Data and code from: Environmental tolerances and habitat association of three Procambarus crayfish in Texas

Walker, Andrew1; Banta, Joshua 1 ; Shartau, Ryan2

Published Aug 05, 2026 on Dryad. https://doi.org/10.5061/dryad.q2bvq841t

Data files

Aug 05, 2026 version files 947.66 KB

Crayfish_Dryad_Analysis_Code.zip

89.03 KB
Crayfish_Dryad_Data.zip

837.62 KB
README.md

21 KB

Abstract

This dataset contains field-survey, habitat, distribution, and laboratory physiological data for four crayfish species in Texas: Procambarus acutus, P. fayettei, P. nueces, and P. texanus. Field data include surveyed sites, species-occurrence records, geographic coordinates, and physicochemical habitat measurements used in species-specific logistic-regression and AICc model-selection analyses. Laboratory data include repeated critical thermal maximum measurements following acclimation at 24, 27, and 30 °C; percent dissolved oxygen at loss of equilibrium during hypoxia trials; repeated oxygen-consumption measurements used to estimate standard metabolic rate, maximum metabolic rate, and aerobic scope; trial-level measurements used to estimate critical oxygen tension using segmented regression; and pH at loss of equilibrium during progressive acidification. The deposit also includes R scripts that reproduce data cleaning, derived variables, mixed-effects and fixed-effects analyses, habitat models, diagnostic outputs, maps, figures, and publication tables.

Overview

This Dryad deposit contains field-survey, habitat, distribution, laboratory physiological, and R analysis materials for four Texas crayfish species: Procambarus acutus, P. fayettei, P. nueces, and P. texanus. The study evaluated habitat associations and physiological responses to temperature, hypoxia, metabolism, critical oxygen tension, and progressive acidification.

There is no associated journal manuscript or article at the time of this Dryad submission. The project is associated with a technical report.

The deposit is organized as two separate ZIP files uploaded directly to Dryad:

Crayfish_Dryad_Data.zip — primary data, open-format CSV copies, metadata, a data dictionary, and methods documentation.
Crayfish_Dryad_Analysis_Code.zip — R scripts, package requirements, and reproduction instructions.

What each ZIP file creates when extracted

Extract both ZIP files into the same parent working directory. Each archive creates a different set of folders and files.

`Crayfish_Dryad_Data.zip`

This ZIP creates:

data/ — the seven script-compatible primary data files and their open-format CSV equivalents.
documentation/ — the dry-site missing-value explanation and the cell-level zero-to-NA correction log.

It also places the following files at the extraction root:

README.md
DATA_DICTIONARY.csv
DRYAD_METADATA.md
DRYAD_UPLOAD_INSTRUCTIONS.md
METHODS_SUMMARY.md
FILE_MANIFEST.csv
SHA256SUMS.txt

`Crayfish_Dryad_Analysis_Code.zip`

This ZIP creates:

R/ — all R analysis and plotting scripts, including unified_style.R.

It also places the following files at the extraction root:

README.md
RUN_ORDER.md
R_PACKAGE_REQUIREMENTS.md
CC0_NOTICE.txt
FILE_MANIFEST.csv
SHA256SUMS.txt

After both ZIP files are extracted into the same parent directory, the main project folders should be:

data/
documentation/
R/

The same README is included in both ZIP files so that either package can be understood independently. Both ZIP files are intended for direct publication in Dryad under Dryad's CC0 waiver. No Zenodo deposit is intended because the funding agency does not permit deposition in Zenodo.

Authors

Joshua Banta — principal investigator and corresponding author
Ryan Shartau — co-principal investigator
Jared Dickson
Andrew Walker

Complete affiliations, ORCID identifiers, and the corresponding-author email are supplied through the Dryad metadata form.

Data package

Primary files and open-format equivalents

The data/ directory contains the following seven script-compatible primary files:

AW Crawfish trapping 24-25.xlsx
crayfish map.xlsx
corrected CTmax copy.csv
hypoxia_ANCOVA copy.csv
All MO2 values.xlsx
Fixed Pcrit values.xlsx
pH mass plot 7-24.xlsx

Open-format CSV equivalents are provided as follows:

Open-format file	Corresponding primary file or worksheet
`field_habitat_all_sites.csv`	`AW Crawfish trapping 24-25.xlsx`, worksheet `All sites`
`field_habitat_capture_sites.csv`	`AW Crawfish trapping 24-25.xlsx`, worksheet `Capture sites`
`mapping_surveyed_sites.csv`	`crayfish map.xlsx`, worksheet `surveyed sites`
`mapping_occurrence_sites.csv`	`crayfish map.xlsx`, worksheet `occurrence sites`
`ctmax_trials.csv`	`corrected CTmax copy.csv`
`hypoxia_loss_of_equilibrium.csv`	`hypoxia_ANCOVA copy.csv`
`metabolic_rate_measurements.csv`	`All MO2 values.xlsx`, first worksheet
`pcrit_respirometry_measurements.csv`	`Fixed Pcrit values.xlsx`, first worksheet
`ph_loss_of_equilibrium.csv`	`pH mass plot 7-24.xlsx`, first worksheet

The CSV equivalents contain the same scientific variables as the corresponding primary files. Variable definitions below therefore apply to both versions.

