Joint telemetry and mark-recapture model reveals resource selection affects Northern Bobwhite (Colinus virginianus) chick survival
Data files
Jun 24, 2026 version files 97.45 MB
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BroodIDs.csv
61.09 KB
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cap_age.csv
7.15 KB
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chick_2018_19_capture_history_5state.csv
65.96 KB
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chick_trap_data_orton.csv
26.66 KB
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forage_model_032525_.RData
5.41 MB
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foraging_inp.csv
4.63 MB
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foraging_rsf_betas_correctedID.csv
37.26 KB
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FW_fates.csv
15.35 KB
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Multistate_survival_foraging.R
27.86 KB
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Multistate_survival_roosting.R
41.46 KB
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read_me.txt
5.59 KB
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README.md
6.86 KB
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roost_model_032525_.RData
87.03 MB
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roosting_rsf_betas.csv
80.65 KB
Abstract
We used two integrated-hierarchical models to examine the effects of (1) nocturnal and (2) foraging habitat selection, as well as age, and year on bobwhite chick survival rates (11-84 days), while also estimating tag-retention rates of backpack-suture style radios. Both models incorporate three unique data sets (chick telemetry, adult telemetry, seasonal trapping efforts).
Each R script is fully annotated. Models are in a Bayesian framework and executed via the Nimble package. All input files are included and described in the ReadMe file
Dataset DOI: https://doi.org/10.5061/dryad.9p8cz8wtz
Dataset Description
This dataset supports analyses examining whether roost-site and foraging-site selection by Northern Bobwhite (Colinus virginianus) chicks influences survival. The survival models integrate multiple data sources, including telemetry and mark–recapture observations, to account for transmitter loss and imperfect detection.
Files and Variable Descriptions
File: BroodIDs.csv
Description: Unique brood identifiers associated with individual chicks on each day of monitoring.
Variables:
- Column 1: Chick identifier consisting of the last four digits of the radio-transmitter frequency and the chick band ID (
transmitterID_bandID). - Remaining columns: Daily brood identifiers.
- Column 2 = first day of tracking.
- Column 3 = second day of tracking.
- Subsequent columns correspond to subsequent tracking days.
- Note: If a chick was censored or observed dead, the brood ID remains associated with that chick for those days and all subsequent days.
File: cap_age.csv
Description: Capture information for radio-tagged Northern Bobwhite chicks monitored during 2018 and 2019.
Variables:
ID: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).year: Year of capture (2018 or 2019).Capture.Date: Capture date (MM/DD/YYYY).age.cap: Age at capture (days).Chick.ID: Unique chick band ID.Freq: Radio-transmitter frequency (Hz).
File: chick_2018_19_capture_history_5state.csv
Description: Radio-telemetry encounter histories for tagged chicks during 2018 and 2019.
Variables:
ID: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).year: Year of observation (2018 or 2019).- Date columns (MM/DD/YYYY):
NA: Not observed.1: Alive.3: Transmitter recovered.4: Not detected (likely transmitter failure).5: Not detectable.
File: chick_trap_data_orton.csv
Description: Seasonal trapping observations for radio-tagged chicks during 2018 and 2019.
Variables:
ID: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).year: Year of observation (2018 or 2019).- Date columns (MM/DD/YYYY):
1: Alive (captured or observed during trapping).4: Not detected.5: Not detectable.
File: foraging_inp.csv
Description: Intensive telemetry tracking data used to determine age at first intensive tracking and estimate foraging behavior.
Variables:
- First 12 columns: Retained from a previous foraging resource-selection analysis and not used in the survival analyses.
ID: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).date: Tracking date (MM/DD/YYYY).use:1: Used location.0: Random location.
age: Chick age (days).brood.id: Unique brood identifier.year: Year of observation (2018 or 2019).
File: foraging_rsf_betas_correctedID.csv
Description: Foraging-site habitat-selection coefficients for radio-tagged Northern Bobwhite chicks. Data and descriptions originate from Hill et al. (2023).
Variables:
id: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).- Variables ending in
_mu: Posterior mean habitat-selection estimates. - Variables ending in
_lci: Lower 95% credible intervals. - Variables ending in
_uci: Upper 95% credible intervals. - Habitat codes:
up: Unburned upland.b_up: Burned upland.rd_dist: Distance to feedline.bf: Fallow field.db: Drain/bay.gf: Unburned grass field.b_gf: Burned grass field.NDVI: Normalized Difference Vegetation Index.NDVI2: Quadratic effect of NDVI.
File: FW_fates.csv
Description: Fall–winter telemetry data for tagged Northern Bobwhite monitored during 2018–2019.
Variables:
Capture date: Date the bird entered the telemetry sample (MM/DD/YYYY).ID: Unique bird band ID.sex:M: Male.F: Female.
age:A: Adult.J: Juvenile.
weight: Body mass (g).freq: Radio-transmitter frequency.fate: Fate determined via telemetry. Blank cells indicate the bird was alive at the end of monitoring.fate date: Date the bird was censored or confirmed dead (MM/DD/YYYY).Year: Sampling year (2018 or 2019).
File: Multistate_survival_foraging.R
Description: Annotated R script that formats associated datasets and conducts the multistate survival analysis evaluating foraging-site selection using Nimble.
Contents:
- Formats and prepares model input data.
- Fits the multistate survival model.
- Summarizes model output.
- Generates figures used in the associated manuscript.
File: Multistate_survival_roosting.R
Description: Annotated R script that formats associated datasets and conducts multistate survival analyses evaluating roost-site selection and known-fate telemetry analyses using Nimble.
Contents:
- Formats and prepares model input data.
- Fits the multistate survival and known-fate models.
- Summarizes model output.
- Generates figures used in the associated manuscript.
File: roosting_rsf_betas.csv
Description: Roost-site habitat-selection coefficients for radio-tagged Northern Bobwhite chicks. Data and descriptions originate from Hill et al. (2023).
Variables:
id: Last four digits of the radio-transmitter frequency and chick band ID (transmitterID_bandID).- Variables ending in
_mu: Posterior mean habitat-selection estimates. - Variables ending in
_lci: Lower 95% credible intervals. - Variables ending in
_uci: Upper 95% credible intervals. - Habitat codes:
up: Unburned upland.b_up: Burned upland.rd_dist: Distance to feedline.bf: Fallow field.db: Drain/bay.gf: Unburned grass field.b_gf: Burned grass field.NDVI: Normalized Difference Vegetation Index.NDVI2: Quadratic effect of NDVI.
File: forage_model_032525_.RData
Description: R workspace containing formatted data objects and model output generated by Multistate_survival_foraging.R.
Contents:
- Formatted analysis datasets.
- Model objects.
- Posterior summaries and derived outputs.
File: roost_model_032525_.RData
Description: R workspace containing formatted data objects and model output generated by Multistate_survival_roosting.R.
Contents:
- Formatted analysis datasets.
- Model objects.
- Posterior summaries and derived outputs.
Software Requirements
- R
- RStudio
- Microsoft Works