batwintor: batwintor: A pacakge for computing the metabolic costs of...

In cReedHranac/batwintor: Tool for bat hibernation energetics

Description

The batwintor package includes 4 groups of functions, Arrousal Functions, Torpor Functions, Model Functions, and Plot Functions. In addition there are 3 data sets built into the package that allow you to explore the majorit of the packages functions.

Data

There are 3 data sets included within the package. bat.params, mylu.params, and fung.params. 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 Myotis lucifugus(mylu) is extracted from bat.params as an example and stored as mylu.params. fung.params contains the parameters required to calculate and scale the growth of Pseduogymnoascans destructans, the psycrophilic fungal agent responsable for WNS.

Torpor Functions

The Torpor Fucntions are used to calculate how long a bat will maintain a torpid metabolic state (torporTime), which is dependent largley on ewl, and torporEnergy is used to determine the energy expended during those bouts of torpor.

Arousal Functions

The Arousal Functions are designed to explane the energry expendatures between bouts of torpor. arousalTime and arousalEnergy document the return from torpid body temperatures to euthermia. The functions euthermicEnergy describes energy expendature during euthermia, and the flyingTime and flyingEnergy functions describe ammendments made to encourperate the metabolic costs of flight during arousals. The coolTime and coolEnergy functions handle the return from eutheria to torpid state and complete the arousal cycle.

Model Functions

The model functions are the heart of the package and are composed of: buildEnv, hibernationModel, and batDynamic. The 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 hibernationModel takes the supplied environment, the parameters passed in and formats the data for the batDynamic which solves the differential equations. hibernationModel then formats, and outputs the results for post-processing and plotting

Plot Tools

The plotting tools built in are currently quite inflexable and more designed to generate consistant plots for publication. dangerZone plots the difference in maximal winter hibernation time between infected and uninfected individuals. survivalPlotter and 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 getDistribution) and a surface represing the length of witner. The survivalHistogram tallies the cell values within these rasters and plots how the a species median survival capasity will shift with the introduction of WNS. survivalMultiplot combines survivalPlotter outputs of infected and uninfected along with survivalHistogram to make one nice picture.

cReedHranac/batwintor documentation built on Jan. 27, 2020, 7:39 p.m.