DOI: 10.5061/dryad.zgmsbccp7
title: Density-dependent declines of Wisconsin bats from white-nose syndrome

description: White-nose syndrome is a fungal infection that affects hibernating bats in
 North America. The disease caused signficant declines in multiple species
 of bats, including the once common little brown bat (Myotis lucifugus).
 Though density dependence These data and analyses 
description: # Density-dependent declines of Wisconsin bats from white-nose syndrome
 [https://doi.org/10.5061/dryad.zgmsbccp7](https://doi.org/10.5061/dryad.zgmsbccp7) ## Description of the data and file structure This dataset is comprised of colony counts of little brown bat summer roosts and winter hibernation sites in Wisconsin during the invasion of the bat fungal disease white-nose syndrome (WNS). These are the data used in the manuscript entitled *Positive density-dependence promotes host persistence in the face of infectious disease*. Bat colony counts from summer (summerdeclines_dataall_Nov2021.csv) and winter (midwest_density_dependence_analysesNEW.csv) sites were used to analyze population growth rates (lambda) during white-nose syndrome invasion in Wisconsin. Data were collected over 11 years from 2011-2021. The summer and winter datasets contain year of survey, population size during year of survey, population growth rate, years since WNS arrival for each site, and landscape and site-level variables for summer dataset. Due to the sensitivity of the bat sites, location information is removed, and site names are anonymized. ### Files and variables #### File: midwest_density_dependence_analysesNew.csv **Description:** Dataset of bat winter sites used in population growth rate models. Data cells with "NA" indicates not applicable.  ##### Variables * site: anonymized names * date: date of bat count * clustersize: Myotis lucifigus (little brown bat) count for that year * yoa: year of arrival of white-nose syndrome * wyear: survey year * season: season of hibernaculum survey (early or late winter) * ysw: years since white-nose syndrome arrival * max.clustersize: largest count of little brown bats in site * state: state of hibernaculum (Wisconsin, Michigan, Illinois)  * month: month survey took place * clustersize2: Little brown bat count with continuity correction of 1 * lambda: growth rate * previous.colony.size: Little brown bat count from previous year for calculating lambda * perc.change: yearly percent change of population (lambda -1) #### File: SummerDeclines_DataAll_Nov2021.csv **Description:** Dataset of bat summer sites used in population growth rate models. Data cells with "NA" indicates not applicable. ##### Variables * Site_num: Numerical value of site * Site: anonymized site name * Year: year of survey * YearssinceWNS: year since white-nose syndrome arrived in closest large hibernaculum * Mean_pop: mean count of little brown bats at each site for that year  * lambda: growth rate * Pop_prevyr: Little brown bat count from previous year for calculating lambda * Roost_type: Type of roost site structure (bat house, barn, attic, bridge) * Roost_typenum: numerical value of roost type * Num_roosts: number of roosts at each site (number of bat houses) * Age_roost: estimated age of roost site in years, how long bats have been using site * Dist_maj_hibkm: distance in km from roost site to closest major hibernation site * Closest_hib: anonymized name of closest hibernaculum * Pdyear: year white-nose syndrome arrived in winter site * WNS_hib_yrpls1: year white-nose syndrome arrived in winter site +1 * Hib_lambda: growth rate of winter site during impacts from white-nose syndrome * PreWNS_hibpop: little brown bat count at winter site before arrival of white-nose syndrome * Dist_water_m: distance in meters between summer roost site and closest water body * Closest_watertype: type of water body (river, lake) * Clos_water_num: numerical value of water body type ## Code/software Analyses were completed in R version 4.3.1. Required packages: tidyverse, ggplot2, viridis, ggthemes, lme4, plyr, dplyr, effects, glmmTMB, cowplot, grid, ggpubr. Winter and summer datasets were analyzed separately. In R script `heather_kate_summer_density_dependence_ms_NEW.R`, summer data is uploaded as "sumdec" and winter data as "mw". Code filters NA values, generates log10 values for population counts, lambda values and distances, and parses data into groups based on phase of white-nose syndrome - "pre-WNS": prior to arrival of wns year &lt;0; "wns arrival":  year 0 arrival of wns in sites; "declines": years when population declines from the disease are observed years 1-2; and "post-wns": years &gt;3 after arrival of wns.  Code plots yearly growth rates for both winter and summer sites grouped by wns phase and analyzes growth rates for both summer and winter sites against colony size and against distance to water for summer sites.  ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a