Dataset DOI: 10.5061/dryad.hmgqnk9zp

We have submitted the following four raw data files: Dryad_MASTER_Juv_Capture_History_CJS.csv, Dryad_Logit_exposure_data_2026.csv, Dryad_MASTER_Veg_survey_data.csv and Dryad_MASTER_Nest_TIMO_2023.csv 

These datasets can be used in collaboration with the following three R scripts:  Dryad_LogisticExposureModel_2026.R, Dryad_TIMO_CJScode_ms.R, Dryad_Monarch_nest_analysis.R

Description of the data and file structure:

These files constitute the data scripts needed to reproduce results from the associated manuscript. This manuscript concerned the reproductive ecology of the Tinian monarch. Primarily, we looked at nest site selection and success, and juvenile survival.  

Files:

File: Dryad_MASTER_Juv_Capture_History_CJS.csv

Variables:

• ch: capture history-1 indicates the bird was detected, 0 indicates it was not. Time between detections is found in the Time_interval column. 
• Tag: Individual marker code. The color codes are comprised of three single letter color codes and the "S" federal marker. G=green, O=Orange, Y=Yellow, W=White, Bk=Black, B=Blue, Gy=Grey, R=Red.
• Territory: Unique two-letter code for territory identity. Can be referenced against  "NEST_ID" and "TERRITORY" columns in Dryad_MASTER_Nest_TIMO_2023.csv for full name and relationship to other nesting metrics. 
• RIV_Classification: Nest-site habitat designation based on basal area and tree density data to calculate the relative importance value (RIV) of native trees, non-native trees, and tangantangan trees in each plot, following the methods of Chavez et al 2020. We considered native forest plots to be those with a native forest RIV score of >0.6, tangantangan plots to be those with a tangantangan RIV score of >0.6, and secondary forest to be all other forest plots with canopy cover >20%. We considered any plots with <21% canopy cover as open land. N/As indicate sites for which required vegetation surveys were not conducted. Use original habitat designations in this case.
• OG_Habitat: Original landscape-level habitat designation 
• Time_interval: days between relights 

File: Dryad_Logit_exposure_data_2026.csv

Variables:

• Study site: Local name for study area
• Territory_Name: Full name for individual territory
• Nest_ID: Alphanumeric nest code. Unique for every nest. First two letters match the territory name, followed by year nest found, followed by order of nest in that year (A-Z)
• RIV_Classification: RIV_Classification: Nest-site habitat designation based on basal area and tree density data to calculate the relative importance value (RIV) of native trees, non-native trees, and tangantangan trees in each plot, following the methods of Chavez et al 2020. We considered native forest plots to be those with a native forest RIV score of >0.6, tangantangan plots to be those with a tangantangan RIV score of >0.6, and secondary forest to be all other forest plots with canopy cover >20%. We considered any plots with <21% canopy cover as open land.
• Total.exposure: Days nest was exposed. Calculated via Mayfield 1975 method
• NEST_FATE: whether nest fledged at least one young or failed
• FATE_Binary: 0/1 success or failure
• Nest_plant: Local Chamorro or English name for nest plant
• Scientific_name: Scientific name for nest plant
• NestPlant_Native: Native or non-native designation
• Nest_height_.cm.: Nest height measured from rim to ground 
• Plant_height_.cm.: Plant height from ground to apex
• Number_of_branches_supporting _nest: Number of nest support branches
• Canopy_height: Estimation of canopy height
• Number_of_stems.*vines_ect.*Within.5m: Measured assesibility to arboreal predators. We counted the number of “branches”, which included stems/trunks, and vines >4 mm in diameter within a 0.5 m radius sphere around the nest
• Average_visibility: An average of % visibility taken from all 4 cardinal directions
• Percent_canopy_cover_: Estimation of percent canopy cover
• Tallest_tree_in_plot: Apex height of tallest tree in nest plot
• Scientific_name: Scientific_name of called tree in plot
• Apex_height_.m.: Height of tallest tree in plot
• Distance_from_tallest_tree_to_nest_.m.: Distance from tallest tree to nest
• Number_of_saplings: Total saplings (sapling= <5cm Diameter breast height) in plot

• Number_of_trees: Total trees in plot (tree= >5cm DBH)

File: Dryad_MASTER_Veg_survey_data.csv

Variables:

