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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-incidence-1.7.3/vignettes/overview.Rmd-291-These models are very good approximation of these data, showing a doubling time
r-cran-incidence-1.7.3/vignettes/overview.Rmd:292:of `r round(get_info(best.fit$fit, "doubling"), 1)` days during the first
r-cran-incidence-1.7.3/vignettes/overview.Rmd:293:phase, and a halving time of `r round(get_info(best.fit$fit, "halving"), 1)`
r-cran-incidence-1.7.3/vignettes/overview.Rmd-294-days during the second.
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-33-
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:34: - `$model`: The model fit to an `incidence` object. Currently, this represents a
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-35- log-linear model, but it can be any model.
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:36: - `$info`: Information derived from the model
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-37- - `r` The growth rate
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-46- - `halving.conf` the confidence interval of the halving time
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:47: - `$origin`: the date corresponding to day '0'
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-48-
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-65-As you can see, the `incidence_fit` object has a print method and a plot method.
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:66:If you want to access individual elements in the `$info` element, you can use
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-67-the `get_info()` function:
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-101-
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:102:If we compare that to the `$model` element produced from `fit()`, we can see that
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-103-it is identical:
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-108-
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:109:### Step 2: creation of the `$info` list:
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-110-
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:111:The `$info` list is created directly from the model itself:
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-112-
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-179-The function `fit_optim_split()` attempts to find the optimal split point in an
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd:180:epicurve, producing an `incidence_fit_list` object in the `$fit` element of the
r-cran-incidence-1.7.3/vignettes/incidence_fit_class.Rmd-181-returned list:
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-81-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:82:## `$dates`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-83-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:84:The `$dates` component contains a vector for all the dates for which incidence
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-85-have been computed, in the format of the input dataset (e.g. `Date`, `numeric`,
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-128-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:129:## `$counts`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-130-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:131:The `$counts` component contains the actual incidence, i.e. counts of events
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-132-for the defined bins. It is a `matrix` of `integers` where rows correspond to
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-188-default, which will pool all missing groups into a separate group, in which
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:189:case it will be a separate column in `$counts`.
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-190-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:191:## `$timespan`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-192-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:193:The `$timespan` component stores the length of the time period covered by the
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-194-object:
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-201-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:202:## `$interval`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-203-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:204:The `$interval` component contains the length of the time interval for the bins:
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-205-
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-210-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:211:## `$n`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-212-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:213:The `$n` component stores the total number of events in the data:
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-214-
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-224-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:225:## `$weeks`
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-226-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:227:The `$weeks` component is optional, and used to store
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-228-[aweek](https://www.repidemicsconsortium.org/aweek/) objects whenever they have
##############################################
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-239-
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd:240:Because `$weeks` is an optional element, it does not have a dedicated
r-cran-incidence-1.7.3/vignettes/incidence_class.Rmd-241-accessor. If the element is not present, attempting to access it will result in
##############################################
r-cran-incidence-1.7.3/R/scale_x_incidence.R-2-#' [ggplot2::scale_x_datetime()], or [ggplot2::scale_x_continuous()], depending
r-cran-incidence-1.7.3/R/scale_x_incidence.R:3:#' on how the `$date` element is stored in the incidence object.
r-cran-incidence-1.7.3/R/scale_x_incidence.R-4-#' @export
##############################################
r-cran-incidence-1.7.3/R/fit.R-22-#'
r-cran-incidence-1.7.3/R/fit.R:23:#' - `$model`: the fitted linear model
r-cran-incidence-1.7.3/R/fit.R:24:#' - `$info`: a list containing various information extracted from the model
r-cran-incidence-1.7.3/R/fit.R-25-#' (detailed further)
r-cran-incidence-1.7.3/R/fit.R:26:#' - `$origin`: the date corresponding to day '0'
r-cran-incidence-1.7.3/R/fit.R-27-#'
r-cran-incidence-1.7.3/R/fit.R:28:#' The `$info` item is a list containing:
r-cran-incidence-1.7.3/R/fit.R-29-#'
##############################################
r-cran-incidence-1.7.3/R/conversion.R-29-#' original dates are not available. In such case, the argument `x`
r-cran-incidence-1.7.3/R/conversion.R:30:#' should be a matrix corresponding to the `$counts` element of an
r-cran-incidence-1.7.3/R/conversion.R-31-#' `incidence` object, i.e. giving counts with time intervals in rows and
##############################################
r-cran-incidence-1.7.3/R/get_interval.R-7-#' - `get_interval()` if `integer = TRUE`: an integer vector, otherwise: the
r-cran-incidence-1.7.3/R/get_interval.R:8:#' value stored in `x$interval`
r-cran-incidence-1.7.3/R/get_interval.R-9-#' @export
##############################################
r-cran-incidence-1.7.3/NEWS.md-35- (see https://github.com/reconhub/incidence/issues/55#issuecomment-405297526)
r-cran-incidence-1.7.3/NEWS.md:36: * the item `$weeks` is now added to the incidence object, which contains an
r-cran-incidence-1.7.3/NEWS.md-37- "aweek" class
##############################################
r-cran-incidence-1.7.3/NEWS.md-51- `labels_week`
r-cran-incidence-1.7.3/NEWS.md:52: * Incidence objects will still have `$isoweeks` if the weeks are ISO 8601
r-cran-incidence-1.7.3/NEWS.md:53: standard, but users should rely intead on `$weeks` instead. The `$isoweeks`
r-cran-incidence-1.7.3/NEWS.md-54- element will be removed in a future version of incidence.