Missing-value conventions

Empty cells have been retained where replacing them with text such as n/a would change column types or interfere with the supplied R scripts. An empty cell never represents a measured numerical zero unless an explicit 0 is present.

Field habitat files: Empty environmental-measurement cells mean that a measurement was unavailable or not recorded. At dry sites, water-quality measurements could not be obtained, so pH, dissolved oxygen, conductivity, resistivity, total dissolved solids, salinity, turbidity, and water temperature are blank rather than zero. Empty trap, capture, species, location, date, time, or notes fields mean that no value was entered in the source record; they should not automatically be interpreted as zero. Text entries such as NA, na, None, and none were retained as originally recorded.
CTmax files: Four records have empty Sex and Mass_g values because those attributes were not recorded. The records are retained, but the model scripts use complete cases for analyses requiring those variables.
Hypoxia files: Empty O2_LOE and hours cells identify trials in which the animal did not experience loss of equilibrium, so neither an LOE endpoint nor an associated elapsed time was available. These blanks are not zero values and are excluded from the reported ANCOVA.
Mapping, metabolic-rate, Pcrit-respirometry, and pH-loss-of-equilibrium files: The deposited tabular records contain no empty scientific-data cells.

The field-specific dry-site correction is documented in:

documentation/DRY_SITE_MISSING_VALUE_NOTE.md
documentation/DRY_SITE_ZERO_TO_NA_LOG.csv

Geographic coordinates

Latitude and longitude are the original field coordinates recorded by the project and have not been generalized or rounded. Coordinates are in World Geodetic System 1984 (WGS84) geographic coordinates, EPSG:4326. Free-text field notes are retained.

Variable definitions

Field habitat data

Files: AW Crawfish trapping 24-25.xlsx, field_habitat_all_sites.csv, and field_habitat_capture_sites.csv.

Variable	Definition	Units or coding
`Site ID`	Identifier assigned to the sampled field site.	Text identifier.
`Date`	Date of the field visit.	Calendar date.
`Quarter/year`	Field-season or reporting-period label recorded by the project.	Text retained as recorded.
`# traps set`	Number of crayfish traps deployed at the site.	Count.
`crayfish caught`	Indicator of whether crayfish were recorded as captured.	Primarily `yes`, `no`, or source-recorded `NA`.
`amount caught`	Number of crayfish recorded in the `All sites` worksheet.	Count retained as recorded.
`# caught`	Number of crayfish recorded in the `Capture sites` worksheet.	Count retained as recorded.
`Species`	Crayfish species or identification recorded for the visit.	Scientific name or source-recorded text.
`Lat`	Latitude of the field site.	Decimal degrees, WGS84.
`Long`	Longitude of the field site.	Decimal degrees, WGS84.
`County`	Texas county containing the site.	County name.
`pH`	Acidity or alkalinity of the water.	pH units.
`MVpH`	Millivolt output associated with the pH measurement.	Millivolts (mV).
`ORP`	Oxidation-reduction potential.	Millivolts (mV).
`%DO`	Dissolved oxygen as percent saturation.	Percent (%).
`ppm DO`	Dissolved oxygen concentration.	Parts per million (ppm).
`µs/cm`	Specific electrical conductivity.	microsiemens per centimeter (µS/cm).
`Ω/cm`	Electrical resistivity.	Ohm-centimeters (Ω·cm), as recorded.
`ppm Tds`	Total dissolved solids concentration.	Parts per million (ppm).
`PSU`	Salinity expressed in practical salinity units.	Practical salinity units (PSU).
`FNU`	Turbidity expressed in formazin nephelometric units.	FNU.
`˚C`	Water temperature.	Degrees Celsius (°C).
`Ground Temp`	Ground or sediment temperature.	Degrees Celsius (°C).
`Time set`	Local time at which traps were set.	Local time.
`Time retrieved`	Local time at which traps were retrieved.	Local time.
`Notes`	Free-text field observations.	Text.

Distribution and mapping data

Files: crayfish map.xlsx, mapping_surveyed_sites.csv, and mapping_occurrence_sites.csv.

Variable	Definition	Units or coding
`Species`	Target crayfish species recorded at an occurrence site.	Scientific name. Present only in the occurrence-site data.
`Lat`	Latitude of the surveyed or occurrence site.	Decimal degrees, WGS84.
`Long`	Longitude of the surveyed or occurrence site.	Decimal degrees, WGS84.

