DOI: 10.5061/dryad.g1jwstr0v
title: Data and code from: Spatially-explicit foraging by an apex predator linked to nearshore prey and their accessibility in lakes

description: Habitat coupling – where mobile predators forage over broad spatial scales
 and, in doing so, link food webs from semi-discrete habitat patches – has
 emerged as a major structuring force in lake ecosystems. For the
 cold-water apex predator lake trout (Salvelinus namaycush), food-web
 structure and morphometry-driven accessibility to nearshore areas in
 summer strongly determine the degree of littoral-pelagic habitat coupling
 across lakes. Much of the evidence for habitat coupling, however, is based
 on stable isotopes of carbon to estimate littoral energy acquisition,
 whereas spatial data directly linking fish movements and foraging
 behaviour in lakes, on which this theory is based – are limited. Here we
 estimated nearshore prey abundance at sites of different thermal
 accessibility and collected stomach content data, which we combined with
 three-dimensional acoustic telemetry positioning and acceleration data to
 directly measure the spatial location of summer foraging movements and
 habitat coupling by lake trout in lakes with and without an offshore prey
 fish. Both study lakes contained higher abundances of nearshore prey fish
 at the most thermally accessible (i.e., steep) sites monitored. Nearshore
 occupancy accounted for a small proportion of lake trout positions in both
 lakes (&lt;5%), although prey fish were present in most (72%) diets
 sampled. High acceleration events indicative of foraging were concentrated
 in steep, thermally accessible nearshore areas in the lake where offshore
 forage fish were absent, but were located further offshore in the lake
 with offshore prey fish. We directly demonstrate that habitat coupling by
 a wild, apex predator is driven by habitat and prey accessibility.
description: These data include acoustic telemetry observations and diet
 relating to lake trout in two small boreal lakes at IISD-Experimental
 Lakes Area, temperature and dissolved oxygen readings for the same lakes,
 and the code used to process and analyse them. 
description: # Spatially-explicit foraging by an apex predator linked to nearshore prey
 and their accessibility in lakes Dataset DOI:
 [https://doi.org/10.5061/dryad.g1jwstr0v](https://doi.org/10.5061/dryad.g1jwstr0v) ## Description of the data and file structure This data set includes the temperature and telemetry data for Lakes 373 and 626 at IISD-Experimental Lakes Area used to analyse lake trout behaviour for the summers of 2021 and 2022. Data are owned by IISD-ELA except for the NRC sunrise and sunset data, which are downloaded from the NRC website. Code was written by Tazi Rodrigues and all authors collected the diet data. ### Files and variables #### File: RBR\_YSI\_TempDO\_L373\_L626\_2021-2022.csv **Description:** Temperature and dissolved oxygen measurements for the study lakes in the study years. ##### Variables * TimeStamp: time of measurement * Lake: location of measurement * Average Depth (m): depth in metres of measurement * Average Temperature (C): average temperature reading over measurement * Dissolved Oxygen (mg/L): average dissolved oxygen reading over measurement * Comments: any additional comments #### File: Nautical\_Twilight\_2021\_NRC.csv **Description:** sunrise and sunset times observed near IISD-ELA in 2021 ##### Variables * Date: date of observation * Nautical Twilight start: time that nautical twilight begins * Sunrise: sunrise time * Sunset: sunset time  * Nautical Twilight end: time that nautical twilight ends #### File: Nautical\_Twilight\_2022\_NRC.csv **Description:** sunrise and sunset times observed near IISD-ELA in 2022 ##### Variables * Date: date of observation * Nautical Twilight start: time that nautical twilight begins * Sunrise: sunrise time * Sunset: sunset time  * Nautical Twilight end: time that nautical twilight ends #### File: Volumes\_2023-03-09.csv **Description:** lake volumes by bathymetric contour ##### Variables * depth: lake depth * Lake: lake identity * monitoring_location_name: location if not just lake identity * activity_start_date: time measurement began * depth_upper: upper depth of lake layer * depth_lower: lower depth of lake layer * area_interval: area of lake layer * volume_interval: volume of lake layer * update_date: date measurements last updated * Volume: 1/10 of the volume of each layer #### File: TempLogs\_L626\_2021-2022.csv **Description:** temperature logs from temperature strings set in Lake 626 at depth increments indicated in the second row ##### Variables * Date Time, GMT-05:00: date and time of measurement * P-01m through to P-11m: temperature at given depth (i.e., P-01 m == 1 m depth) #### File: Diversion\_Fish\_Data.csv **Description:** metadata for fish with telemetry tags ##### Variables * Lake: location of fish * Year: year that fish was tagged * Tag_Num: telemetry tag number * Fish_ID: fish identifier * Tag Snb: serial number of tag * TagType: type of telemetry tag * Frequency: frequency at which tag signals * Sensor: integrated sensors that align with tag identity * Pulse rate: pulse rate of tag * Species: species of fish tagged * Date Tagged: date that fish was tagged * Date_Released: date that fish was released after tagging * Time_Released: time that fish was released after tagging * PIT#: unique identifier for each fish * Total length (mm): total length of each tagged fish, to end of caudal fin * Fork length (mm): length of each tagged fish to fork in caudal fin, if appropriate * Weight (g): weight of tagged fish at time of tagging * Time in Anaesthetic: length of time tagged fish spent in anaesthetic bath * Surgery start: surgery start time * Surgery end: surgery end time * Time for surgery: length of time fish spent in surgery * Sex: sex of tagged fish if known * Current Condition: tag condition - dead, alive, or failed * Date_Dead: date that tag died or failed * Time_Dead: time that tag died or failed * Surgeon: researcher who conducted the surgery * General Comments: any other comments #### File: L373\_L626\_LT\_surgery\_fish\_data\_2022.csv **Description:** metadata for fish tagged in the last year of this study ##### Variables * Lake: location of fish * Year: year that fish was tagged * Tag_Num: telemetry tag number * Fish_ID: fish identifier * Tag Snb: serial number of tag * TagType: type of telemetry tag * Frequency: frequency at which tag signals * Sensor: integrated sensors that align with tag identity * Pulse rate: pulse rate of tag * Species: species of fish tagged * Date Tagged: date that fish was tagged * Date_Released: date that fish was released after tagging * Time_Released: time that fish was released after tagging * PIT#: unique identifier for each fish * Total length (mm): total length of each tagged fish, to end of caudal fin * Fork length (mm): length of each tagged fish to fork in caudal fin, if appropriate * Weight (g): weight of tagged fish at time of tagging * Time in Anaesthetic: length of time tagged fish spent in anaesthetic bath * Surgery start: surgery start time * Surgery end: surgery end time * Time for surgery: length of time fish spent in surgery * Sex: sex of tagged fish if known * Current Condition: tag condition - dead, alive, or failed * Date_Dead: date that tag died or failed * Time_Dead: time that tag died or failed * Surgeon: researcher who conducted the surgery * General Comments: any other comments #### File: all37303.csv **Description:** VPS readings from Lake 373. All files that begin with "all" follow the same variable format. Characters 4-6 of each file name indicate the lake name. ##### Variables * Transmitter: human-assigned name for transmitter * FullId: code-assigned name for transmitter * Id: short form of FullId * Time: time detected * X: x coordinate * Y: y coordinate * Z: z coordinate * Longitude: longitude of detection  * Latitude: latitude of detection * Depth: depth of detection  * Station: NA * HPE: horizontal position error * HPEm: horizontal position error (m) * RMSE: root mean squared error * TempData: temperature data, where sensor was integrated (NA) * DepthData: depth data, where sensor was integrated * AccelData: accelerometer data, where sensor was integrated * RxDetected: receivers that detected signal * nRxDetected: number of receivers that detected signal * RxUsed: receivers that were used to triangulate position * nRxUsed: number of receivers that were used to triangulate position #### File: all37304.csv **Description:** VPS readings from Lake 373. All files that begin with "all" follow the same variable format. Characters 4-6 of each file name indicate the lake name. ##### Variables * Transmitter: human-assigned name for transmitter * FullId: code-assigned name for transmitter * Id: short form of FullId * Time: time detected * X: x coordinate * Y: y coordinate * Z: z coordinate * Longitude: longitude of detection  * Latitude: latitude of detection * Depth: depth of detection  * Station: NA * HPE: horizontal position error * HPEm: horizontal position error (m) * RMSE: root mean squared error * TempData: temperature data, where sensor was integrated (NA) * DepthData: depth data, where sensor was integrated * AccelData: accelerometer data, where sensor was integrated * RxDetected: receivers that detected signal * nRxDetected: number of receivers that detected signal * RxUsed: receivers that were used to triangulate position * nRxUsed: number of receivers that were used to triangulate position #### File: all37305.csv **Description:** VPS readings from Lake 373. All files that begin with "all" follow the same variable format. Characters 4-6 of each file name indicate the lake name. ##### Variables * Transmitter: human-assigned name for transmitter * FullId: code-assigned name for transmitter * Id: short form of FullId * Time: time detected * X: x coordinate * Y: y coordinate * Z: z coordinate * Longitude: longitude of detection  * Latitude: latitude of detection * Depth: