Data from: Parasite transmission stage abundance varies in lakes over time and space
Data files
Aug 22, 2024 version files 11.92 MB
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BishopMixingDepthCV.csv
2.18 KB
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Cedar_Basin_Nearshore.csv
4.60 MB
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CedarMixingDepthCV.csv
2.14 KB
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CrookedWMixingDepthCV.csv
2.28 KB
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CV_Cedar_LocationsDates.csv
9.04 KB
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CV_Depth_All_Parasites.csv
6.02 KB
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CV_LilAp_LocationsDates.csv
8.90 KB
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CV_Walsh_LocationsDates.csv
10.52 KB
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FeeP.csv
1.97 KB
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LilApMixingDepthCV.csv
2.11 KB
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MillMixingDepthCV.csv
2.04 KB
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README.md
26.68 KB
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SporeConcentrationsByDepthAll.csv
149.02 KB
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SporeConcentrationsByDepthLocations.csv
273.16 KB
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SupportingInformationSporeViability.csv
872 B
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Walsh_Basin_Nearshore.csv
4.54 MB
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Walsh_Basin_Thermal_Profile_2021.csv
2.29 MB
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WalshMixingDepthCV.csv
3 KB
Abstract
Environmentally transmitted parasites produce transmission stages that can remain viable and infective for extended periods of time in the environment where susceptible hosts may encounter them. Although many parasites have this mode of transmission, the abundance and distribution of environmental transmission stages have largely been overlooked, especially in aquatic habitats. Without empirical data to characterize spatial and temporal dynamics of parasite transmission stages in the environment, we might make incorrect assumptions about host-parasite contact rates. For aquatic environments, seasonal habitat structure driven by thermal stratification has been hypothesized to affect the patchiness of transmission stages within the water column, leading to uneven exposure risk to hosts. In this study, we quantified transmission stage concentrations of five common parasites of Daphnia spp. and Ceriodaphnia dubia at every meter of the water column at the deep basin of six lakes in southeastern Michigan every two weeks from June to November 2021. We found that transmission stage concentration varied by orders of magnitude over time and with depth. We investigated several possible drivers of these spatial and temporal patterns. For instance, our results suggest that greater mixing depth decreased transmission stage vertical patchiness within the water column of lakes with lower Fee’s p values. However, horizontal spore patchiness across a lake was not correlated with the nearshore-offshore gradient of our study lakes. Overall, the results of our study show that parasite transmission stage concentrations have spatial and temporal dynamics that could affect disease dynamics within highly structured aquatic environments.
README: Parasite transmission stage abundance varies in lakes over time and space
https://doi.org/10.5061/dryad.s7h44j1gb
Description of the data and file structure
Davenport et al. study on parasite environmental transmission stage distribution in lakes
The files include all the data and code used to create the figures in the Davenport et al. manuscript. Data collection was led by Elizabeth Davenport and supported by Marcin Dziuba, Logan Jacobson, Siobhan Calhoun, and Kira Monell. Elizabeth Davenport and Meghan Duffy of the University of Michigan created figures.
Description of the data and file structure
1. scripts: this contains the code used to create figures.
2. data: this contains the data collected during the study.
Spore Concentrations and Outbreak Data
Data and code for 2021 field study led by Elizabeth Davenport
Citation: Parasite transmission stage abundance varies in lakes over time and space
Authors: Elizabeth S. Davenport 1*, Marcin K. Dziuba 1, Logan E. Jacobson 1, Siobhan K. Calhoun 1, Kira J. Monell 1, and Meghan A. Duffy 1
1 Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
Contact: * Author responsible for writing code related to analyses and figures: davenpe@umich.edu
Date: November 2023
_______________________________________________________________________________________________________________
DATA
BishopMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. MixingDepth = the deepest meter that is being mixed.
CedarMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. MixingDepth = the deepest meter that is being mixed.
CrookedWMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. MixingDepth = the deepest meter that is being mixed.
LilApMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. MixingDepth = the deepest meter that is being mixed.
MillMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. MixingDepth = the deepest meter that is being mixed.
WalshMixingDepthCV.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. Mixing Depth = the deepest meter that is being mixed.
