DOI: 10.5061/dryad.2bvq83c05
title: Data from: Some like it cold: A general habitat association model for smallmouth bass in stratified lakes

description: Associations between fish distribution and environmental or spatial
 gradients at the population level represent habitat use models with
 potential to be transferable if model parameters are stationary among
 populations and over years. Further, population-level habitat use models
 represent the scale of effect – habitat relevant to within population
 distribution and processes. Here we show that for a widely recognized warm
 water fish species (smallmouth bass; Micropterus dolomieu), habitat use
 based on occupancy models extends their distribution in lakes deeper into
 the metalimnion and hypolimnion  – some bass like it cold. Lake
 depth at net sites was the gradient used to model habitat use in a
 comparative lake set (n=11 lakes) and for a large lake with three surveys
 over a decade. Bayesian quantile regression, with lakes as random effects,
 revealed all sizes of bass were present in shallow, warm areas of lakes as
 expected based on thermal preferences. Large adult bass, and not smaller
 fish, were found at deeper, colder depths producing a significant pattern
 of large fish found at deeper sites, thus confirming earlier tracking
 studies. The depth covariate was similar across lakes (no significant
 difference among lakes with one exception) in the comparative lake set.
 Over years, the depth covariate was also similar (no significant
 difference among years) and comparable to the comparative lake set. This
 consistency points to a general stationary habitat model for smallmouth
 bass during the summer season. We provide guidance for habitat managers
 based on this stationarity.
description: All lakes were surveyed using a depth stratified randomized
 netting survey with each depth stratum area based on the aerial coverage
 of a stratum. The netting survey for each lake used a
 depth stratified random design with each lake partitioned into depth
 categories as follows: 1–3 m; 3-6 m; 6–12 m; 12–20 m; 20–x m; more. Net
 sites were allocated based on aerial percent of each stratum in each lake
 and therefore represents a fair sample of bottom habitat in the lake as
 reflected in depth. A net consisted of 8 panels of varying mesh size (38,
 51, 64, 76, 89, 102, 114, and 127mm; totaling to 25m in length X 1.8 m in
 height). See article for availability of depth maps.
 Each net set was comprised of two nets tied together in tandem
 (“strapped”) and separated by approximately 3 m. Netting locations were
 separated by a minimum of 250 m. Nets were set on bottom for one hour with
 each net location separated by a minimum of 250 m to reduce or eliminate
 gear competition. Employing 1-hour sets approached operational limits of
 field crews and was as close to an instantaneous point sample site
 estimate as could be achieved for habitat use analysis. Netting effort on
 all lakes occurred between 07:00 and 16:00. With each net lift, fish
 species were recorded, measured for length (FL, mm), and returned to the
 lake if alive. Each net set included covariates consisting of depth of set
 (m) and temperature at net depth (°C) derived from a spline model of a
 depth: temperature profile recorded in mid-survey for each lake. Our
 definition of metalimnion is the depth range of a temperature profile with
 the highest rate of change in temperature from warm surface waters to deep
 cold water. The thermocline is the single depth of greatest change in
 temperature with the smallest change in depth within the metalimnion
 (greatest Δ temp over smallest Δ depth; based on the minima of the first
 derivative of the spline function using function “deriv”). Dissolved
 oxygen (DO) was above 7 ppm in each lake at all depths so DO was not
 included as a habitat covariate in this study.
description: # Data from: Some like it cold: A general habitat association model for
 smallmouth bass in stratified lakes ## Descriptions of .R Files:
 Comparison_bass_occupancy.R - Code to recreate the occupancy analysis of
 the multi-lake dataset and Figure 4. Uses
 "Comparison_Lake_data.csv" file so make sure working directory
 is set where that file is located. 'ubms' package version used
 in analysis is listed in script and manuscript, newer versions may give
 slightly different results from tweaks to default priors.
 Opeongo_bass_occupancy.R - Code to recreate the occupancy analysis
 specific to lake Opeongo and Figure 6. Uses "Ope_data.csv" file
 so make sure working directory is set where that file is located.
 'ubms' package version used in analysis is listed in script and
 manuscript, newer versions may give slightly different results from tweaks
 to default priors histograms_and_Quantile_regresion.R - Code to create
 Figures 2, 3, and 5 in manuscript. Also contains code to reproduce
 Quantile regression in a previous version of the manuscript (left in for
 those who may be interested). Uses "Bass_Temp_Flen.csv" and
 "Occu_depths.csv" files so make sure working directory is set
 where those files are located. ## Data Definitions for CSV files
 `comparison_lake_data.csv`: Called by Comparison_bass_occupancy.R; this
 file contains pass-level count and presence absence data for smallmouth
 bass in the multi-lake comparison, with site-level depth and temperature
 as well as ID columns for each lake. * PRJ_CD - Project code of each
 netting survey * Site - Code for each site in each netting survey *
 P1_SB_Count -Pass 1, Panel 1 count of Smallmouth Bass * P2_SB_Count -Pass
 1, Panel 2 count of Smallmouth Bass * P3_SB_Count -Pass 2, Panel 1 count
 of Smallmouth Bass * P4_SB_Count -Pass 2, Panel 2 count of Smallmouth Bass
 * P5_SB_Count -Pass 3, Panel 1 count of Smallmouth Bass * P6_SB_Count
 -Pass 3, Panel 2 count of Smallmouth Bass * P1_SB_PA - Pass 1, Panel 1
 presence/absence of Smallmouth Bass * P2_SB_PA - Pass 1, Panel 2
 presence/absence of Smallmouth Bass * P3_SB_PA - Pass 2, Panel 1
 presence/absence of Smallmouth Bass * P4_SB_PA - Pass 2, Panel 2 presence
 / absence of Smallmouth Bass * P5_SB_PA - Pass 3, Panel 1 presence/absence
 of Smallmouth Bass * P6_SB_PA - Pass 3, Panel 2 presence/absence of
 Smallmouth Bass * X - Easting coordinate of net site in meters; UTM zone
 17N * Y - Northing coordinate of net site in meters; UTM zone 17N *
 AVG_Depth - average depth of site in meters * AVG_Temp - average
 temperature of site in degrees Celsius * lk2 - ID for identifying Lauder
 lake survey sites * lk3 - ID for identifying Cache lake survey sites * lk4
 - ID for identifying Canoe lake survey sites * lk5 - ID for identifying
 Rock lake survey sites * lk6 - ID for identifying Tea lake survey sites *
 lk7 - ID for identifying Whitefish lake survey sites * lk8 - ID for
 identifying Happy Isle lake survey sites * lk9 - ID for identifying Ragged
 lake survey sites * lk10 - ID for identifying Cedar lake survey sites *
 lk11 - ID for identifying lake of Two Rivers survey sites `Ope_data.csv`:
 Called by Opeongo_bass_occupancy.R; this file contains pass-level count
 and presence-absence data for smallmouth bass in lake Opeongo across
 multiple years, with site-level depth and temperature as well as a Year
 column that describes survey year. * PRJ_CD - Project code of each netting
 survey * Site - Code for each site in each netting survey * P1_SB_PA -Pass
 1, Panel 1 count of Smallmouth Bass * P2_SB_PA -Pass 1, Panel 2 count of
 Smallmouth Bass * P3_SB_PA -Pass 2, Panel 1 count of Smallmouth Bass *
 P4_SB_PA -Pass 2, Panel 2 count of Smallmouth Bass * P1_SB_Count - Pass 1,
 Panel 1 presence / absence of Smallmouth Bass * P2_SB_Count - Pass 1,
 Panel 2 presence / absence of Smallmouth Bass * P3_SB_Count - Pass 2,
 Panel 1 presence / absence of Smallmouth Bass * P4_SB_Count - Pass 2,
 Panel 2 presence / absence of Smallmouth Bass * X - Easting coordinate of
 net site in meters; UTM zone 17N * Y - Northing coordinate of net site in
 meters; UTM zone 17N * P1_Average_Depth - average depth of first pass of
 site in meters * P2_Average_Depth - average depth of second pass of site
 in meters * AVG_Temp - average temperature of site in degrees Celsius *
 Year - ID for identifying different years' survey sites (A = 2013
 survey, B = 2019 survey, C = 2023 survey) `Bass_Temp_FLEN.csv`: Called by
 histograms_and_Quantile_regresion.R; this data is the temperature at
 capture and fork length of individual bass caught in surveys from the
 multi-lake comparison dataset. * PRJ_CD - Project code of each netting
 survey * SPC - species code from database * AVG_Temp - average temperature
 of capture in degrees Celsius * AVG_tDepth - average depth of capture in
 meters * FLENcm - fork length of Smallmouth bass in centimeters
 `Occu_depths.csv`: Called by histograms_and_Quantile_regresion.R; this
 data is the depth at different modelled occupancy values as well as
 thermocline values for each lake. * Lake - header column of lake name *
 Cache - Depths of Occupancy and thermocline (in meters) for Cache Lake *
 Canoe - Depths of Occupancy and thermocline (in meters) for Canoe Lake *
 Cedar - Depths of Occupancy and thermocline (in meters) for Cedar Lake *
 Happy Isle - Depths of Occupancy and thermocline (in meters) for Happy
 Isle Lake * Lauder - Depths of Occupancy and thermocline (in meters) for
 Lauder Lake * Ragged - Depths of Occupancy and thermocline (in meters) for
 Ragged Lake * Rock - Depths of Occupancy and thermocline (in meters) for
 Rock Lake * Smoke - Depths of Occupancy and thermocline (in meters) for
 Smoke Lake * Tea - Depths of Occupancy and thermocline (in meters) for Tea
 Lake * LOTR - Depths of Occupancy and thermocline (in meters) for Lake of
 Two Rivers * Whitefish - Depths of Occupancy and thermocline (in meters)
 for Whitefish Lake `Temp_DO_data.csv`: This data isn't called by the
 R codes but was included as it is the data used to predict site
 temperature, thermocline depth, and temperature at capture for individual
 fish. * PRJ_CD - Project code of each temperature DO profile survey *
 Location - Location ID of Temp/DO survey * Lake - Lake Name * Date - Date
 of Temp/DO survey (Blank values indicate no available date, but profiles
 were taken during time of survey). * Depth - Depth of Temperature and DO
 measurement (in meters). * Temp - Temperature of water (in degrees
 Celsius) at each depth * DOConc - Dissolved oxygen concentration of water
 (in parts per million) at each depth