DOI: 10.5061/dryad.ffbg79d5r
title: Stable atmospheric conditions underlie a steady pace of nocturnal bird migration in the tropics

description: Seasonal migrations between temperate and tropical latitudes have evolved
 repeatedly across the tree of life, but we know little about how tropical
 environments have shaped this life history strategy. In this first
 aeroecological radar study in South America, we tested whether tropical
 atmospheric stability leads to a more continuous pace of nocturnal bird
 migration across a season than the episodic pulses of migration in
 temperate regions. We estimated and compared the volume, flight
 directions, and heights of birds detected by weather radars and acoustic
 sensors in three regions of Colombia across four years and assessed the
 effects of atmospheric conditions. We found that stable tropical winds
 have distinct effects on migration timing depending on geographic context.
 Within the Andes mountains, supportive winds explain the altitudes at
 which birds fly, but not the volume of birds aloft on a given night,
 resulting in lower nightly variation in migration intensity. However,
 lapses in prevailing headwinds east of the Andes drove higher variation in
 migration intensity similar to temperate latitudes. With a reduced
 relationship between forecastable weather and the magnitude of nightly
 migration, predicting high-volume migration events to target for
 conservation initiatives may be more challenging in tropical climates.
description: # Stable atmospheric conditions underlie a steady pace of nocturnal bird
 migration in the tropics Dataset DOI:
 [10.5061/dryad.ffbg79d5r](10.5061/dryad.ffbg79d5r) ## R source file guide
 Guide to R source files used in four key analyses for "Stable
 atmospheric conditions underlie a steady pace of nocturnal bird migration
 in the tropics". 1. **Quantifying variation and accumulation of
 nightly migration traffic** Uses R source file migration_traffic4pub.R
 Requires "vpi_master_co_il_noc_clean_A8.csv" to plot migration
 traffic accumulation and "vpi_list_allseasons_clean_noc_A8.rds"
 and "vpi_list_usa_noc_A8_20240919.rds" to calculate migration
 traffic summaries. Output of migration traffic summaries with some manual
 annotation of data quality based on reviewing raw imagery in
 "vpi_migration_traffic_summary_A8_20240920.csv", which the
 script also summarizes. Generates results for Fig. 2, Fig. 3a,b, and Table
 1 2. **Quantifying effects of atmospheric conditions on migration across
 nights and altitude** Revisions of GAM analysis of vertically integrated
 profiles ("vpi_thin_props_clean_A8_3.csv") and full vertical
 profiles ("all_radars_thinned_vpts_df_CLEAN_A8_20240714.csv" of
 a single scan per night across the full data set Generates results for
 Figure 3, Figures S4, S5 and S6, and Tables S3 and S4 3. **Quantifying the
 volume and direction of birds and wind** Comparing volumes and directions
 for each site, season, including making rose plots used in figures and
 summary stats for Table 2. Reads
 "all_radars_thinned_vpts_df_CLEAN_A8_20240714.csv",
 "vpi_thin_props_clean_A8_3.csv", and
 "all_radars_thinned_vpi_cfdates_CLEAN_A8.csv" 4. **Comparing
 radar and acoustic data** Compares nocturnal flight call and radar data
 using "vpi_thin_props_clean_A8_3.csv" and
 "night_summary-20231203_redacted.csv", resulting in Figures S5
 and Table S3. Species IDs redacted in this version of the data due to
 ongoing analysis for a different paper. #### File:
 code\_resubmission\_20250314.zip **Description:** Zip file containing R
 source files and accompanying data required for analyses in the paper. ###
 Files and variables contained in
 "code\_resubmission\_20250314.zip" 1.
 **vpi_master_co_il_noc_clean_A8.csv:** Near-complete vertically integrated
 time series for all radars/seasons consolidated into a single data frame
 2. **vpi_list_allseasons_clean_noc_A8.rds:** RDS file containing a list of
 vertically integrated profiles from Colombia for each season/radar used in
 an analysis, separated for inspection and plotting. 3.
 **vpi_list_usa_noc_A8_20240919.rds:** RDS file containing a list of
 vertically integrated profiles from the USA for each season/radar used in
 an analysis, separated for inspection and plotting. 4.
 **vpi_migration_traffic_summary_A8_20240920.csv:** Migration traffic
 summary generated in "migration traffic4pub.R" and subsequently
 annotated with quality information from specting vertical profiles in the
 RDS files above. 5. **vpi_thin_props_clean_A8_3.csv:** Data frame of
 single vertically integrated radar scans per night, used in GAM analysis
 to quantify effects of weather on nightly bird migration. 6.
 **all_radars_thinned_vpts_df_CLEAN_A8_20240714.csv:** Data frame of full
 profiles from single radar scans per night, used in GAM analysis to
 quantify effects of weather on altitude selection. 7.
 **all_radars_thinned_vpi_cfdates_CLEAN_A8.csv:** Data frame of full
 profiles from single radar scans per night and filtered to dates common
 between all Colombian radar stations to directly compare volume and
 directions between sites. 8. **night_summary-20231203_redacted.csv:** Data
 frame of nocturnal flight call detections and sampling effort with nightly
 calls per hour for each species and location. However, species information
 has been redacted prior to publication in a different manuscript and data
 set. Common variables within the above files (see Dokter et al. 2019
 *Ecography* for details). Other variables are explained in the code mtr:
 migration traffic rate, birds/km/hr vid: vertically integrated density,
 birds/km^2 vir: vertically integrated reflectivity, volume/km^2 rtr:
 reflectivity traffic rate, volume/km/hr mt: migration traffic, total
 estimated individual birds per time bin based on radar cross section rt:
 reflectivity traffic, total estimated reflectivity volume per time bin ff:
 bird ground speed dd: bird ground direction u: bird east/west directional
 component v: bird north/south directional component eta: reflectivity,
 cm^2/km^3 noy: night of the year ## Code/software All analyses conducted
 with R version 4.2.1 in R Studio Version 2024.12.0+467