Move resampling methods to 'dimensio'

DESCRIPTION

@@ -56,7 +56,6 @@ Collate:
     'initialize.R'
     'mutators.R'
     'show.R'
-    'statistics.R'
     'subset.R'
     'summary.R'
     'utilities.R'

NAMESPACE

@@ -68,7 +68,6 @@ exportMethods(as_incidence)
 exportMethods(as_long)
 exportMethods(as_occurrence)
 exportMethods(as_stratigraphy)
-exportMethods(bootstrap)
 exportMethods(get_dates)
 exportMethods(get_groups)
 exportMethods(get_samples)
@@ -79,7 +78,6 @@ exportMethods(get_tpq)
 exportMethods(has_dates)
 exportMethods(has_groups)
 exportMethods(has_terminus)
-exportMethods(jackknife)
 exportMethods(remove_Inf)
 exportMethods(remove_NA)
 exportMethods(remove_empty)

NEWS.md

@@ -4,7 +4,6 @@
 * Add `replace_Inf()` to replace infinite values in a `matrix`-like object.
 * Add `replace_zero()` to replace zero in a `matrix`-like object.
 * Add `remove_Inf()` to remove infinite values in a `matrix`-like object.
-* Add resampling methods: `bootstrap()` and `jackknife()`.
 * Add `assert_*()` and `validate()` to validate objects.
 * Add `get_dates()`, `set_dates()<-` to extract/replace `dates` slot.
 * Add `get_terminus()`, `set_terminus()<-`, `get_tpq()`, `set_tpq()<-`, `get_taq()`, `set_taq()<-` to extract/replace `tpq` and `taq` slots.
@@ -14,7 +13,6 @@
 * `AbundanceMatrix` class gained a new slot to store the sample sizes (`totals`).
 * `AbundanceMatrix` class gained two new slots to store chronological information (`dates`, `tpq`, `taq`).
 * Add `AbundanceSummary` class to store summary of an `AbundanceMatrix` object.
-* Add `BootstrapVector` and `JackknifeVector` classes to store bootstrap and jackknife resampling values (inherit from base `numeric`).
 
 # arkhe 0.3.1
 

R/AllClasses.R

@@ -1,18 +1,5 @@
 # CLASSES DEFINITION
 
-# Vector =======================================================================
-.BootstrapVector <- setClass(
-  Class = "BootstrapVector",
-  contains = "numeric"
-)
-.JackknifeVector <- setClass(
-  Class = "JackknifeVector",
-  slots = c(
-    hat = "numeric"
-  ),
-  contains = "numeric"
-)
-
 # AbundanceMatrix ==============================================================
 #' Archaeological Data
 #'

R/AllGenerics.R

@@ -387,87 +387,3 @@ NULL
 #' @name summary
 #' @rdname summary
 NULL
-
-# Statistics ===================================================================
-#' Jackknife Estimation
-#'
-#' @param x A [`numeric`] vector.
-#' @param do A [`function`] that takes `x` as an argument and returns a single
-#'  numeric value.
-#' @param object A `JackknifeVector` object.
-#' @param ... Extra arguments passed to `do`.
-#' @return
-#'  `jackknife()` returns a `JackknifeVector` object (i.e. a `numeric`
-#'  vector of the `n` leave-one-out values of `do`).
-#'
-#'  `summary()` returns a named `numeric` vector with the following elements:
-#'  \describe{
-#'   \item{`mean`}{The jackknife estimate of mean of `do`.}
-#'   \item{`bias`}{The jackknife estimate of bias of `do`.}
-#'   \item{`error`}{he jackknife estimate of standard error of `do`.}
-#'  }
-#' @example inst/examples/ex-statistics.R
-#' @author N. Frerebeau
-#' @docType methods
-#' @family statistics
-#' @name jackknife
-#' @rdname jackknife
-NULL
-
-#' @rdname jackknife
-#' @aliases jackknife-method
-setGeneric(
-  name = "jackknife",
-  def = function(x, ...) standardGeneric("jackknife")
-)
-
-#' Bootstrap Estimation
-#'
-#' Creates \eqn{n} bootstrapped replicates by resampling with replacement from
-#' the original data and applies a function.
-#' @param x A [`numeric`] or an [`integer`] vector (see below).
-#' @param do A [`function`] that takes `x` as an argument
-#'  and returns a single numeric value.
-#' @param n A non-negative [`integer`] giving the number of bootstrap
-#'  replications.
-#' @param object A `BootstrapVector` object.
-#' @param level A length-one [`numeric`] vector giving the confidence level.
-#'  Must be a single number between \eqn{0} and \eqn{1}. If `NULL`, no
-#'  confidence interval are computed.
-#' @param type A [`character`] string giving the type of confidence
-#'  interval to be returned. It must be one "`student`" (default) or
-#'  "`normal`". Any unambiguous substring can be given. Only used if `level`
-#'  is not `NULL`.``
-#' @param probs A [`numeric`] vector of probabilities with values in
-#'  \eqn{[0,1]} (see [stats::quantile()]). If `NULL`, quantiles are not
-#'  computed.
-#' @param na.rm A [`logical`] scalar: should missing values be removed
-#'  from `object` before the sample statistics are computed?
-#' @param ... Extra arguments passed to `do`.
-#' @return
-#'  `bootstrap()` returns a `BootstrapVector` object (i.e. a `numeric`
-#'  vector of the `n` bootstrap values of `do`).
-#'
-#'  `summary()` returns a `numeric` vector with the following elements:
-#'  \describe{
-#'   \item{`min`}{Minimum value.}
-#'   \item{`mean`}{Mean value.}
-#'   \item{`max`}{Maximum value.}
-#'   \item{`lower`}{Lower bound of the confidence interval.}
-#'   \item{`upper`}{Upper bound of the confidence interval.}
-#'   \item{`Q*`}{Sample quantile to `*` probability.}
-#'  }
-#' @example inst/examples/ex-statistics.R
-#' @author N. Frerebeau
-#' @docType methods
-#' @family statistics
-#' @name bootstrap
-#' @rdname bootstrap
-NULL
-
-#' @rdname bootstrap
-#' @aliases bootstrap-method
-setGeneric(
-  name = "bootstrap",
-  def = function(x, ...) standardGeneric("bootstrap")
-)

codemeta.json

@@ -124,7 +124,7 @@
       "name": "utils"
     }
   ],
-  "fileSize": "890.918KB",
+  "fileSize": "876.091KB",
   "contIntegration": "https://codecov.io/gh/tesselle/arkhe",
   "developmentStatus": "https://www.repostatus.org/#active",
   "keywords": [