DOI: 10.5061/dryad.qbzkh18x0
title: Data from: Prealternate molt intensity and timing in six Nearctic-Neotropical migratory warblers

description: 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 the Journal of Field Ornithology publication of the
 same title (2025) and the R code for our analyses. See the publication for
 detailed methods on how the data and code were applied.
description: # Data from: Prealternate molt intensity and timing in six
 Nearctic-Neotropical migratory warblers Dataset DOI:
 [10.5061/dryad.qbzkh18x0](https://doi.org/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