depth of detection  * Station: NA * HPE: horizontal position error * HPEm: horizontal position error (m) * RMSE: root mean squared error * TempData: temperature data, where sensor was integrated (NA) * DepthData: depth data, where sensor was integrated * AccelData: accelerometer data, where sensor was integrated * RxDetected: receivers that detected signal * nRxDetected: number of receivers that detected signal * RxUsed: receivers that were used to triangulate position * nRxUsed: number of receivers that were used to triangulate position #### File: all62601.csv **Description:** VPS readings from Lake 626. All files that begin with "all" follow the same variable format. Characters 4-6 of each file name indicate the lake name. ##### Variables * Transmitter: human-assigned name for transmitter * FullId: code-assigned name for transmitter * Id: short form of FullId * Time: time detected * X: x coordinate * Y: y coordinate * Z: z coordinate * Longitude: longitude of detection  * Latitude: latitude of detection * Depth: depth of detection  * Station: NA * HPE: horizontal position error * HPEm: horizontal position error (m) * RMSE: root mean squared error * TempData: temperature data, where sensor was integrated (NA) * DepthData: depth data, where sensor was integrated * AccelData: accelerometer data, where sensor was integrated * RxDetected: receivers that detected signal * nRxDetected: number of receivers that detected signal * RxUsed: receivers that were used to triangulate position * nRxUsed: number of receivers that were used to triangulate position #### File: all62602.csv **Description:** VPS readings from Lake 626. All files that begin with "all" follow the same variable format. Characters 4-6 of each file name indicate the lake name. ##### Variables * Transmitter: human-assigned name for transmitter * FullId: code-assigned name for transmitter * Id: short form of FullId * Time: time detected * X: x coordinate * Y: y coordinate * Z: z coordinate * Longitude: longitude of detection  * Latitude: latitude of detection * Depth: depth of detection  * Station: NA * HPE: horizontal position error * HPEm: horizontal position error (m) * RMSE: root mean squared error * TempData: temperature data, where sensor was integrated (NA) * DepthData: depth data, where sensor was integrated * AccelData: accelerometer data, where sensor was integrated * RxDetected: receivers that detected signal * nRxDetected: number of receivers that detected signal * RxUsed: receivers that were used to triangulate position * nRxUsed: number of receivers that were used to triangulate position #### File: stations373.csv **Description:** acoustic telemetry receiver station metadata ##### Variables * Serial: serial number of receiver * StationName: human-assigned station name * Start: date of deployment * End: date receiver pulled, if applicable * Latitude: latitude of receiver * Longitude: longitude of receiver * Depth: depth of receiver * X: x coordinate used for positioning * Y: y coordinate used for positioning  * Z: depth reading used for positioning #### File: stations626.csv **Description:** acoustic telemetry receiver station metadata ##### Variables * Serial: serial number of receiver * StationName: human-assigned station name * Start: date of deployment * End: date receiver pulled, if applicable * Latitude: latitude of receiver * Longitude: longitude of receiver * Depth: depth of receiver * X: x coordinate used for positioning * Y: y coordinate used for positioning  * Z: depth reading used for positioning #### File: VR2\_Data\_up\_to\_2022\_TR\_20240319.csv **Description:** processed telemetry detections from VR2 receivers ##### Variables * Transmitter: transmitter ID for tagged fish * SensorType: type of sensor reading, if applicable * Slope: slope for calculating readings in meaningful units * Intercept: intercept for calculating readings in meaningful units * Sensor.Value: value transmitted by sensor * Sensor.Unit: unit that applies to sensor type * DateTime: date and time of detection * diff: difference in seconds from previous reading * FISH: short ID from transmitter * True.Sensor.Value: calibrated sensor value #### File: L626\_VR2\_Data\_Processed\_2024.csv **Description:** processed telemetry detections from VR2 receivers ##### Variables * Transmitter: transmitter ID for tagged fish * SensorType: type of sensor reading, if applicable * Slope: slope for calculating readings in meaningful units * Intercept: intercept for calculating readings in meaningful units * Sensor.Value: value transmitted by sensor * Sensor.Unit: unit that applies to sensor type * DateTime: date and time of detection * diff: difference in seconds from previous reading * FISH: short ID from transmitter * True.Sensor.Value: calibrated sensor value #### File: Minnow\_Trap\_Collections.xlsx\_-\_Subsampling.csv **Description:** minnow trap data for traps where subsampling occurred ##### Variables * Lake: where the minnow traps were located * Date: date of collection * Crew: initials of people