Critical thermal maximum data

Files: corrected CTmax copy.csv and ctmax_trials.csv.

Variable	Definition	Units or coding
`Species`	Crayfish species.	Scientific name.
`IndividualID`	Identifier for the individual crayfish.	Text identifier; combined with species in the scripts to create `SubjectID`.
`AcclimTemp`	Temperature at which the individual was acclimated before testing.	Degrees Celsius; categorical levels 24, 27, and 30.
`Sex`	Recorded sex of the individual.	Male or female; common text variants are normalized by the scripts.
`Mass_g`	Body mass recorded for the trial.	Grams (g).
`CTmax`	Critical thermal maximum, measured as temperature at loss of equilibrium during progressive warming.	Degrees Celsius (°C).

Hypoxia loss-of-equilibrium data

Files: hypoxia_ANCOVA copy.csv and hypoxia_loss_of_equilibrium.csv.

Variable	Definition	Units or coding
`ID`	Identifier for the individual crayfish.	Text identifier.
`species`	Species code.	`A` = P. acutus; `F` = P. fayettei; `N` = P. nueces; `T` = P. texanus.
`sex`	Recorded sex of the individual.	`M` = male; `F` = female.
`weight`	Body mass of the individual.	Grams (g).
`O2_LOE`	Dissolved oxygen at loss of equilibrium (LOE).	Percent dissolved oxygen. Empty when LOE did not occur.
`hours`	Elapsed duration of the hypoxia trial.	Hours. Retained in the data but not included in the reported ANCOVA.

Metabolic-rate data

Files: All MO2 values.xlsx and metabolic_rate_measurements.csv.

Variable	Definition	Units or coding
`species`	Crayfish species.	Scientific name.
`ID`	Identifier for the individual crayfish.	Text identifier.
`trial`	Replicate respirometry trial number.	Integer replicate identifier.
`O2_Max`	Upper oxygen-rate value for the measurement interval.	µmol O₂ h⁻¹, as specified by the project investigators.
`O2_Min`	Lower oxygen-rate value for the measurement interval.	µmol O₂ h⁻¹, as specified by the project investigators.
`MO2`	Measured oxygen-consumption rate.	µmol O₂ h⁻¹.
`mass`	Body mass of the individual.	Grams (g).
`sex`	Recorded sex of the individual.	`M` = male; `F` = female.

Highlighted rows in `All MO2 values.xlsx`

The colored rows are visual boundary markers for three contiguous individual-trial blocks. Yellow marks the first and last records for individual A14, green marks the first and last records for A17, and light peach marks the first and last records for A18. The highlighting does not identify excluded observations, treatments, quality-control failures, or analytical weights. The R scripts use cell values only and do not read or use spreadsheet formatting.

Critical oxygen tension respirometry data

Files: Fixed Pcrit values.xlsx and pcrit_respirometry_measurements.csv.

Variable	Definition	Units or coding
`species`	Crayfish species.	Scientific name.
`ID`	Identifier for the individual crayfish.	Text identifier.
`trial`	Replicate trial number used to define separate Pcrit-estimation groups.	Integer replicate identifier.
`O2_Max`	Upper oxygen-rate value for the measurement interval.	µmol O₂ h⁻¹, as specified by the project investigators.
`O2_Min`	Lower oxygen-rate value used as the predictor in segmented regression.	µmol O₂ h⁻¹, as specified by the project investigators.
`MO2`	Measured oxygen-consumption rate.	µmol O₂ h⁻¹.
`mass`	Body mass of the individual.	Grams (g).
`sex`	Recorded sex of the individual.	`M` = male; `F` = female.

Progressive-acidification data

Files: pH mass plot 7-24.xlsx and ph_loss_of_equilibrium.csv.

Variable	Definition	Units or coding
`ID`	Repository identifier for the individual crayfish.	Text identifier. The eight originally nonunique `T` records were assigned `T_pH_01` through `T_pH_08`.
`Original_ID`	Identifier as recorded in the source workbook.	Text; `T` denotes separate P. texanus individuals used only in the pH trials.
`Species`	Crayfish species.	Scientific name.
`Sex`	Recorded sex of the individual.	`M` = male; `F` = female.
`Mass_g`	Body mass of the individual.	Grams (g).
`pH_LOE`	pH at loss of equilibrium during progressive acidification.	pH units.

Abbreviations

AICc: Akaike information criterion corrected for small sample size.
ANCOVA: analysis of covariance.
CTmax: critical thermal maximum.
DO: dissolved oxygen.
EPSG: European Petroleum Survey Group coordinate-reference-system identifier.
FNU: formazin nephelometric units.
LOE: loss of equilibrium.
MMR: maximum metabolic rate.
MO2: oxygen-consumption rate.
ORP: oxidation-reduction potential.
Pcrit: critical oxygen tension.
PSU: practical salinity units.
SMR: standard metabolic rate.
TDS: total dissolved solids.
WGS84: World Geodetic System 1984.

