Luke J. Eberhart-Phillips, Clemens Küpper, María Cristina Carmona-Isunza, Orsolya Vincze, Sama Zefania, Medardo Cruz-López, András Kosztolányi, Tom E. X. Miller, Zoltán Barta, Innes C. Cuthill, Terry Burke, Tamás Székely, Joseph I. Hoffman, and Oliver Krüger
In this repository you can find all the necessary files needed to reproduce the analyses presented in our paper.
(Supplementary Material Appendix A)
R/
- Eberhart_Phillips_et_al_SM_Appendix_A.pdf and Eberhart_Phillips_et_al_SM_Appendix_A.Rmd contains the documented code for all analyses, which can be implemented after downloading the datasets provided in the
data/andoutput/folders.
(Supplementary Material Appendix B)
data/
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Appendix_B_juvenile_adult_mark-recapture_data.txt contains the mark-recapture field data of juveniles and adults. Each row is a single uniquely marked individual identified by their bird_ID. The annual encounter history of an individual is expressed in their ch, where a "1" indicates that an individual was encountered and "0" indicates it was not encountered. sex describes the molecular sex-type of an individual with "M" for males and "F" for females. age describes the stage at which an individual was initially captured, where "J" indicates it was first captured as a chick, and "A" indicates it was first captured as an adult. population describes the population in which the individual was sampled from ("KIP" = Kittlitz's plover, "MP" = Madagascar plover, "WFP" = white-fronted plover, "KPT" = Kentish plover Tuzla, "KPM" = Kentish plover Maio, and "SP" = snowy plover).
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Appendix_B_breeding_data.txt contains the individual reproductive histories of all marked breeding adults in the population. Each row is a nesting attempt uniquely identified by the family_ID. no_chicks expresses the number of chicks that hatched from the nest. clutch_size indicates the number of eggs in the nest when it was initially discovered. year describes the year in which the nest was active. male and female indicates the unique identity of the father and mother, respectively, with "male_NA" and "female_NA" describing cases in which the other mate was not identified. population describes the population in which the individual was sampled from (same notation as above).
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Appendix_B_hatching_sex_ratio_data.txt contains the sex and origin of each chick included in our analysis to assess hatching sex ratio. Each row is a chick uniquely identified by their chick_ID. The family of origin for each chick is shown in their family_ID. year describes the year in which the chick hatched. A "1" in either the male or female column indicates the molecular sex-type of a given chick. population describes the population in which the chick was sampled (same notation as above).
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Appendix_B_parental_care_data.txt contains the behavioral observations of the care-system for each family. Each row is an observation of a unique family (family_ID) within a given population (same notation as above). care_system expresses the parental care recorded on a given observation (i.e. "male_care", "female_care", or "both_care". hatch_date indicates the date on which a given brood hatched. date indicates the date on which the observation was made.
output/
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AIC_table_juvenile_adult_boot_out.txt contains the bootstrap output for model selection of juvenile and adult survival based on the mark-recapture analysis run in Program MARK. Each row is a model fitted via maximum likelihood to the bootstrapped data sample of each iteration (iter). Phi describes the model structure for fitting annual survival. p describes the model structure for fitting annual encounter probability. npar reveals the number of parameters used in a given model. AICc is the Akaike Information Criteria statistic corrected for small sample size. DeltaAICc is the difference in AICc between a given model and the best fit model of a given iteration. weight describes the AIC weight of a given model. Deviance describes the deviance of a given model. population specifies the population from which the analysis of the iteration was based on (same notation as above).
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ASR_boot_out_final.txt contains the adult sex ratio estimates (ASR_boot_out) of each iteration of the bootstrap procedure. Each row represents an iteration (iter). population specifies the population from which the analysis of the iteration was based on (same notation as above).
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survival_rates_boot_out_final.txt contains the sex- and stage-specific survival estimates (estimate) of each iteration (iter) in the bootstrap procedure. Each row represents a given sex and stage (sex_age) in a given iteration. population specifies the population from which the analysis of the iteration was based on (same notation as above).
Last updated: February 20, 2018