Data and code from: Can tropical birds withstand climate change? An empirical test of the microclimate refugia hypothesis in Amazonian forests
Data files
Nov 10, 2026 version files 2.65 MB
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2024_longterm_hobos.csv
710.52 KB
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2024_shortterm_hobos.csv
1.75 MB
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all_paired_captures_082724.csv
99.53 KB
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BDFFP_species_attributes_102726.csv
14.74 KB
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capture_rates.csv
16.97 KB
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ekr_microclimates_netcoord_112224.csv
1.60 KB
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nh_per_station.csv
1.25 KB
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oikos_stats_updated_072326.R
46.81 KB
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README.md
8.83 KB
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site_class_121424.csv
365 B
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stations_grouped.csv
334 B
Abstract
Dataset DOI: 10.5061/dryad.6q573n6g0
Files and variables
File: 2024_longterm_hobos.csv
Description: Microclimate hobo datalogger data. Dataloggers recorded continuously over multiple days and data was combined and averaged with short term data.
Variables
- new_dttm: converted date-time column year-month-day hour(24):min:sec
- temp: ambient temperature reading (celsius)
- rh: ambient relative humidity (%) reading
- station: banding station code
- plateau_igarape: microclimate classification (igarape = riparian)
- fazenda: research area in which stations were grouped into
- primary_secondary: forest age classification
File: all_paired_captures_082724.csv
Description: Banding data for bird captures.
Variables
- capture_id: Capture number. Every capture in our dataset has a unique number.
- capture_time: Time bird was extracted from net (24 hour).
- recorder: Initials of recorder.
- bander: Initials of bander.
- code: Recapture, new capture, unbanded, same-day recapture
- band_size: Band size
- band_number: Band number
- sci_name: Scientific name
- sp_code: A 6 letter code composed of the first 3 letters of the genus and the first 3 letters of the species.
- cp: Cloacal protuberance (rated on a 1-5 scale)
- bp: Brood patch (rated on a 1-5 scale)
- fat: Fat score (0-100%)
- body_molt: Body molt (0-100%)
- tail_molt: Tail molt (asymmetrical / symmetrical / none)
- wing_molt: Wing molt (asymmetrical / symmetrical / none)
- ff_wear: Flight feather wear (rated on a 1-5 scale)
- molt_limit: Presence or absence of a molt limit and if present, where that limit is visible.
- skull: Skull ossification (0-100%)
- wing_cord: Wing chord (measured unflattened)
- tail_length: Tail length (measured from the central rectrices)
- mass: Mass of bird in grams
- cycle: Cycle based on W-R-P system
- how_cycle: How cycle was determined
- sex: Sex of bird (if known)
- how_sex: How sex was determined
- status: Status of bird (uninjured, injured)
- ketone: Blood ketone reading
- ketone_time: Time ketone reading was taken
- day: Day
- month: Month
- year: Year
- station: Specific banding station in which the bird was captured.
- site_type: Microclimate type (igarape/plateau)
- fazenda: General sampling location at the BDFFP.
- forest_struct: Forest age of station (primary / secondary)
- net: Net number in which the bird was captured.
- temp_1: First temperature reading (°C)
- temp_2: Second temperature reading (°C)
- temp_3: Third temperature reading (°C)
- avg_temp: Average temperature of 3 temperature readings (°C)
- gape: Presence or absence of gape
- striations: Striations (0-100%) for hummingbirds only.
- tarsus: Left tarsus, mm
- bill: Nares to tip of bill, mm
- notes: general notes
Missing data: empty cells indicate that the information was not recoded for that specific capture. These cells have intentionally been left blank rather than filled with "NA" or another placeholder. Please do not convert blanks to NA before running the provided R script, as the script expects empty cells and replacing them will cause errors.
File: 2024_shortterm_hobos.csv
Description: Microclimate hobo datalogger data. Dataloggers recorded microclimate data only during banding hours and data was combined and averaged with long term data. See longterm_hobos for variable descriptions.
File: BDFFP_species_attributes_102726.csv
Description: Document with relevant characteristics for all species captured.
Variables
- species_pter: Outdated scientific name
- species_sacc: Updated scientific name
- eng_name: English common name
- family: Family
- guild: Guild
- vertical_stratum: Vertical stratum which they occupy within the forest.