Analysis overview

Habitat associations

Species-specific binomial logistic-regression models evaluate all additive combinations of standardized water temperature, turbidity, salinity, conductivity, total dissolved solids, and pH, including the null model. Candidate models are ranked using AICc.

Distribution maps

The mapping workflow uses the deposited exact WGS84 coordinates and adds public county and watershed context layers.

Critical thermal maximum

CTmax is analyzed using a repeated-measures mixed-effects ANCOVA with categorical acclimation temperature and random intercepts for SubjectID and SubjectID-by-acclimation-temperature combinations.

The primary fixed-effects structure is:

CTmax ~ Species + AcclimTemp + Sex + Mass_c + Species:AcclimTemp + Species:Sex + Species:Mass_c

with random effects:

(1 | SubjectID) + (1 | SubjectID:AcclimTemp)

Hypoxia tolerance

The reported ANCOVA uses species, sex, centered body weight, Species × Sex, and Species × Body Weight:

O2_LOE ~ species + sex + weight_c + species:sex + species:weight_c

The hours column is retained but intentionally not included in the reported model.

Metabolic responses

Standard metabolic rate (SMR) is the mean of the lowest 10% of observed MO2 measurements within an individual. Maximum metabolic rate (MMR) is the maximum observed MO2, and aerobic scope is MMR minus SMR.

The SMR, MMR, and aerobic-scope ANCOVAs include species, sex, centered body mass, Species × Sex, and Species × Body Mass.

Critical oxygen tension

Pcrit is estimated separately for each species-by-individual-by-trial group using segmented regression of MO2 on O2_Min. Trial is a replicate identifier rather than a fixed effect.

Pcrit is analyzed using the mixed-effects ANCOVA:

Pcrit ~ species + sex + mass_c + species:sex + species:mass_c + (1 | SubjectID)

Acidity tolerance

The Panel D script and the combined seven-response ANCOVA table use the same fixed-effects structure:

ph_loe ~ species + sex + mass_c + species:sex + species:mass_c

The Panel D figure displays observed points and sex-averaged model predictions with confidence intervals. The only figure output created by the Panel D script is Acidity_PanelD.png.

Analysis-code package

Setup

Extract Crayfish_Dryad_Data.zip and Crayfish_Dryad_Analysis_Code.zip into the same working directory. Preserve the script-compatible data filenames and keep unified_style.R in the same directory as the plotting scripts.

Recommended run order

R/01_habitat_associations_AICc.R
R/02_habitat_summary_table.R
R/03_distribution_maps.R
R/05_CTmax_publication_outputs.R
R/06_CTmax_panel_A.R
R/07_hypoxia_ANCOVA.R
R/08_metabolism_SMR_MMR_scope.R
R/09_aerobic_scope_panel_B.R
R/10_Pcrit_primary_mixed_model.R
R/11_Pcrit_panel_C.R
R/12_pH_panel_D.R
R/13_combined_ANCOVA_table.R

R/04_CTmax_primary_mixed_model.R is the detailed numbered-output CTmax workflow and uses the same repeated-measures model structure as the publication-output script.

Pipeline dependencies

R/02_habitat_summary_table.R requires the cross-species summary generated by R/01_habitat_associations_AICc.R.

The combined ANCOVA table requires CSV outputs generated by the CTmax, hypoxia, metabolism, and Pcrit primary scripts. The pH ANCOVA is recalculated internally from pH mass plot 7-24.xlsx.

Several plotting scripts require R/unified_style.R.

The distribution-mapping script may require internet access during its first run to retrieve public county and watershed context layers.

Software requirements

The scripts use R and packages listed in R_PACKAGE_REQUIREMENTS.md. The combined PDF table also requires a working LaTeX installation.

Execution note

The scripts were statically inspected, and known filename and model inconsistencies were corrected. R was not installed in the packaging environment, so the complete workflow must be run in a clean R environment before final submission.

Supporting documentation

The data ZIP also contains:

DATA_DICTIONARY.csv
DRYAD_METADATA.md
DRYAD_UPLOAD_INSTRUCTIONS.md
METHODS_SUMMARY.md
FILE_MANIFEST.csv
SHA256SUMS.txt

The code ZIP also contains:

RUN_ORDER.md
R_PACKAGE_REQUIREMENTS.md
CC0_NOTICE.txt
FILE_MANIFEST.csv
SHA256SUMS.txt

Rights and reuse

Both ZIP files are intended for direct publication in Dryad under the Creative Commons Zero (CC0) waiver. Users should cite the Dryad dataset DOI and the associated technical report when reusing the data or analysis materials.