batwintor: Tool for bat hibernation energetics

#' batwintor: A pacakge for computing the metabolic costs of hibernation on bats.
#'
#' The batwintor package is designed to use the principals of hibernation physiology
#' to compute the total energentic requirements of hibernation for bats. This package
#' also includes tools to address how these energetic costs may change when
#' hibernators are infected with the etiological agent of White-nose syndrome
#' \emph{Pseudogymnoascus destructans}. This package includes 4 primary groups
#' of functions, \code{Arrousal Functions}, \code{Torpor Functions},
#' \code{Model Functions}, and \code{Plot Functions}. In addition there are 3
#' data sets built into the package that allow you to explore the majority of
#'  the packages functions.
#' @section Data:
#' There are 3 data sets included within the package.
#' \code{\link{bat.params}}, \code{\link{mylu.params}}, and
#' \code{\link{fung.params}}. \code{bat.params} contains all of the parameter
#' estimations necessary to run the primary model for 12 species of North
#' American bats. Bat species involved are listed by their four letter code
#' (first two letters genus and species) as we got tired of writing out the
#' whole name every time. The parameters for \emph{Myotis
#' lucifugus}(\code{mylu}) is extracted from \code{bat.params} as an example
#' and stored as \code{\link{mylu.params}}. \code{\link{fung.params}} contains
#' the parameters required to calculate and scale the growth of
#' \emph{Pseduogymnoascans destructans}, the psycrophilic fungal agent
#' responsable for WNS.
#'
#' @section Torpor Functions:
#' The \code{Torpor Fucntions} are used to calculate
#' how long a bat will maintain a torpid metabolic state
#' (\code{\link{torporTime}}), which is dependent largley on
#' \code{\link{ewl}}, and \code{\link{torporEnergy}} is used to
#' determine the energy expended during those bouts of torpor.
#'
#' @section Arousal Functions:
#' The \code{Arousal Functions} are designed to
#' explane the energry expendatures between bouts of torpor.
#' \code{\link{arousalTime}} and \code{\link{arousalEnergy}} document
#' the return from torpid body temperatures to euthermia. The functions
#' \code{\link{euthermicEnergy}} describes energy expendature during
#' euthermia, and the \code{\link{flyingTime}} and
#' \code{\link{flyingEnergy}} functions describe ammendments made to encourperate
#' the metabolic costs of flight during arousals. The \code{\link{coolTime}}
#' and \code{\link{coolEnergy}} functions handle the return from eutheria
#' to torpid state and complete the arousal cycle.
#'
#' @section Model Functions:
#' The model functions are the heart of the package and are composed of:
#' \code{\link{buildEnv}}, \code{\link{hibernationModel}}, and
#' \code{\link{batDynamic}}. The \code{\link{buildEnv}} function allows you to create your
#' the parameter space that your model will run across in the form of
#' environmental spave and a time vector. The \code{\link{hibernationModel}} takes
#' the supplied environment, the parameters passed in and formats the data
#' for the \code{\link{batDynamic}} which solves the differential equations.
#' \code{\link{hibernationModel}} then formats, and outputs the results for post-processing
#' and plotting
#'
#' @section Plot Tools:
#' The plotting tools built in are currently quite inflexable and more designed to
#' generate consistant plots for publication. \code{\link{dangerZone}} plots the difference
#' in maximal winter hibernation time between infected and uninfected individuals.
#' \code{\link{survivalPlotter}} and \code{\link{survivalRaster}} used to infer the
#' model microclimate results across the geographic range of the species. This
#' function relies on the user supplying temperature and humidity data as well
#' as a distributional range (see \code{\link{getDistribution}}) and a surface
#' represing the length of witner. The \code{\link{survivalHistogram}} tallies
#' the cell values within these rasters and plots how the a species median
#' survival capasity will shift with the introduction of WNS. \code{\link{survivalMultiplot}}
#' combines \code{\link{survivalPlotter}} outputs of infected and uninfected along
#' with \code{\link{survivalHistogram}} to make one nice picture.
#'
#' @docType package
#' @name batwintor
NULL