• Study site: Local name for study area
• Habitat_type: Original, landscape-scale designation for nest-site habitat type. Options included Tangan, Native, and Secondary forest types
• Microsite_habitat: Nest-site-scale designation for habitat type. Determined by proportion of tangan and native tree types. Tangan forest= >50% tangan trees, Native forest= >50% native trees, secondary forest= everything else. 
• Territory_Name: Full name for individual territory
• Nest_ID: Alphanumeric nest code. Unique for every nest. First two letters match the territory name, followed by year nest found, followed by order of nest in that year (A-Z)
• RIV_Classification: RIV_Classification: Nest-site habitat designation based on basal area and tree density data to calculate the relative importance value (RIV) of native trees, non-native trees, and tangantangan trees in each plot, following the methods of Chavez et al 2020. We considered native forest plots to be those with a native forest RIV score of >0.6, tangantangan plots to be those with a tangantangan RIV score of >0.6, and secondary forest to be all other forest plots with canopy cover >20%. We considered any plots with <21% canopy cover as open land.
• Date: Date vegetation survey was conducted. Format: MM/D/YY. The Dryad_MASTER_Nest_TIMO_2023.csv has code to help R manage the date. 
• Time: Time vegetation survey was conducted
• Paired_site?: No= nest site, Yes=paired sites. Paired sites were randomly chosen locations 25 m from nest sites where forest structure elements were measured
• Nest_plant: Local Chamorro or English name for nest plant
• Scientific_name: Scientific name for nest plant
• Native: Indicates if nest plant is native or non-native. Yes=Native, No=Non-native, N/A=No nest tree (i.e. for paired plots)
• Nest_height_.cm.: Nest height measured from rim to ground 
• Plant_height_cm: Nest plant height measured from ground to apex of tree. In cases where the nest associated stem was a propagule of a strangler tree (primarily Ficus tinctoria), the apex height was measured for the associated stem, and not the parent tree. 
• Plant_diameter_below_nest_cup_(mm): Diameter of stem measured directly below nest
• Number_of_branches_supporting _nest: Number of nest support branches
• Diameter_of_branch_1_(mm): This and the following 6 columns (Diameter of branch 1-7) are measurements of the support branches. Nest trees had 2-7 support branches. N/A indicates the absence of a support branch. 
• Distance_to_plant_edge_(cm): Distance from center of nest to host plant edge
• Distance_to_main_trunk_(cm): Distance from center of nest to main trunk
• Canopy_heigh_(cm): Estimation of canopy height above next cup
• Number_of_stems_vines_ect.Within.5m: Measurement of accessibility of nest to arboreal predators (rats). We counted the number of “branches”, which included stems/trunks, and vines >4 mm in diameter within a 0.5 m radius sphere around the nest
• Percent_visible_N (following columns are N-W): Estimation of nest visibility from all 4 cardinal directions. Taken from 1 m away at eye level. 
• Percent_bare_ground: An estimation of the portion of bare ground in the plot 
• Percent_litter: An estimation of the portion of plant litter on the ground in the plot 
• Percent_rock: An estimation of the portion of plant litter on the ground in the plot 
• Percent_plant_cover: An estimation of the proportion of vegetative ground cover (plants <1m tall) in the plot
• Canopy_cover_at_10_m: Estimation of percent canopy cover sited directly upwards with an ocular tube 10 m from the nest
• Canopy_cover_at_8_m: Estimation of percent canopy cover sited directly upwards with an ocular tube 8 m from the nest
• Canopy_cover_at_6_m: Estimation of percent canopy cover sited directly upwards with an ocular tube 6 m from the nest
• Canopy_cover_at_4_m: Estimation of percent canopy cover sited directly upwards with an ocular tube 4 m from the nest
• Canopy_cover_at_2_m: Estimation of percent canopy cover sited directly upwards with an ocular tube 2 m from the nest
• Percent ground cover estimate: Total estimate of ground cover for the plot
• Percent_sub_canopy_cover_estimate: Estimate of canopy cover at the sub-canopy (sometimes called T2) layer
• Percent_upper_canopy_cover_estimation: Estimate of canopy cover at the top-canopy (sometimes called T1) layer
• Tallest_tree_in_plot: Apex height of tallest tree in nest plot
• Scientific_name: Scientific_name of called tree in plot
• Apex_height_.m.: Height of tallest tree in plot
• Distance_from_tallest_tree_to_nest_.m.: Distance from tallest tree to nest
• Number_of_old_nests: Count of visible, inactive nests on plot
• Number_of_saplings: Total saplings in plot (sapling= <5cm Diameter breast height)

• Number_of_trees: Total trees in plot (tree= >5cm DBH)
• Tree_Survery_recycled_from_previous_nest?: In cases where nests were built within 5m of a previously measured plot, we reused tree data from the previously measured plot. Entry indicates all entries other than Yes with a description of the nest ID should be interpreted as no's. 
• Notes: Any related notes about the entry 

File: Dryad_MASTER_Nest_TIMO_2023.csv

Variables:

• YEAR: Year nest was initiated 
• NEST_ID: Alphanumeric nest code. Unique for every nest. First two letters match the territory name, followed by year nest found, followed by order of nest in that year (A-Z)
• RIV_Classification: Nest-site habitat designation
• FIRST_NEST: Y/N first documented nest
• NEST_ATTEMPT: Numerical order of nest attempts across years of study (2021-2022)
• DATE_FOUND: Date nest found by observers. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• TIME: Time nest found by observers
• HABITAT: Original, landscape-scale habitat designation
• TERRITORY: Full territory name
• "FEMALE_ID" and "MALE_ID":  Individual banding code. The color codes are comprised of three single letter color codes and the "S" federal marker. G=green, O=Orange, Y=Yellow, W=White, Bk=Black, B=Blue, Gy=Grey, R=Red. UB=Unbanded.
• Pair last seen together: Date paired last documented together as of 2024. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• Time pair together since fist nest initiation: Days elapsed between first detection of pair and last resight together on the territory
• JUV_ID: Individual banding code for attending juvenile, if present. Most territories did not have attending juveniles during nesting periods
• LAY_DATE: Exact or back-calculated lay date. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• LAY_MONTH: Month first egg was laid, if known
• Time Since previous nest termination calc: Function that calculates difference between lay date of current nest and termination date of previous nest
• Exact_Lay: Whether or not the exact lay date is known or was back calculated. Exact lay dats could only be ascertained when the nest was checked with a single egg, followed the next day by a second egg
• CLUTCH_SIZE: total eggs laid
• HATCH_DAY: Date first egg hatched. Could only be calculated exactly via camera traps, or if a nest was found with one hatched nestling followed the next day by a second. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• Exact_hatch: Indicates whether the date is known exactly or was back calculated based on typical incubation period 
• BROOD_SIZE: Number of nestling in the nest
• NESTLING 1 BAND: Individual banding code
• NESTLING_1_BODY_CONDITION: Scale of subjective nestling body condition good-poor
• NESTLING 2 BAND: Individual banding code
• NESTLING_2_BODY_CONDITION: Scale of subjective nestling body condition good-poor
• NEST_FATE: whether nest fledged at least one young or failed
• CONFIRMED FLEDGLINGS: Indicates number of relighted or camera trap indicated number of success fledglings from the nest
• 2ND TO LAST CHECK (cam or nest check): Date of 2nd to last check. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• LAST_NEST_CHECK (cam or nest check): Date of last time nest was observed either by physical nest-check, or last date of activity on the camera trap. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• DATE_CONFIRMED_FAILED_OR_FLEDGED: Date an outcome was determined, if possible. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• FINAL_ACTIVITY: Date of final activity calculated with Mayfield 1975 method. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• Rebuild_time: Time to rebuild a new nest
• Previous nest successful: Yes/No whether previous nest attempt (if there was one) was successful
• Post-predation renest: Indicates if current nest follows a previous nest attempt that was eaten by predators 
• FINAL_ACTIVITY_clean: Copy Past of previous column without function. Data format: MM/DD/YY. The #DEAL WITH DATES code block at the beginning of the Dryad_Monarch nest analysis.R addresses date conversion issues between the csv and R. 
• PREDATOR ID: Identification of predator if possible 
• CAUSE OF FAILURE SPECIFIC: The specific cause of failure (ex: type of predator: type of environmental impact, etc)
• CAUSE OF FAILURE GENERAL: Category of failure: predation, environmental, abandoned or unknown
• CAMERA TRAP?: Y/N indicates whether a camera trap was deployed to monitor the nest
• PREDATION ON CAMERA: Indicates if the moment and identify of predator was captured on the camera trap 
• VEG SURVEY: Indicates if a vegetation survey was conducted on the plot after nest termination 
• REBUILD: Indicated if nest is a rebuild of a previous nest (i.e. was a previous nest physically repaired for a new clutch)
• Consecutive rebuild: Indicates whether a rebuild had already been attempted
• Distance_from_previous_nest_meters: Measurement of distance to previous nest if known

• COMMENTS: Misc. notes 

Scripts:

File: Dryad_LogisticExposureModel_2026.R

Required packages: lme4, MASS

Required data: Dryad_Logit_exposure_data_2026.csv

File: Dryad_TIMO_CJScode_ms.R

Required packages: rjags, jagsUI

Required data: Dryad_MASTER_Juv_Capture_History_CJS.csv

File: Dryad_Monarch_nest_analysis.R

Required and suggested packages: tidyverse, readxl, janitor, stringr, hms, lubridate, ggplot2, dplyr, plyr

Required data: Dryad_MASTER_Veg_survey_data.csv and Dryad_MASTER_Nest_TIMO_2023.csv 

Code/software

• R-Studio Version 1.3.1056,  for CJS: JAGS 4.3.1 (Plummer 2003) through the R package ‘rjags’ (Plummer et al. 2019)