Cedar_Basin_Nearshore.csv: this data file contains the temperature data collected from thermistor chains deployed at the deep basin and at a nearshore location. Water temperature at 1-meter intervals was measured every 5 minutes. The temperature difference was calculated using the temperature data collected at the same depth at the deep basin and nearshore location. Date = datetime of temperature measurements. B1 = temperature recorded at 1 meter at the deep basin. B2 = temperature recorded at 2 meters at the deep basin. B3 = temperature recorded at 3 meters at the deep basin. B4 = temperature recorded at 4 meters at the deep basin. B5 = temperature recorded at 5 meters at the deep basin. Bsurf = temperature recorded at 0 meters at the deep basin. NS1 = temperature recorded at 1 meter nearshore. NS2 = temperature recorded at 2 meters nearshore. NS3 = temperature recorded at 3 meters nearshore. NS3 = temperature recorded at 3 meter2 nearshore. NSSurf = temperature recorded at 0 meters nearshore. Diff.1 = temperature difference between deep basin and nearshore at 1 meter. Diff.2 = temperature difference between deep basin and nearshore at 2 meters. Diff.3 = temperature difference between deep basin and nearshore at 3 meters.
Walsh_Basin_Nearshore.csv: this data file contains the temperature data collected from thermistor chains deployed at the deep basin and at a nearshore location. Water temperature at 1-meter intervals was measured every 5 minutes. The temperature difference was calculated using the temperature data collected at the same depth at the deep basin and nearshore location. Date = datetime of temperature measurements. B1 = temperature recorded at 1 meter at the deep basin. B2 = temperature recorded at 2 meters at the deep basin. B3 = temperature recorded at 3 meters at the deep basin. B4 = temperature recorded at 4 meters at the deep basin. B5 = temperature recorded at 5 meters at the deep basin. Bsurf = temperature recorded at 0 meters at the deep basin. NS1 = temperature recorded at 1 meter nearshore. NS2 = temperature recorded at 2 meters nearshore. NS3 = temperature recorded at 3 meters nearshore. NS3 = temperature recorded at 3 meter2 nearshore. NSSurf = temperature recorded at 0 meters nearshore. Diff.1 = temperature difference between deep basin and nearshore at 1 meter. Diff.2 = temperature difference between deep basin and nearshore at 2 meters. Diff.3 = temperature difference between deep basin and nearshore at 3 meters.
CV_Cedar_LocationsDates.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. Locations = the location sampled within the lake (deep basin, intermediate location, nearshore location).
CV_LilAp_LocationsDates.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. Location = the location sampled within the lake (deep basin, intermediate location, nearshore location).
CV_Walsh_LocationsDates.csv: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake. Parasite = name of the parasite species quantified. Round = temporal sampling round. Lake = name of the lake sampled. CV = coefficient of variation. Location = the location sampled within the lake (deep basin, intermediate location, nearshore location).
CV_Depth_All_Parasites.csv: this data file contains the coefficient of variation of the spore concentration at specific depths through time. Lake = name of the lake sampled. Parasite = name of the parasite species quantified. Depth = meter of the water column sampled. CV = coefficient of variation of spore concentration measuring variation over time at a specific depth.
SporeConcentrationsByDepthAll.csv: this data file contains the spore concentration for all five parasites at every meter of the water column at the deep basin of our six study lakes. Sample = unique sample ID. Round = sampling round number. Depth = meter of the water column sampled. Date = date of sampling. Lake = name of the lake sampled. Parasite = name of the parasite species quantified. Concentration = number of spores per liter. ConcentrationLog10Plus1 = log of the number of spores per liter plus one.
SporeConcentrationsByDepthLocations.csv: this data file contains the spore concentration for all five parasites at every meter of the water column at all locations across our six study lakes. Sample = unique sample ID. Round = sampling round number. Depth = meter of the water column sampled. Date = date of sampling. Lake = name of the lake sampled. Location = specific location within the lake being sampled (deep basin, intermediate location, and nearshore location). Parasite = name of the parasite species quantified. Concentration = number of spores per liter. ConcentrationLog10Plus1 = log of the number of spores per liter plus one.
Walsh_Basin_Thermal_Profile_2021.csv: this data file contains the temperature data collected from the thermistor chains deployed at the deep basin of Walsh Lake. Water temperature at 1-meter intervals was measured every 5 minutes. Date = datetime of temperature measurements. B1 = temperature recorded at 1 meter at the deep basin. B2 = temperature recorded at 2 meters at the deep basin. B3 = temperature recorded at 3 meters at the deep basin. B4 = temperature recorded at 4 meters at the deep basin. B5 = temperature recorded at 5 meters at the deep basin. Surface = temperature recorded at 0 meters at the deep basin.
SupportingInformationSporeViability.csv: this data file contains the concentration of Metschnikowia bicuspidata spores (copies/uL) in samples that were assigned to one of three treatments (controls, frozen, or UV-exposure) and the percent infection when Daphnia dentifera were exposed to spores from these three treatments. SampleID = individual sample identifier. Treatment = treatment of spores (control, froze, or UV). Concentration = number of spores (copies/uL). PercentInfection = percent of exposed Daphnia dentifera that becomes infected with Metschnikowia bicuspidata.
FeeP.csv: this data file contains the Fee's p value for each lake for every sampling date. When lakes were fully mixing, Fee's p could not be calculated, so these values are represented with NAs. Date = sampling date. Lake = lake name. FeeP = Fee's p value.
Files and variables
File: BishopMixingDepthCV.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data.
Variables
- Parasite: name of the parasite species quantified
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: CedarMixingDepthCV.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data.
Variables
- Parasite: name of the parasite species quantified
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: CrookedWMixingDepthCV.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data.
Variables
- Parasite: name of the parasite species quantified
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: CV_Cedar_LocationsDates.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake.
Variables
- Parasite = name of the parasite species quantified.
- Round = temporal sampling round.
- Lake = name of the lake sampled.
- CV = coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- Locations = the location sampled within the lake (deep basin, intermediate location, nearshore location)
File: CV_LilAp_LocationsDates.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake.
Variables
- Parasite = name of the parasite species quantified.
- Round = temporal sampling round.
- Lake = name of the lake sampled.
- CV = coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- Locations = the location sampled within the lake (deep basin, intermediate location, nearshore location)
File: CV_Depth_All_Parasites.csv
Description: this data file contains the coefficient of variation of the spore concentration at specific depths through time
Variables
- Lake = name of the lake sampled.
- Parasite = name of the parasite species quantified.
- Depth = meter of the water column sampled.
- CV = coefficient of variation of spore concentration measuring variation over time at a specific depth; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
File: FeeP.csv
Description: this data file contains the Fee's p value for each lake for every sampling date. When lakes were fully mixing, Fee's p could not be calculated, so these values are represented with NAs.
Variables
- Date = sampling date.
- Lake = lake name.
- FeeP = Fee's p value; NA values refer to dates on which the lakes were turning over and there was not a thermocline, which would be factored into the calculation for Fee's p.
File: CV_Walsh_LocationsDates.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column at multiple locations across the lake
Variables
- Parasite = name of the parasite species quantified.
- Round = temporal sampling round.
- Lake = name of the lake sampled.
- CV = coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- Location = the location sampled within the lake (deep basin, intermediate location, nearshore location).
File: LilApMixingDepthCV.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data.
Variables
- Parasite: name of the parasite species quantified
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: MillMixingDepthCV.csv
Description: this data file contains the coefficient of variation of the spore concentration vertically through the water column and the depth of mixing through the water column based on temperature data.
Variables
- Parasite: name of the parasite species quantified
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: SupportingInformationSporeViability.csv
Description: this data file contains the concentration of Metschnikowia bicuspidata spores (copies/uL) in samples that were assigned to one of three treatments (controls, frozen, or UV-exposure) and the percent infection when Daphnia dentifera were exposed to spores from these three treatments.
Variables
- SampleID = individual sample identifier.
- Treatment = treatment of spores (control, froze, or UV).
- Concentration = number of spores (copies/uL).
- PercentInfection = percent of exposed Daphnia dentifera that becomes infected with Metschnikowia bicuspidata.
File: SporeConcentrationsByDepthAll.csv
Description: this data file contains the spore concentration for all five parasites at every meter of the water column at the deep basin of our six study lakes.
Variables
- Sample = unique sample ID.
- Round = sampling round number.
- Depth = meter of the water column sampled.
- Date = date of sampling.
- Lake = name of the lake sampled.
- Parasite = name of the parasite species quantified.
- Concentration = number of spores per liter.
- ConcentrationLog10Plus1 = log of the number of spores per liter plus one.
File: SporeConcentrationsByDepthLocations.csv
Description: this data file contains the spore concentration for all five parasites at every meter of the water column at all locations across our six study lakes.
Variables
- Sample = unique sample ID.
- Round = sampling round number.
- Depth = meter of the water column sampled.
- Date = date of sampling.
- Lake = name of the lake sampled.
- Location = specific location within the lake being sampled (deep basin, intermediate location, and nearshore location).
- Parasite = name of the parasite species quantified.
- Concentration = number of spores per liter.
- ConcentrationLog10Plus1 = log of the number of spores per liter plus one.
File: Walsh_Basin_Thermal_Profile_2021.csv
Description: this data file contains the temperature data collected from the thermistor chains deployed at the deep basin of Walsh Lake. Water temperature at 1-meter intervals was measured every 5 minutes.
Variables
- Date = datetime of temperature measurements.
- B1 = temperature recorded at 1 meter at the deep basin.
- B2 = temperature recorded at 2 meters at the deep basin.
