Resource allocation underlies parental decision-making during incubation in the Manx shearwater

Natasha Gillies, Oliver Padget, Martyna Syposz, Sarah Bond, Tim Guilford

Overview

This folder contains codes and data to reproduce both the main and supplementary results of the paper, published in Ornithology (2022); https://doi.org/10.1093/ornithology/ukac006.

There are 2 folders: "Data_inputs" and "Scripts". As this is a large and multi-year dataset that may be currently used by other members of the project or collaborators, we would appreciate if you could contact Natasha Gillies (gilliesne@gmail.com) if you would like to make use of the dataset. This will reduce duplication of effort and ensure that we can give you any additional information that may be useful for analysis or interpretation.

Scripts

• 1_MASH-incubation_main-analysis.R This script contains all the code necessary to reproduce the main results and figures presented in the manuscript.
• 2_MASH-incubation_functions.R This script contains additional functions to run the analyses in script 1.

Data inputs

There are 6 datasets used in the analysis.

• MASH2015-2019_daily-active-nests.csv Contains the number of active nests per day and year, and is used to define the simulated changeovers for the randomisation analysis. The columns are:

  • date Date where active nests recorded
  • nburrows Number of active nests
  • year Year of recording

• MASH2015-2019_daily-foraging-data.csv Summarised activity for birds across individual foraging trips. The columns are:

  • ring Individual ring identity of bird
  • stintID Unique identity of individual stint
  • sex Female (F) or male (M)
  • burrow Identity of nest
  • start_mass Mass (g) at beginning of foraging trip
  • year Year of recording
  • end_mass Mass (g) at end of foraging trip
  • foragetrip Duration (days) of foraging trip
  • forageGain Mass (g) gained across duration of foraging trip
  • neglect Whether the trip followed neglect (YES) or not (NO)
  • prop_rest Proportion of foraging trip spent resting
  • prop_flight Proportion of foraging trip spent in flight
  • prop_forage Proportion of foraging trip spent foraging
  • phase What phase of the trip the bird was in, commuting (commute) or foraging (forage)

• MASH2015-2019_daily-mass-change.csv Contains daily mass changes for all birds for which mass data were collected. The columns are:

  • year Year data was collected
  • ring Individual identity of bird
  • sex Female (F) or male (M)
  • stintID Denotes unique identity of stint (within bird)
  • DSL ‘Days Since Laying’, indicates time since egg was laid
  • stintday Day of stint
  • mass_chg Difference in mass (g) from previous day
  • mass_chgPer Difference in mass (g) from previous day as a percentage of body mass
  • exp Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP)

• MASH2015-2019_forage-data-by-trip.csv Contains summarised data from individual foraging trips. The columns are:

  • burrow Individual identity of nest
  • year Year data were collected
  • stintID Denotes unique identity of stint (within bird)
  • ring Individual identity of bird
  • sex Female (F) or male (M)
  • start_mass Mass of bird (g) at beginning of foraging trip
  • DSL ‘Days Since Laying’, indicates time since egg was laid
  • foragetrip Duration of foraging trip (days)
  • partnerincoming Mass of returning partner (g) upon departure on foraging trip
  • exp Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP)

• MASH2015-2019_incub-data-by-shift.csv Contains summarised data from individual incubation shifts. The columns are:

  • burrow Individual identity of nest
  • year Year data were collected
  • stintID Denotes unique identity of stint (within bird)
  • start_date Date that the incubation shift began
  • ring Individual identity of bird
  • sex Female (F) or male (M)
  • start_mass Mass of bird (g) at beginning of foraging trip
  • burrowID Denotes identity of nest within a given year
  • stintlength Duration of incubation shift (days)
  • DSL ‘Days Since Laying’, indicates time since egg was laid
  • end_mass Mass of bird (g) at end of incubation shift
  • endsInNeglect Whether bird neglected egg at end of stint (YES) or not (NO)
  • followsNeglect Whether incubation shift commenced following neglect (YES) or not (NO)
  • exp Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP)
  • whoFirst Factor denoting whether the female (F) or male (M) took the first incubation shift. If the first incubation shift was not recorded for that nest, recorded as ‘nostart’

• MASH2015-2019_nest-data.csv Contains summarised data for entire incubation attempts for each nest used in the study. The columns are:

  • year Year the data were collected
  • burrow Denotes individual identity of nest
  • outcome Whether the incubation attempt was successful (HATCHED) or not (FAILED)
  • incDur Total duration (days) from egg laying to egg hatching (or failure)
  • count.F Number of incubation shifts taken by the female
  • count.M Number of incubation shifts taken by the male
  • NO.BIRD Number of days neither parent was recorded at the nest
  • femper Proportion of incubation days taken by female
  • malper Proportion of incubation days taken by male
  • exp Pair experience, unknown (UNKNOWN), newly formed (NEW) or experienced (EXP)
  • julian Lay date recorded as Julian date
  • whoFirst Factor denoting whether the female (F) or male (M) took the first incubation shift. If the first incubation shift was not recorded for that nest, recorded as ‘nostart’