involved in field sampling that day * Access: one of low, medium, or high related to thermal accessibility * Depth: depth of minnow trap * Contour: bathymetric contour at which minnow trap was set * Species: species code * Total Number: tallied number of fish + 30 * Tally (alive): number of fish after 30 that were alive, of that species and trap * Tally (dead): number of fish that were dead of that species and trap * Notes: any extra comments #### **File: Minnow\_Trap\_Collections\_-\_Fall\_Data\_Entry\_TR.csv** **Description:** minnow trap metadata  ##### Variables * Date Set: date minnow trap was set * Lake: where minnow trap was set * Access: thermal accessibility of minnow trap set (low, medium, or high) * Contour: bathymetric contour where minnow trap was set * Set: which day of the three consecutive days the minnow trap was set * Time Set: time that minnow trap was set * Date Collected: date that minnow trap was collected * Time Collected: time that minnow trap was collected #### **File: Lavage\_Weigh\_Sheet\_Oikos.csv** **Description:** weights of diet items from gastric lavage ##### Variables * Lake: where fish was caught * Date: which date fish was caught * PIT: unique identifier for each fish * Sample: sample number * Sample ID: lake and sample number * Taxon: identification of lavage item * Tin ID: letter written on tin to keep track in oven * Tin Mass: how much the tin weighed * DateTime In: when the tin was put in oven * Wet + Tin (g): weight of tin and wet sample * DateTime Out: when the tin was taken from oven * Dry + Tin (g): weight of tin and dry sample * Notes: extra comments * Number: number of prey items * SecondTin: dry weight of tin, if taken separately #### File: L373\_L626\_LT\_lavage\_fish\_data\_2021-22.csv **Description:** metadata for fish included in gastric lavage sampling ##### Variables * LAKE: lake where sample was taken * SPECIES: species of fish from which sample was taken * sample ID: unique number for sample * DATE: date that sample was taken * YEAR: year that sample was taken * CREW: initials of people involved in field work that day * PIT: unique identifier for fish * WEIGHT (g): mass of fish * Total lemgth (mm): length of fish to tip of tail * Fork length (mm):  length of fish to fork in caudal fin * SEX: sex of fish if known * GUT CONTENT DESCRIP: field comments regarding gut contents * MULTIPLE?: whether fish had already been sampled * COMMENTS: extra comments ##### File: Minnow\_Trap\_Collections.xlsx\_-*Animals*(5).csv **Description:** measurements for animals collected in minnow traps ##### Variables * Lake: lake where sample was taken * Date: date on which sample was taken * Crew: people involved in field work that day * Access: thermal accessibility (low, medium, high) * Depth: depth at which minnow trap was set * Contour: bathymetric contour where minnow trap was set * Species: fish species * Mass: mass of each individual fish * Standard Length: standard length of individual fish * Fork Length: length to fork in caudal fin of individual fish, if appropriate * Sex: sex of individual fish, if known * Dead: whether or not the fish was dead at time of sampling * Notes: extra comments * SIA: whether or not the fish was taken for stable isotope analysis * Confirmed: if data input was triple-checked ##### File: 01-library-oikos.Rmd **Description:** Establishes functions that are used in the remaining R Markdown files. ##### File: 02-temp-do-oikos.Rmd **Description:** Reads and processes temperature and dissolved oxygen files. ##### File: 03-slope-calculations-oikos.Rmd **Description:** Calculates slope values for the lake rasters. ##### File: 04-nearshore-prey-oikos.Rmd **Description:** Processing and analysis of data associated with the minnow trap data collection. ##### File: 05-lavage-oikos.Rmd **Description:** Processing and analysis of data associated with gastric lavage. ##### File: 06-read-vps-oikos.Rmd **Description:** Reads and processes spatial lake trout movement data. ##### File: 07-read-vr2-oikos.Rmd **Description:** Reads and processes detection data for lake trout. ##### File: 08-spatial-processing-oikos.Rmd **Description:** Spatial processing of spatial lake trout movement data, including assigning slope values and distance to shore to each position. ##### File: 09-hyp1-oikos.Rmd **Description:** Produces Figure 1 of associated paper and performs kernel-based calculations. ##### File: 10-hyp2-hyp3-oikos.Rmd **Description:** Analysis of the effect of slope on lake trout movement patterns. ## Code/software To view these data, use the associated R Markdown files using the programming language R. Scripts should be read in numbered order from 1-10. Bathymetric data used in these scripts can be found at the following location:  IISD Experimental Lakes Area. 2022. IISD Experimental Lakes Area: Bathymetry Data Package, 1968-2022 ver 3. Environmental Data Initiative. [https://doi.org/10.6073/pasta/e9898c78448cbbe544057e689d3c06df](https://doi.org/10.6073/pasta/e9898c78448cbbe544057e689d3c06df).