- B3 = temperature recorded at 3 meters at the deep basin.
- B4 = temperature recorded at 4 meters at the deep basin.
- B5 = temperature recorded at 5 meters at the deep basin.
- Surface = temperature recorded at 0 meters at the deep basin; NA values indicate dates we did not track temperature at this depth. We started tracking temperature at 0 meters about halfway through the sampling period.
File: WalshMixingDepthCV.csv
Description:
Variables
- Parasite: name of the parasite species quantified
- Date: date of sampling
- Round: temporal sampling round
- Lake: name of the lake sampled
- CV: coefficient of variation; NA values refer to dates on which the spore concentrations were zero throughout the water column, which prevented calculation of a coefficient of variation.
- MixingDepth: the deepest meter that is being mixed
File: Cedar_Basin_Nearshore.csv
Description: this data file contains the temperature data collected from thermistor chains deployed at the deep basin and at a nearshore location. Water temperature at 1-meter intervals was measured every 5 minutes. The temperature difference was calculated using the temperature data collected at the same depth at the deep basin and nearshore location.
Variables
- Date = datetime of temperature measurements.
- B1 = temperature recorded at 1 meter at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B2 = temperature recorded at 2 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B3 = temperature recorded at 3 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B4 = temperature recorded at 4 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B5 = temperature recorded at 5 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- Bsurf = temperature recorded at 0 meters at the deep basin; NA values indicate dates we did not track temperature at this depth or dates when we temporarily removed the data loggers from the lake to download data. We started tracking temperature at 0 meters about halfway through the sampling period.
- NS1 = temperature recorded at 1 meter nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS2 = temperature recorded at 2 meters nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS3 = temperature recorded at 3 meters nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS3 = temperature recorded at 3 meter2 nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NSSurf = temperature recorded at 0 meters nearshore; NA values indicate dates we did not track temperature at this depth. We started tracking temperature at 0 meters about halfway through the sampling period.
- Diff.1 = temperature difference between deep basin and nearshore at 1 meter. NA values indicate dates when we temporarily removed the data loggers from the lake to download data, so no temperature difference could be calculated.
- Diff.2 = temperature difference between deep basin and nearshore at 2 meters. NA values indicate dates when we temporarily removed the data loggers from the lake to download data, so no temperature difference could be calculated.
- Diff.3 = temperature difference between deep basin and nearshore at 3 meters, so no temperature difference could be calculated.
File: Walsh_Basin_Nearshore.csv
Description: this data file contains the temperature data collected from thermistor chains deployed at the deep basin and at a nearshore location. Water temperature at 1-meter intervals was measured every 5 minutes. The temperature difference was calculated using the temperature data collected at the same depth at the deep basin and nearshore location.
Variables
- Date = datetime of temperature measurements.
- B1 = temperature recorded at 1 meter at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B2 = temperature recorded at 2 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B3 = temperature recorded at 3 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B4 = temperature recorded at 4 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- B5 = temperature recorded at 5 meters at the deep basin. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- Bsurf = temperature recorded at 0 meters at the deep basin; NA values indicate dates we did not track temperature at this depth. We started tracking temperature at 0 meters about halfway through the sampling period.
- NS1 = temperature recorded at 1 meter nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS2 = temperature recorded at 2 meters nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS3 = temperature recorded at 3 meters nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NS3 = temperature recorded at 3 meter2 nearshore. NA values indicate dates when we temporarily removed the data loggers from the lake to download data.
- NSSurf = temperature recorded at 0 meters nearshore; NA values indicate dates we did not track temperature at this depth. We started tracking temperature at 0 meters about halfway through the sampling period.
- Diff.1 = temperature difference between deep basin and nearshore at 1 meter. NA values indicate dates when we temporarily removed the data loggers from the lake to download data, so no temperature difference could be calculated.
- Diff.2 = temperature difference between deep basin and nearshore at 2 meters. NA values indicate dates when we temporarily removed the data loggers from the lake to download data, so no temperature difference could be calculated.
- Diff.3 = temperature difference between deep basin and nearshore at 3 meters. NA values indicate dates when we temporarily removed the data loggers from the lake to download data, so no temperature difference could be calculated.
Code/software
We used the R statistical environment with R version 3.6.2 (R Core Team). We conducted statistical analyses and created plots using packages rstatix (Kassambara 2023), ggplot2 (Wickham 2016), tidyverse (Wickham et al. 2019), dyplr (Wickham et al. 2021), lubridate (Grolemund and Wickham 2011), scales (Wickham and Seidel 2019), ggpubr (Kassambara 2020), and reshape2 (Wickham 2007).