##############################################
r-cran-incidence-1.7.3/NEWS.md-130-
r-cran-incidence-1.7.3/NEWS.md:131:* `print.incidence()` will now print isoweeks even if the `$interval` element is
r-cran-incidence-1.7.3/NEWS.md-132- "week".
##############################################
r-cran-incidence-1.7.3/NEWS.md-160-* `group_names()` allows the user to retrieve and set the group names.
r-cran-incidence-1.7.3/NEWS.md:161:* `get_timespan()` returns the `$timespan` element.
r-cran-incidence-1.7.3/NEWS.md:162:* `get_n()` returns the `$n` element.
r-cran-incidence-1.7.3/NEWS.md-163-* `dim()`, `nrow()`, and `ncol()` are now available for incidence objects,
##############################################
r-cran-incidence-1.7.3/NEWS.md-198-
r-cran-incidence-1.7.3/NEWS.md:199:* The `$lm` field of the `incidence_fit` class is now named `$model` to clearly
r-cran-incidence-1.7.3/NEWS.md-200- indicate that this can contain any model.
##############################################
r-cran-incidence-1.7.3/NEWS.md-214- `incidence_fit` objects within a nested list. This is the class returned by
r-cran-incidence-1.7.3/NEWS.md:215: in the `$fit` element of `fit_optim_split()`.
r-cran-incidence-1.7.3/NEWS.md-216-
##############################################
r-cran-incidence-1.7.3/NEWS.md-237-
r-cran-incidence-1.7.3/NEWS.md:238:* `get_info()` returns information stored in the `$info` element of an
r-cran-incidence-1.7.3/NEWS.md-239- `incidence_fit`/`incidence_fit_list` object.
##############################################
r-cran-incidence-1.7.3/NEWS.md-253-
r-cran-incidence-1.7.3/NEWS.md:254:* The `$timespan` item in the incidence object from Dates was not type-stable
r-cran-incidence-1.7.3/NEWS.md-255- and would change if subsetted. A re-working of the incidence constructor
##############################################
r-cran-incidence-1.7.3/inst/doc/overview.Rmd-291-These models are very good approximation of these data, showing a doubling time
r-cran-incidence-1.7.3/inst/doc/overview.Rmd:292:of `r round(get_info(best.fit$fit, "doubling"), 1)` days during the first
r-cran-incidence-1.7.3/inst/doc/overview.Rmd:293:phase, and a halving time of `r round(get_info(best.fit$fit, "halving"), 1)`
r-cran-incidence-1.7.3/inst/doc/overview.Rmd-294-days during the second.
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-33-
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:34: - `$model`: The model fit to an `incidence` object. Currently, this represents a
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-35- log-linear model, but it can be any model.
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:36: - `$info`: Information derived from the model
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-37- - `r` The growth rate
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-46- - `halving.conf` the confidence interval of the halving time
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:47: - `$origin`: the date corresponding to day '0'
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-48-
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-65-As you can see, the `incidence_fit` object has a print method and a plot method.
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:66:If you want to access individual elements in the `$info` element, you can use
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-67-the `get_info()` function:
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-101-
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:102:If we compare that to the `$model` element produced from `fit()`, we can see that
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-103-it is identical:
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-108-
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:109:### Step 2: creation of the `$info` list:
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-110-
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:111:The `$info` list is created directly from the model itself:
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-112-
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-179-The function `fit_optim_split()` attempts to find the optimal split point in an
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd:180:epicurve, producing an `incidence_fit_list` object in the `$fit` element of the
r-cran-incidence-1.7.3/inst/doc/incidence_fit_class.Rmd-181-returned list:
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-81-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:82:## `$dates`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-83-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:84:The `$dates` component contains a vector for all the dates for which incidence
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-85-have been computed, in the format of the input dataset (e.g. `Date`, `numeric`,
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-128-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:129:## `$counts`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-130-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:131:The `$counts` component contains the actual incidence, i.e. counts of events
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-132-for the defined bins. It is a `matrix` of `integers` where rows correspond to
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-188-default, which will pool all missing groups into a separate group, in which
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:189:case it will be a separate column in `$counts`.
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-190-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:191:## `$timespan`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-192-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:193:The `$timespan` component stores the length of the time period covered by the
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-194-object:
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-201-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:202:## `$interval`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-203-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:204:The `$interval` component contains the length of the time interval for the bins:
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-205-
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-210-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:211:## `$n`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-212-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:213:The `$n` component stores the total number of events in the data:
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-214-
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-224-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:225:## `$weeks`
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-226-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:227:The `$weeks` component is optional, and used to store
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-228-[aweek](https://www.repidemicsconsortium.org/aweek/) objects whenever they have
##############################################
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-239-
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd:240:Because `$weeks` is an optional element, it does not have a dedicated
r-cran-incidence-1.7.3/inst/doc/incidence_class.Rmd-241-accessor. If the element is not present, attempting to access it will result in
##############################################
r-cran-incidence-1.7.3/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-cran-incidence-1.7.3/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX`
r-cran-incidence-1.7.3/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM