R/flycircuit-package.r

In natverse/flycircuit: Functions to support the analysis of the FlyCircuit single neuron dataset

#' Support functions for analysis of raw image data provided by flycircuit.tw
#'
#' @section Additional data: You can find out more about the data processing
#'   that we carried out by visiting the companion website for the NBLAST paper
#'   \url{https://bit.ly/flybrains}. This includes detailed instructions for the
#'   \href{http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/nblast_desktop/#data}{associated
#'   data downloads}.
#'   
#' @section Package options:
#'
#'   flycircuit uses the following \code{\link{options}} to configure behaviour:
#'
#'   \itemize{
#'
#'   \item \code{flycircuit.datadir}: path to directory where downloaded data
#'   will be stored. Defaults to package's \code{extdata} folder.
#'
#'   \item \code{flycircuit.dbdir}: location to which dataframes caching
#'   database tables will be downloaded.
#'
#'   \item \code{flycircuit.ffdir}: location of \code{ff} objects used for all
#'   by all score matrices.
#'
#'   \item \code{flycircuit.bigmatdir}: location of \code{big.matrix} objects
#'   previously used for all by all score matrices.
#'
#'   \item \code{flycircuit.scoremat}: character vector naming the default
#'   regular or \code{ff} matrix object containing nblast scores. Note that
#'   although it is is permissible to set this to the actual score matrix rather
#'   than a character vector naming the matrix, this turns out to have
#'   substantial performance penalties for large matrices.
#'
#'   \item \code{flycircuit.remote_overwrite}: Determines how local cached
#'   versions of data available on the web are updated. When \code{NULL} (i.e.
#'   unset) the web version is checked and, if it is newer, it is donwloaded and
#'   used to overwrite the cached copy. When \code{FALSE} the exisiting local
#'   copy is used; when \code{TRUE} the remote version is always downloaded.
#'
#'   }
#'
#' @import nat
#' @examples
#' # Show state of flycircuit package options
#' options()[grep('^flycircuit', names(options()))]
#'
#' @keywords internal
"_PACKAGE"

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