- diet: Diet
- substrate: Foraging substrate
- foraging_mode: Foraging method
- sociality: Sociality (especially for army-ant followers)
Missing data: empty cells indicate that the information is not provided for a particular species. These cells have intentionally been left blank rather than filled with "NA" or another placeholder. Please do not convert blanks to NA before running the provided R script, as the script expects empty cells and replacing them will cause errors.
File: capture_rates.csv
Description: Calculations for capture rates of each species at each banding station.
Variables
- sci_name: Scientific name
- station: Banding station
- count: number of captures / banding station
- sum_nh: sum of 2024 and 2025 net-hours for that station (see description of nethours below).
- capt_rate: capture rate (# captures / sum_nh)
File: ekr_microclimates_netcoord_112224.csv
Description: Net coordinates for microclimate mistnets (used in distance analysis).
Variables
- station: Unique code for banding station
- point name: banding station code with specific net number
- long: Longitude
- lat: Latitude
- elev: Elevation (meters)
- fazenda: Sampling site (contains multiple banding stations)
- forest_struct: Forest age (primary / secondary)
- site_type: Microclimate type (igarape / plateau)
File: nh_per_station.csv
Description: Calculations for net-hours variables (nethours = #nets open / # hours open per station)
Variables
- station: Unique code given to each banding station.
- class: A grouping variable showing microclimate type and forest age.
- site_type: Microclimate type (plateau or igarape)
- forest_struct: Forest age (primary or secondary)
- nh_2023: net-hours calculation for 2024 field season.
- nh_2024: net-hours calculation for 2025 field season.
- sum_nh: Sum of 2024 & 2025 net-hours.
File: site_class_121424.csv
Description: Used to classify each station by microclimate type, forest age, and "class" (a combination of microclimate type and forest age).
Variables
- site: (unique code given to each banding station)
- site_type: Microclimate type (plateau or igarape)
- forest_struct: Forest age (primary or secondary)
- class: Combination of microclimate type and forest age.
File: stations_grouped.csv
Description: Used to group banding stations into larger groupings.
Variables
- station: Unique name given to each banding station.
- station_grouped: New grouping for each banding station.
File: oikos_stats_updated_072326.R
Description: This R script walks through all the statistical models, data transformations, and figure generation for this study. Requires the data files to be read in with blanks preserved as empty cells (see "Missing data" above). Do not recode blanks as NA.
Required R packages
tidyverse: the core suite (dplyr, ggplot2, tidyr, readr, etc.) for data manipulation and plottingpurrr: functional programming tools for iterating over lists and columnslubridate: working with dates and timeshms: handling time-of-day values (hours:minutes:seconds)lme4: linear and generalized linear mixed-effects models (lmer,glmer)afex: an interface for ANOVA and mixed models, with p-values for mixed modelsMASS: negative binomial GLMs (glm.nb) andstepAICcar: ANOVA tables, VIF for collinearity, Levene’s test, and regression diagnosticsemmeans: estimated marginal means and post-hoc pairwise comparisonsAICcmodavg: AICc-based model selection and model averagingperformance: model checks such as R², overdispersion, residual diagnostics, and collinearitysandwichandlmtest: robust (heteroskedasticity-consistent) standard errorsRVAideMemoire: assorted stats helpers, including post-hoc tests and overdispersion checks for mixed modelsvegan: ordination such as NMDS, PERMANOVA, and dissimilarity matricesbetapart: partitioning beta diversity into turnover and nestedness componentsgeosphere: distances and geometry between geographic coordinates (e.g., site-to-site distances)ggrepel: non-overlapping text labels on ggplot figuresGGally: extensions to ggplot2patchwork: combining multiple ggplots into a single multi-panel figureflextable: formatting tables for Word, PowerPoint, or HTML output
Code/software
R studio Version 2026.01.1+403 was used for statistical analyses. All loaded packages and workflow for each analysis are included in the R script provided.
Access information
Other publicly accessible locations of the data:
- n/a
Data was derived from the following sources:
- Species attributes were derived from the Open Traits Network AVONET database (https://opentraits.org/datasets/avonet.html)
