Physiological constraints and cognitive chunking in Zebra Finch songs: Data and R script

Learned bird songs often have a hierarchical organization. In the case of zebra finches, each bird’s song is made up of a string of notes delivered in a stereotyped sequence to form a “motif”, and motifs are repeated to form a song bout. During song learning, young males copy “chunks” of two or more consecutive notes from their tutors’ songs. These chunks are represented as distinct units within memory (during learning) and within motor systems (during song production). During song performance, motifs may deviate from the learned sequence by stopping short, starting late, or by skipping, inserting or repeating notes. We measured acoustic and temporal variables related to the respiratory and vocal physiology of song production and asked how they related to deviations from each bird’s “canonical” sequence. The best predictor of deviations from that sequence was the duration of the silent interval between notes, when inspiration normally occurs. Deviations from the canonical motif occurred..., Subjects:  The subjects were 50 adult male zebra finches (Taeniopygia guttata) bred and raised in the Williams College colony. Birds were hatched in aviaries that housed at least three breeding pairs, and so could copy songs from their fathers or from other adult males. Young males in their own and other broods could also influence song development (Tchernichovski & Nottebohm, 1998) or be the source of song material, and both young and older females were present and could influence song development (Carouso-Peck & Goldstein, 2019). When birds reached maturity (approximately 90 days) they were removed from their natal aviaries and housed in single-sex cages, grouped by age cohort, in a colony room that also housed females and older males. All procedures were approved by the Williams College Institutional Animal Care and Use Committee (Williams College IACUC protocol WH-A).
Song Recording:   Recordings of female-directed song were obtained by placing a caged adult male (> 120 d..., R, with the following packages: ggplot2, Rcpp, Matrix, lme4, reshape2, sciplot, lattice, plyr, magrittr, MuMIn, Amelia, pscl, readr, performance, dplyr, tidyverse, ggeasy, car, glmmTMB, bbmle, GLMMadaptive, sandwich, lmtest, MASS, DescTools (all are open-source), \# **Physiological Constraints and Cognitive Chunking in Zebra Finch Songs: Data and R script**

The data set for the associated paper was obtained by analyzing an average of more than 100 songs from each of 50 zebra finches. Zebra finches have a stereotyped song consisting of approximately ten notes, which are delivered in a stereotyped sequence called a motif. The full sequence is the canonical motif. To address the question of what physiological and cognitive factors are associated with deviations of the canonical motif sequence, we scored deviations as start, stop, and other (repeats, skips, insertions) and counted their occurrence at each transition between notes in each birds canonical motif. We then characterized the acoustic and temporal properties of each transition between notes. Finally, we characterized the cognitive chunks within the song by looking at 21 birds songs that were copies of the same motif, and noting where the copied songs did not match; the transitions where t...