Neotropical birds respond innately to unfamiliar acoustic signals dataset

Here we included the files for Sandoval and Wilson manuscript entitled "Neotropical birds respond innately to unfamiliar acoustic signals." which is publish in The American Naturalist. The name of each file is followed by a description of the file's contents in the file Read me. : 

SWanalysis.R - The R script used to produce all statistical analyses and figures presented in the manuscript. This file is dependent on the following files described below:

SWtreeF2.nex

SWnames.csv

SWtreePGLM.nex

SWdataPGLM.csv

SWtrialData.csv

SWsppData.csv

SWcallF1.wav

SWsongF1.wav

Methods
SWanalysis.R - The R script used to produce all statistical analyses and figures presented in the manuscript. This file is dependent on the following files described below:

SWtreeF2.nex

SWnames.csv

SWtreePGLM.nex

SWdataPGLM.csv

SWtrialData.csv

SWsppData.csv

SWcallF1.wav

SWsongF1.wav

SWtreeF2.nex --- A nexus file containing 10,000 phylogenetic trees. Trees were generated from birdtree.org using all the species that overlapped with at least one of the playback sites used in our study. Although 692 species are sympatric with the sites, only 689 are shown in the trees because three species recognized by the American Ornithological Society's checklists (Arremon atricapillus, Buteo plagiatus, Momotus subrufescens) were not included in the phylogenies provided by birdtree.org. Trees were created using the Hackett backbone.

SWnames.csv --- A data file containing taxonomic information used to create Figure 2 in the manuscript. It includes the following variables:

AOS: species names shown in Figure 2, based on the American Ornithological Society

birdtree: species names used in the phylogenies created by birdtree.org

AOSorder: taxonomic order of each species, based on the American Ornithological Society

colour: numbers (Alphabet colour palette) to colour code species of the same taxonomic order

SWtreePGLM.nex --- A nexus file containing 10,000 phylogenetic trees. Trees were generated from birdtree.org using the 38 species that responded to the chick-a-dee call treatment of at least one trial (shown in red in figure 2 of the paper), as well as 38 phylogenetically matched non-respondent species (shown in blue in figure 2 of the paper). These trees are used in the phylogenetic logistic regressions presented in the paper. Trees were created using the Hackett backbone.

SWdataPGLM.csv --- A data file containing species traits used in the phylogenetic logistic regressions. The following variables are shown for each species that responded to the chick-a-dee calls of at least one trial (N = 38 species), and for 38 phylogenetically matched species that did not respond:

birdtree: species names used by birdtree.org

respond: whether the species responded to the chick-a-dee calls of at least one trial

corr: median cross-correlation coefficients (0-1) comparing a species' calls to chick-a-dee calls

mass: mean body mass of the species (grams)

SWtrialData.csv --- A data file containing the raw data collected during 414 trial-treatments. These data are used in the analysis of whether experimental treatment affected the number of resident species that approached the playback speaker. Variables in the datafile include:

migrants: North American migrants were either present or absent

country: trials were conducted in Brazil, Colombia, or Costa Rica

site: trials were conducted at 21 sites in Brazil, 27 sites in Colombia, and 30 sites in Costa Rica

block: a block included three playback treatments played at a given site over ~20 minutes

trt: playback treatments included a chick-a-dee call, fee bee song, and silence

latency: time (s) from start of playback until first bird approached within 5 m of speaker

dist: minimum distance (m) of any bird to speaker during the trial-treatment

spp: number of resident species to approach within 5 m of speaker during trial-treatment

inds: sum of # individuals of each resident species within 5 m of speaker during trial-treatment

SWsppData.csv --- A data file containing the raw data collected during the 88 trials in which at least one resident species responded during at least one of the three treatments. For each trial-treatment, data are included separately for each species that ultimately responded to any of the three treatments in the trial. These data are used in the analyses of whether experimental treatment affected a given species' probability of response, their latency to respond, and their minimum approach distance. Variables in the datafile include:

migrants: North American migrants were either present or absent

country: trials were conducted in Brazil, Colombia, or Costa Rica

site: trials were conducted at 21 sites in Brazil, 27 sites in Colombia, and 30 sites in Costa Rica

block: a block included three playback treatments played at a given site over ~20 minutes

trt: playback treatments included a chick-a-dee call, fee bee song, and silence

latency: time (s) from start of playback until first bird of the species approached within 5 m of speaker

dist: minimum distance (m) of the species to speaker during the trial-treatment

focal: scientific name of the species; taxonomy follows American Ornithological Society

respond: did focal species approach within 5 m of speaker during the treatment (0=no; 1=yes)

SWcallF1.wav --- Audio recording (44.1 kHz sampling rate, 16-bit amplitude encoding, WAVE format) of a chick-a-dee call used to create Figure 1a.

SWsongF1.wav --- Audio recording (44.1 kHz sampling rate, 16-bit amplitude encoding, WAVE format) of a fee bee song used to create Figure 1b.

SWsounds.csv --- A list of audio files obtained from public libraries of sound. One call within each recording was used either as a playback stimulus or in a spectrogram cross-correlation to determine the structural similarity between the species' call and the chick-a-dee call. Cross correlation coefficients were then used in a phylogenetic logistic regression predicting a species' probability of response. Variables in the data file include:

species: scientific name of the species; taxonomy follows American Ornithological Society

ID: the catalogue numbers of recordings from Macaulay Library (ML) and Xeno Canto (XC)

onset: time (s) within recording when call begins

offset: time (s) within recording when call ends

role: each call was used either as a stimulus or in the phylogenetic logistic regression (PGLR)