R_median <- res$R$`Median(R)`[win] r-cran-epiestim-2.2-3+dfsg/R/sample_posterior_R.R:35:#' R_CrI <- c(res$R$`Quantile.0.025(R)`[win], res$R$`Quantile.0.975(R)`[win]) r-cran-epiestim-2.2-3+dfsg/R/sample_posterior_R.R-36-#' ############################################## r-cran-epiestim-2.2-3+dfsg/R/estimate_r.R-250-#' ## sample (either internally to EpiEstim or externally) r-cran-epiestim-2.2-3+dfsg/R/estimate_r.R:251:#' all(R_si_from_sample$R$`Mean(R)` == R_si_from_data$R$`Mean(R)`) r-cran-epiestim-2.2-3+dfsg/R/estimate_r.R-252-#' } ############################################## r-cran-epiestim-2.2-3+dfsg/NEWS.md-76- and sets defaults where arguments are missing. In particular, if argument r-cran-epiestim-2.2-3+dfsg/NEWS.md:77: `incid` is not `NULL`, by default `config$t_start` and `config$t_end` will be r-cran-epiestim-2.2-3+dfsg/NEWS.md-78- set so that, when the configuration is used inside `estimate_R` function, the ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-76-For i), the default behavior is to estimate R over weekly sliding windows. r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:77:This can be changed through the `config$t_start` and `config$t_end` arguments r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-78-(see below, "Changing the time windows for estimation"). ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-135-Note that you can obtain such a full distribution of the serial interval using r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:136:`discr_si` function (this is how `Flu2009$si_distr` was obtained, with r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-137-additional rounding): ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-167-compute. You can adjust the parameters governing the sample sizes by altering r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:168:the default values of `config$n1` and `config$n2` (`n1` is the number of pairs r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-169-of mean and sd of the SI that are drawn and `n2` is the size of the posterior ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-263-## sample (either internally to EpiEstim or externally) r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:264:all(res_si_from_sample$R$`Mean(R)` == res_si_from_data$R$`Mean(R)`) r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-265-``` ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-268- r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:269:The time window can be specified through arguments `config$t_start` and r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd:270:`config$t_end`. For instance, the default weekly sliding windows can also be r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.Rmd-271-obtained by specifying: ############################################## r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.R-128-## sample (either internally to EpiEstim or externally) r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.R:129:all(res_si_from_sample$R$`Mean(R)` == res_si_from_data$R$`Mean(R)`) r-cran-epiestim-2.2-3+dfsg/inst/doc/demo.R-130- ############################################## r-cran-epiestim-2.2-3+dfsg/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then r-cran-epiestim-2.2-3+dfsg/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX` r-cran-epiestim-2.2-3+dfsg/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM