Data and code from: Shifting gears in a shifting climate: birds adjust migration speed in response to spring vegetation green-up

Amaral, Bruna 1 ; Youngflesh, Casey 2 ; Tingley, Morgan 3 ; Miller, David 1

Published Jun 01, 2026 on Dryad. https://doi.org/10.5061/dryad.ttdz08m6w

Data files

Jun 01, 2026 version files 90.35 MB

Amaral_etal_2025dd_repo.zip

90.31 MB
README.md

35.22 KB

Abstract

Aim: Investigate whether birds use vegetation green-up, a measure of spring arrival, as a cue to shift their migration speed in response to climate change by examining: (1) how green-up moves in the landscape, (2) how bird migratory speed responds to green-up, (3) how species traits affect migratory speed, and (4) how migration speed affects arrival time at breeding sites.

Location: Eastern North America.

Time period: 2002 to 2017.

Major taxa studied: 55 species of eastern North American Passerines.

Methods: We calculated speed at the migration front using arrival dates derived from 16 years of eBird data with a linear regression. Similarly, we calculated the advancement speed of forest vegetation green-up using satellite data. Green-up effects on bird speed were tested using generalized additive models.

Results: On average, songbirds migrate northward during spring at a mean speed of 63 km/day. We observed strong non-linear effects of latitude, with bird migration speed accelerated, and green-up speed slowed as the distance from the equator increased. Annual and spatial variation in bird migration speed depended on the local green-up date and how quickly green-up was advancing northward: years with earlier and faster green-up were associated with higher migration speeds. Bird arrival relative to green-up was strongly influenced by two variables: how early green-up was, and how fast birds were migrating.

Main conclusions: The variation of bird migration speed with green-up suggests birds can shift migration speed to ‘catch up’ with earlier springs. However, the stronger effect of green-up date compared to migration speed suggests that birds do not fully compensate for arrival time by simply migrating more quickly. Climate change will likely outpace birds’ ability to speed up their migration and adapt to new phenological regimes.

Bruna R. Amaral, Casey Youngflesh, Morgan Tingley, and David A. Miller

Publication on Diversity and Distributions

Dryad: https://doi.org/10.5061/dryad.ttdz08m6w

GitHub: https://github.com/br-amaral/BirdMigrationSpeed

This repository contains code to calculate bird migration and green-up speeds, fit models, and make figures and predictions of bird migration front speed. All the code (numbered in order of execution), data necessary to run the analysis, and output are provided. Files are compressed in a single .zip folder called Amaral_etal_2025dd_repo.zip

Folder structure:

code: all the R script files used to run the analysis, numbered according to the order they should be executed. Details on the specific files used as input or output can be found in the<b>data</b> folder description.
data: all the data used in the analysis, including our output. Divided into:
- source: files from different studies used in our analysis:
  - Speed_data: folder with data from the literature on species' active flight migratory speeds.
  - philo_tree: folder with the phylogenetic tree of all species in our study¹.
  - traits: folder with data on species gathered from the literature.
- res: model results output for the 4 analyses we conducted.
figures: folder with figures from the manuscript, which also serves as a placeholder when running the code to generate the figures.
tables: folder with tables from the manuscript.
appendix: folder with the appendix S1 from the manuscript.

Code

1_GetEstimates.R: code to import phenological mismatch data (results from Youngflesh et al 2021, available in their Zenodo repository) and create matrices with bird and green-up velocity to run models in 3_ModelPlots.R

Input:

Output:

2_AddSpsData.R: code to add species traits data from the literature and also calculate extra traits from the data

Input:

Output:

data/final.rds

3_ModelPlots.R: code to analyze how bird arrival date speed is affected by green-up, bird traits, and latitude, which factors contribute to anomalies in lag, and how green-up varies according to latitude. Model summaries and figures are created here.

Source:

5_Maps.R

Input:

Output:

4_PredictSpsSpeed.R: code to predict how much species speed will change with 1 sd of green-up date or speed

Input:

5_Maps.R: code to make maps with migration speed and direction for species and green-up

Source:
map.R: function to create maps
Input:

        - data/data_arr.rds
        - data/source/traits/data_sensi.rds
        - data/species_Grid.RData
        - data/fit_df_tab5.rds
        - data/master_cell_grid.rds
        - data/for_green-up_dl.rds

Input:

6_StopoverTime.R: code to calculate stopover time based on our speed estimates and bird flight speeds from the literature

Input:

Output:

data/stopover_percent.csv

7_PhyloRes.R: code to check for the effect of phylogenic relationships on our results

Input:

SUP_sensiana: code to run sensitivity analysis
Input:

data

data/birdgreen.rds: tibble with bird and green-up speed calculations from 1_GetEstimates.R
data/birdgreen_st3000.rds: tibble with bird and green-up speed calculations filtering species faster than 3000
data/cell_grid_master.rds: grid cell information
data/cellcoor.rds: tibble with XY coordinates of each cell, and a cell id number
data/cellnumbs.rds: tibble with cell numbers that start at 1
data/data_arr.rds: tibble with arrival date estimates (Youngflesh et al. [2021])
data/final.rds: tibble with bird and green-up information, plus species traits
data/fit_df_tab5.rds: average sensitivity for species
data/for_green-up_dl.rds: estimates of green-up date (Youngflesh et al. [2021])
data/master_cell_grid.rds: information about the grid cell locations
data/species_Grid.RData: map grid for each species (migratory and breeding cell information)
data/stopover_percent.csv: matrix with the stopover time for species according to their flight speed and our estimates
data/velocityB.rds: tibble with calculated bird speeds from 1_GetEstimates.R

data/source
data/source/philo_tree/tree-pruner-c9524fe9-2d15-4b45-a65a-03b4fa85e4e9/output.nex: phylogenetic tree for birds
data/source/sps_list: list of bird species
data/source/Speed_data/Speed_table_small.csv: flight speed for birds from the literature (specific references on Appendix S1)
data/source/spskey.csv: species common and scientific names
data/source/traits/birds_HWI.csv: bird hand-wing index gathered from Sheard et al. 2020
data/source/traits/data_sensi.rds: bird sensitivity data gathered from Youngflesh et al. 2021
data/source/traits/gcb14540-sup-0001-supinfo_mass.csv: bird body mass data from Horton et al. 2019 found on supplementary materials
data/source/traits/jane13345-sup-0002-tables1_diet.csv: bird diet data from La Sorte & Graham 2021 found on supplementary materials
data/source/traits/species_tax_ord.csv: bird family data from BirdTree.org
data/source/traits/sps_migtime.csv: Bird migration time data.
data/source/traits/Table_S1.csv: bird overwinter latitude data from Youngflesh et al. 2021

data/res
data/res/mod_lat_guspe.rds: model one results
data/res/mod_gu.rds: model two results
data/res/mod_tra.rds: model three results
data/res/mod_lag.rds: model four results

figures

Figure 1: Bird migration velocity (direction (a) and speed (b)) in the Eastern flyway in North America. (a) Arrows represent median bird migration direction according to latitude across years (2002 to 2017) for all species combined. Birds are mostly moving north, as seen in the arrows showing migration direction. (b) Median bird migration speed according to latitude across years (2002 to 2017) for all species combined is represented in the shades of purple and yellow. Birds move faster in higher latitudes as seen by the yellow781 coloured cells in the plot in the north. Species have different occurrence ranges and data available for different cells and years; the migration speed and direction in a cell might represent different sets of species.
Figure 2: Species and trait-specific bird front migration speed (km/day). Bird migration speed estimates in the Eastern flyway in North America for each species grouped mean estimates distribution (histogram, log scale y-axis). Each boxplot represents a species in a year and a cell (25th and 75th percentiles), and species are ordered according to their median speed. The squares on the bottom represent the data used in model 3 to estimate bird migration speed (details in Table 1, legend on the bottom right), except for species diet and migration time. Both variables were removed from the model due to the lack of many species in each category.
Figure 3: Mean bird migration speed (in pink, log(km/day)) varying according to latitude estimated by model 2 (details on Table 1). Vegetation green-up speed varied according to latitude (in green, log(km/day)) according to model 1. Bird speed tends to increase with latitude, while green-up speed decreases with latitude in the Eastern flyway in North America. Lines represent mean estimate, and the shaded region the 95% confidence interval.
Figure 4: Effect of vegetation green-up on bird migration speed (km/day) in the breeding (yellow and solid) and migratory range (orange and dashed) Eastern flyway in North America (model 2). Lines (a, b) and dots (c) represent the mean estimate, and the shaded areas (a, b) and whiskers (c) represent the 95% confidence interval. (a) Anomaly in green-up date (ordinal day, scaled) effect on bird migration speed. Early green-up years were associated with a faster migration pace. (b) Anomaly in green-up speed (km/day, base 10 logarithm and scaled) effect on bird migration speed. Fast green-up years were associated with a fast migration pace. (c) Bird migration speed varied according to bird range type. Birds moved slower in breeding cells than in migratory cells.
Figure 5: Bird traits that influenced migration speed in the Eastern flyway in North America. The pink line indicates the average relationships, while the shaded area indicates the 0.95 confidence interval. The first arrival date was positively associated with bird migration speed, with birds migrating faster when they arrive later.
Figure 6: Coefficient effects of model 4 (details in Table 1) on anomaly on bird relative arrival (vegetation green-up arrival date minus bird arrival date, scaled). Positive values of anomaly on relative arrival (y-axis) represent birds arriving earlier than green-up, whereas negative values represent birds arriving behind green-up. The green dashed line represents the effect of the green-up date z-score on the relative arrival anomaly. Early green-up years are strongly associated with birds arriving relatively later than average, relative to green-up. The pink dashed line represents the effect of bird migration speed prior to arrival (km/day, z-score) on relative arrival anomaly. Birds are migrating slower on average (negative z-score); they are late in relation to green-up. The blue dashed line shows the effect of the first-arrival date (ordinal date z-score) on anomalies on relative arrival anomaly. First-arrival date and anomalies in relative arrival presented a very weak relationship. Even though both the green-up date and bird migration speed prior to arrival were associated with relative arrival anomaly, the effect size of the green-up date was almost twice the effect of bird migration speed prior to arrival.

tables

Table 1: Generalised additive models and their response variables, predictors, and results. Coefficient estimates and confidence intervals are shown for the linear fixed effects of the four models that investigated variation in bird migratory and green-up speed. For the random effects and smooth terms, we show how much variance they are explaining, as well as the residual variance estimate. Bold estimates indicate coefficient estimates with 95% confidence intervals that do not overlap zero in the fixed effects; for the non-linear and non-fixed effects, bold font indicates a p-value smaller than 0.05 in the likelihood ratio test that uses a reference distribution to test a null hypothesis (that the variance is 0) using the estimated degrees of freedom and maximum degrees of freedom for each term.

appendix

Appendix S1 (ddi70033-sup-0001-AppendixS1.docx): file with supplementary tables, figures, and equations.

Description of all columns of each file of the data:

data/birdgreen_st3000.rds

year (numeric): year of sampling
cell (numeric): cell id number
species (character): bird species scientific name
mig_cell (logical): TRUE if the cell is within the breeding range of the species
breed_cell (logical): TRUE if the cell is within the migratory range of the species (note that some cells can be both breeding and migratory)
cell_lat (numeric): latitude scaled of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
arr_GAM_mean (numeric): estimate of the posterior mean arrival date (calendar day) of a species in a cell
arr_GAM_sd (numeric): estimate of the posterior standard deviation arrival date (calendar day) of a species in a cell
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from the MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within the cell
NArr (numeric): number of neighboring cell with bird arrival data
vArrMag (numeric): bird velocity magnitude (speed, km/day)
vArrAng (numeric): bird velocity angle (direction, radians)
angB (numeric): bird velocity angle in degrees
xB (numeric): x coordinate of the direction of bird migration for a given cell
yB (numeric): y coordinate of the direction of bird migration for a given cell
NGr (numeric): number of neighboring cell with green-up data
vGrMag (numeric): green-up velocity magnitude (speed, km/day)
vGrAng (numeric): green-up velocity angle (direction, radians)
angG (numeric): green-up velocity angle in degrees
xG (numeric): x coordinate of the direction of green-up for a given cell
yG (numeric): y coordinate of the direction of green-up for a given cell
lag (numeric): bird arrival date minus green-up date (days)
AnomDArr (numeric): bird arrival date anomaly (scaled bird arrival date)
AnomDGr (numeric): green-up date anomaly (scaled green-up date)
AnomVArr (numeric): bird speed anomaly (scaled bird speed)
AnomVGr (numeric): green-up speed anomaly (scaled green-up speed )
AnomLag (numeric): lag anomaly (scaled lag)
cell_lat2 (numeric): latitude in degrees of cell centroid

data/birdgreen.rds

year (numeric): year of sampling
cell (numeric): cell id number
species (character): bird species scientific name
mig_cell (logical): TRUE if the cell is within the breeding range of the species
breed_cell (logical): TRUE if the cell is within the migratory range of the species (note that some cells can be both breeding and migratory)
cell_lat (numeric): latitude scaled of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
arr_GAM_mean (numeric): estimate of the posterior mean arrival date (calendar day) of a species in a cell
arr_GAM_sd (numeric): estimate of the posterior standard deviation arrival date (calendar day) of a species in a cell
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within cell
NArr (numeric): number of neighboring cell with bird arrival data
vArrMag (numeric): bird velocity magnitude (speed, km/day)
vArrAng (numeric): bird velocity angle (direction, radians)
angB (numeric): bird velocity angle in degrees
xB (numeric): x coordinate of the direction of bird migration for a given cell
yB (numeric): y coordinate of the direction of bird migration for a given cell
NGr (numeric): number of neighboring cell with green-up data
vGrMag (numeric): green-up velocity magnitude (speed, km/day)
vGrAng (numeric): green-up velocity angle (direction, radians)
angG (numeric): green-up velocity angle in degrees
xG (numeric): x coordinate of the direction of green-up for a given cell
yG (numeric): y coordinate of the direction of green-up for a given cell
lag (numeric): bird arrival date minus green-up date (days)
AnomDArr (numeric): bird arrival date anomaly (scaled bird arrival date)
AnomDGr (numeric): green-up date anomaly (scaled green-up date)
AnomVArr (numeric): bird speed anomaly (scaled bird speed)
AnomVGr (numeric): green-up speed anomaly (scaled green-up speed )
AnomLag (numeric): lag anomaly (scaled lag)
cell_lat2 (numeric): latitude in degrees of cell centroid

data/cellcoor.rds

cell (numeric): cell id number
cell_lat (numeric): latitude in degrees of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid

data/cellnumbs.rds

cell (numeric): cell id number
cell2 (numeric): cell id number starting from 1

data/final.rds

year (numeric): year of sampling
cell (numeric): cell id number
species (character): bird species scientific name
mig_cell (logical): TRUE if the cell is within the breeding range of the species
breed_cell (logical): TRUE if the cell is within the migratory range of the species (note that some cells can be both breeding and migratory)
cell_lat (numeric): latitude scaled of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
arr_GAM_mean (numeric): estimate of the posterior mean arrival date (calendar day) of a species in a cell
arr_GAM_sd (numeric): estimate of the posterior standard deviation arrival date (calendar day) of a species in a cell
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within cell
NArr (numeric): number of neighboring cell with bird arrival data
vArrMag (numeric): bird velocity magnitude (speed, km/day)
vArrAng (numeric): bird velocity angle (direction, radians)
angB (numeric): bird velocity angle in degrees
xB (numeric): x coordinate of the direction of bird migration for a given cell
yB (numeric): y coordinate of the direction of bird migration for a given cell
NGr (numeric): number of neighboring cell with green-up data
vGrMag (numeric): green-up velocity magnitude (speed, km/day)
vGrAng (numeric): green-up velocity angle (direction, radians)
angG (numeric): green-up velocity angle in degrees
xG (numeric): x coordinate of the direction of green-up for a given cell
yG (numeric): y coordinate of the direction of green-up for a given cell
lag (numeric): bird arrival date minus green-up date (days)
AnomDArr (numeric): bird arrival date anomaly (scaled bird arrival date)
AnomDGr (numeric): green-up date anomaly (scaled green-up date)
AnomVArr (numeric): bird speed anomaly (scaled bird speed)
AnomVGr (numeric): green-up speed anomaly (scaled green-up speed )
AnomLag (numeric): lag anomaly (scaled lag)
cell_lat2 (numeric): latitude in degrees of cell centroid
winlat (numeric): mean latitude in which species overwinter
species2 (character): species name with space and not underscore
xi_mean (numeric): posterior mean of estimate for species-specific sensitivity (days/day) to green-up for each cell
sensi_mean (numeric): mean species sensitivity (days/day) for all cells
sensi_sd (numeric): standard deviation of bird sensitivity (days/day)
Order (character): species taxonomic order
Family (character): species taxonomic family
Body_mass_g (numeric): species average body mass in grams
Time (character): time of the day that species migrate (diurnal or nocturnal)
Diet (character): species diet
FamilyColor (character): color according to species family
TaxOrder (numeric): number for each taxonimic family to order figures
HWI (numeric): hand-wing index for each species
ea_lat_m (numeric): mean first arrival date for a species accross all years for all cells
ea_lat (numeric): : mean first arrival date for a species in each cell
ea_lat_yr (numeric): mean first arrival date for a species at each year for all cells
ea_lat_yr_ano (numeric): anomaly of mean first arrival date for a species at each year for all cells
ea_lat_ano (numeric): anomaly of mean first arrival date for a species accross all years for all cells

data/fit_df_tab5.rds

species (character): bird species scientific name
slat (numeric): scaled cell centroid latitude
lat (numeric): latitude in degrees of cell centroid
sensim (numeric): posterior mean of estimate for species-specific sensitivity (days/day) to green-up for each cell

data/for_green-up_dl.rds

year (numeric): year of sampling
cell (numeric): cell id number
cell_lat (numeric): latitude in degrees of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within cell
gr_pcell (numeric)
gr_type (character): type of greenup - MidGreenup here, which is 50% of maximum (see MCD12Q2 product guide for details)

data/master_cell_grid.rds

long (numeric): longitude in degrees of cell centroid
lat (numeric): latitude in degrees of cell centroid
order (numeric): number of which of the 6 corners of the hexagon the coordinates are
hole (logical): indicates if there are any missing coordinates
piece (numeric): indicates if we all the points of the hexagon are present
group (numeric): group which a row belongs to
cell (numeric): cell id number

data/species_Grid.RData

species_Grid (character): list with the names of all species grid cell maps that represent their distribution, and cells with data

data/stopover_percent.csv

Species name (character): bird species scientific name with space
Flight Speed (numeric): bird active flight speed (km/day)
Migratory Speed (numeric): bird migratory flight speed (km/day)
Migration distance (numeric): distance which birds migrate from overwintering latitude (km)
Proportion of time at stopover site (numeric): proportion of time that birds spend not flying during migration

data/velocityB.rds

species (character): bird species scientific name
year (numeric): year of sampling
cell (numeric): cell id number
NArr (numeric): number of neighboring cell with bird arrival data
vArrMag (numeric): bird velocity magnitude (speed, km/day)
vArrAng (numeric): bird velocity angle (direction, radians)
angB (numeric): bird velocity angle in degrees
xB (numeric): x coordinate of the direction of bird migration for a given cell
yB (numeric): y coordinate of the direction of bird migration for a given cell

data/res/data_trait.rds

year (numeric): year of sampling
cell (numeric): cell id number
species (character): bird species scientific name
mig_cell (logical): TRUE if the cell is within the breeding range of the species
breed_cell (logical): TRUE if the cell is within the migratory range of the species (note that some cells can be both breeding and migratory)
cell_lat (numeric): latitude scaled of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
arr_GAM_mean (numeric): estimate of the posterior mean arrival date (calendar day) of a species in a cell
arr_GAM_sd (numeric): estimate of the posterior standard deviation arrival date (calendar day) of a species in a cell
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within cell
NArr (numeric): number of neighboring cell with bird arrival data
vArrMag (numeric): bird velocity magnitude (speed, km/day)
vArrAng (numeric): bird velocity angle (direction, radians)
angB (numeric): bird velocity angle in degrees
xB (numeric): x coordinate of the direction of bird migration for a given cell
yB (numeric): y coordinate of the direction of bird migration for a given cell
NGr (numeric): number of neighboring cell with green-up data
vGrMag (numeric): green-up velocity magnitude (speed, km/day)
vGrAng (numeric): green-up velocity angle (direction, radians)
angG (numeric): green-up velocity angle in degrees
xG (numeric): x coordinate of the direction of green-up for a given cell
yG (numeric): y coordinate of the direction of green-up for a given cell
lag (numeric): bird arrival date minus green-up date (days)
AnomDArr (numeric): bird arrival date anomaly (scaled bird arrival date)
AnomDGr (numeric): green-up date anomaly (scaled green-up date)
AnomVArr (numeric): bird speed anomaly (scaled bird speed)
AnomVGr (numeric): green-up speed anomaly (scaled green-up speed )
AnomLag (numeric): lag anomaly (scaled lag)
cell_lat2 (numeric): latitude in degrees of cell centroid
winlat (numeric): mean latitude in which species overwinter
species2 (character): species name with space and not underscore
sensi (numeric): posterior mean of estimate for species-specific sensitivity (days/day) to green-up for each cell
sensi_mean (numeric): mean species sensitivity (days/day) for all cells
sensi_sd (numeric): standard deviation of bird sensitivity (days/day)
Order (character): species taxonomic order
Family (character): species taxonomic family
Body_mass_g (numeric): species average body mass in grams
Time (character): time of the day that species migrate (diurnal or nocturnal)
Diet (character): species diet
FamilyColor (character): color according to species family
TaxOrder (numeric): number for each taxonomic family to order figures
HWI (numeric): hand-wing index for each species
ea_lat_m (numeric): mean first arrival date for a species across all years for all cells
ea_lat (numeric): mean first arrival date for a species in each cell
ea_lat_yr (numeric): mean first arrival date for a species at each year for all cells
ea_lat_yr_ano (numeric): anomaly of mean first arrival date for a species at each year for all cells
ea_lat_ano (numeric): anomaly of mean first arrival date for a species across all years for all cells
sps_cell (numeric): unique combination of each species in each cell
xi_mean (numeric): posterior mean of species-level sensitivity
xi_sd (numeric): posterior sd of species-level sensitivity
ea_lat2 (numeric): mean first arrival date for a species in each cell in degrees

data/res/mod_gu.rds

gam object with results for model 2

data/res/mod_lag.rds

gam object with results for model 4

data/res/mod_lat_guspe.rds

gam object with results for model 1

data/res/mod_tra.rds

gam object with results for model 3

data/source/arrival_master_2020-07-21.csv

species (character): bird species scientific name
cell (numeric): cell id number
mig_cell (logical): TRUE if the cell is within the breeding range of the species
breed_cell (logical): TRUE if the cell is within the migratory range of the species (note that some cells can be both breeding and migratory)
cell_lat (numeric): latitude in degrees of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
arr_GAM_mean (numeric): estimate of the posterior mean arrival date (calendar day) of a species in a cell
arr_GAM_sd (numeric): estimate of the posterior standard deviation arrival date (calendar day) of a species in a cell
valid_GAM (logical): denotes whether a spcies-cell-year had a valid GAM estimate. Can be used to filter IAR-derived estimates for downstream analyses (see below).
arr_IAR_mean (numeric): posterior mean of IAR-derived arrival estimate
arr_IAR_sd (numeric): posterior mean of IAR-derived arrival estimate

data/source/MidGreenup_2020-08-06-forest.csv

year (numeric): year of sampling
cell (numeric): cell id number
cell_lat (numeric): latitude in degrees of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
gr_mn (numeric): posterior mean 'midgreen-up' date (calendar day) for all pixels classified as 'good' or 'best' that fall within cell that were classified as forest - green-up dates derived from the MCD12Q2 data product - land cover information derived from MCD12Q1 data product
gr_ncell (numeric): number of green-up pixels that met filtering criteria that fell within cell

data/source/Speed_data/Speed_table_small.csv

species (character): bird species scientific name
flight_speed (numeric): bird active flight flight speed (km/day)

data/source/spskey.csv

species (character): bird species common name
sci_name (character): bird species scientific name

data/source/traits/birds_HWI.csv

Species-ID (numeric): species unique number ID
Order (character): species taxonomic order
Species name (character): bird species scientific name
IUCN name (character): bird species scientific name according to the IUCN
Tree name (character): bird species phylogenectic name
HWI (numeric): hand-wing index for each species
species (character): bird species scientific name

data/source/traits/data_sensi.rds

sci_name (character): bird species scientific name
species (character): bird species common name
cell (numeric): cell id number
cell_lat (numeric): latitude in degrees of cell centroid
cell_lng (numeric): longitude in degrees of cell centroid
beta_mean (numeric): posterior mean of species/cell specific sensitivity of arrival to green-up
beta_sd (numeric): posterior sd of species/cell specific sensitivity of arrival to green-up
xi_mean (numeric): posterior mean of species-level sensitivity
xi_sd (numeric): posterior sd of species-level sensitivity
gamma_mean (numeric): posterior mean of the effect of latitude on xi
gamma_sd (numeric): posterior sd of the effect of latitude on xi

data/source/traits/species_tax_ord.csv

FamilyColor (character): color according to species family
species (character): bird species scientific name
TaxOrder (numeric): number for each taxonomic family to order figures

data/source/traits/sps_migtime.csv

CommonName (character): bird species common name
species (character): bird species scientific name
Order (character): species taxonomic order
Family (character): species taxonomic family
Time (character): time of the day that species migrate (diurnal or nocturnal)

data/source/traits/Table_S1.csv

Species (character): bird species scientific name with space
Common name (character): bird species common name with space
Order (character): species taxonomic order
Included (logical): species included in the analysis (original, not this paper)
Mig Pace (numeric): how fast species moved (days/deg latitude)
Arr date (numeric): species mean arrival date (ordinal date)
Overwinterlatitude (numeric): mean latitude in which species overwinter
PC1 (numeric): trais PC1 score for each species (migration pace, arrival date, overwinter latitude)
species (character): bird species scientific name

1 - phylogenetic tree data from Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491:444-448

Data and code from: Shifting gears in a shifting climate: birds adjust migration speed in response to spring vegetation green-up

Data files

Abstract

README: Data and code from: Shifting gears in a shifting climate: birds adjust migration speed in response to spring vegetation green-up

Folder structure:

Code

data

data/source

data/res

figures

tables

appendix