Dataset DOI: 10.5061/dryad.qbzkh18x0

Description of the data and file structure

In this study, we provided a detailed quantification of the timing and intensity of prealternate molt for six species of warbler (Family: Parulidae) on their nonbreeding grounds in Jamaica: Ovenbird (Seiurus aurocapilla), Northern Waterthrush (Parkesia noveboracensis), Black-and-white Warbler (Mniotilta varia), American Redstart (Setophaga ruticilla), Northern Parula (Setophaga americana), and Prairie Warbler (Setophaga discolor). We examined how molt intensity varied across the molting period and tested whether molt intensity varied across species, age, and sex classes. This repository contains the data (collected in winter 2023) used in this Journal of Field Ornithology publication and the R code for our analyses.

Files and variables

File: PAMolt.csv

Description: prealternate molt intensity and explanatory variables values used in the R script PAMolt_analysis.R

Variables:

• JULDATE: Julian date in the year 2023
• SPECIES: species AOU code (AMRE = American Redstart, BAWW = Black-and-white Warbler, NOPA = Northern Parula, NOWA = Northern Waterthrush, OVEN = Ovenbird, PRAW = Prairie Warbler)
• BAND: USGS leg band number. NA values indicate individuals that were not banded.
• AGE: age class (ASY = after-second-year / definitive-cycle, SY = second-year /first-cycle). NA values indicate individuals for which age was not determined.
• SEX: sex class (F = female, M = male, U = unknown). NA values indicate individuals for which sex could not be determined in the field by plumage characteristics or wing length.
• CROWN: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• BCK.OF.HEAD: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• CHEEK: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• CHIN: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• THROAT: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• NAPE.NECK: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• BREAST: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• BELLY: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• VENT: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• FLANKS: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• LEGS: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• UNDRTAIL: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• UPPRTAIL: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• BACK: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• RUMP: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• SHLDRS: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• WNGPTS: molt intensity score measured in the field for this feather patch; measured as the percentage of feathers in active molt on a scale of zero to four, where 0 = 0%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75%, 4 = 76-100%. NA values indicate individuals for which molt was not scored in this patch.
• CCMI: numerical combined contour molt index (CCMI) used to measure individual molt intensity. In the field, we scored each of 17 feather patches for the percentage of feathers in active molt, as described above for each feather patch (e.g., CROWN variable). For each bird, we took the sum of all feather patch scores divided by the total number of feather patches (17) to assign a CCMI score on an ordinal scale from zero to four. NA values indicate individuals for which CCMI could not be calculated because molt was not scored in one or more feather patches.
• CCMI.HEAD: numerical combined contour molt index used to measure individual molt intensity, only for feather patches on the head (6 patches). Followed method as described above for CCMI variable, included only feather patches on the head. NA values indicate individuals for which CCMI could not be calculated because molt was not scored in one or more feather patches.
• CCMI.BODY: numerical combined contour molt index used to measure individual molt intensity, only for feather patches on the body (11 patches). Followed method as described above for CCMI variable, included only feather patches on the head. NA values indicate individuals for which CCMI could not be calculated because molt was not scored in one or more feather patches.
• CAPCATEGORY: represents the capture record for the individual bird (FIRST = first capture, SECOND = second capture, as in first recapture, THIRD = third capture, as in second recapture, and so on)
• MOULT: a binary value for whether the bird was molting at capture (1) or not (0)
• A.FILTER: used to filter individual American Redstarts and Prairie Warblers for 1) first capture after the observed onset of molt for the species (A.FILTER = A) and 2) second capture after the observed onset of molt for the species (A.FILTER = B). A.FILTER = C was used to exclude one bird which was captured one day after first capture, after the onset of molt for the species.

File: PAMoltAnalysis.R

Description: the R script used to complete the analysis using R software version 4.4.0