This collection contains files associated with data analysis of Dunlin brood survival found in Saalfeld, S.T., B.L. Hill, C.M. Hunter, C.J. Frost, and R.B. Lanctot. 2021. Warming Arctic summers unlikely to increase productivity of shorebirds through renesting. Nature Scientific Reports 11:15277.
Directories include: input_files, output_files, R_code, program_mark_files, and figure_files. Found in the analysis_output folder on the RDR.
Information for the Dunlin brood survival project were obtained concurrently with information obtained for the Utqiagvik shorebird project and information on chicks and nests included in these files may also be contained within the Utqiagvik shorebird project archive (file://ifw7ro-file.fws.doi.net/datamgt/mbm/mbmsh_009_Utqiagvik_shorebird_project).
The data providers have invested considerable effort in QA/QC, but it is possible that undetected errors remain. It is strongly recommended that careful attention be paid to the contents of the metadata file associated with these data to evaluate data set limitations, restrictions, or intended use. The originators of this dataset shall not be held liable for improper or incorrect use of the data described and/or contained herein.
Potential users of these data should first contact the data authors listed below, as potential biases may occur within the data depending on the intended use. Therefore, potential users should contact the data authors to discuss intended use and how these data may or may not be applicable.
input_files: this folder contains input files for analyses including:1) beta: this file provides beta estimates from top-ranked model (HD x age2 + I) from Program Mark to estimate daily survival rates of Dunlin chicks and probability of surviving to 15 days of age as a function of invertebrate biomass, chick age, and hatch date. Daily survival rates and survival probabilities, as well as associated errors were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I) using the R code MVN_analysis_figure3, MVN_anlaysis_figure4, and MVN_analysis_figure 5.
Variables include:Parameter: parameter from top-ranked model
Beta: beta estimate from top-ranked model
SE: SE of beta estimate from top-ranked model
2) vcov: this file provides the variance-covariance matrix from the top-ranked model (HD x age2 + I) from Program Mark to estimate daily survival rates of Dunlin chicks and probability of surviving to 15 days of age as a function of invertebrate biomass, chick age, and hatch date. Daily survival rates and survival probabilities, as well as associated errors were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I) using the R code MVN_analysis_figure3, MVN_anlaysis_figure4, and MVN_analysis_figure 5.
This file does not have headers and each row and column represents estimates for each parameter in the same order as the beta file (Intercept, Hatch Date, Age, Age x Age, Insect, Hatch Date x Age, and Hatch Date x Age x Age)
3) predications_figure3: this file provides parameters values to estimate daily survival rates of Dunlin chicks as a function of invertebrate biomass for chick ages (2 and 7 days) and average hatch date for initial (3 July) and replacement (15 July) nests. Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distributon and the variance-covariance matrix from the top-ranked model (HD x age2 + I) using the R code MVN_analysis_figure3.
Variables include:A: age used for calculations where age at hatch = 1, age
age used for manuscript where age at hatch = 0
Hatch: hatch date, where 1 = 27 June
Insect: values of insect biomass (mg/trap/day)
4) predications_figure4: this file provides parameter values to estimate daily survival rates of Dunlin chicks as a function of age for average hatch date for initial (3 July) and replacement (15 July) nests, and invertebrate biomass (1 and 25 mg/trap/day). Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I) using the R code MVN_analysis_figure4.
Variables include:A: age used for calculations where age at hatch = 1
age: age used for manuscript where age at hatch = 0
Hatch: hatch date, where 1 = 27 June
Insect: values of insect biomass (mg/trap/day)
5) predictions_figure5: This file provides parameter values to estimate the probability of a Dunlin chick surviving to 15 days of age as a function of hatch date. Survival probabilities and associated CIs were estimated using average invertebrate biomass estimates based on date and 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I) using the R code MVN_analysis_figure5.
Variables include:A: age used for calculations where age at hatch = 1
age: age used for manuscript where age at hatch = 0
Hatch: hatch date, where 1 = 27 June
Insect: values of insect biomass (mg/trap/day). These are average values among the two years of the study for a given date. For example, if hatch date is 1 and age is 0, this value represents the average invertebrate biomass on 27 June, if the hatch date is 1 and age is 1 then this value represents the average invertebrate biomass on 28 June, etc. Although no invertebrate data were available after 4 August in 2008 and 8 August in 2009, we assumed these values would be close to zero due to prior trends.
output_files: this folder contains output files from analyses including:1) plot_data_figure3: this file provides estimated daily survival rates of Dunlin chicks as a function of invertebrate biomass for chick ages (2 and 7 days) and average hatch date for initial (3 July) and replacement (15 July) nests. Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). These values were obtained using the R code MVN_analysis_figure3.
The values represented by ‘dsr’ are mean, variance, L95, U95, and standard deviation. ID represents order of estimates for given values of age, hatch date, and insect biomass as given in the input file predictions_figure3.
2) plot_data_figure4: this file provides estimated daily survival rates of Dunlin chicks as a function of age for average hatch date for initial (3 July) and replacement (15 July) nests, and invertebrate biomass (1 and 25 mg/trap/day). Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). These values were obtained using the R code MVN_analysis_figure4.
The values represented by ‘dsr’ are mean, variance, L95, U95, and standard deviation. ID represents order of estimates for given values of age, hatch date, and insect biomass as given in the input file predictions_figure4.
3) plot_data_figure5: this file provides estimated probability of a Dunlin chick surviving to 15 days of age as a function of hatch date. Survival probabilities and associated CIs were estimated using average invertebrate biomass estimates based on date and 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). Although no invertebrate data were available after 4 August in 2008 and 8 August in 2009, we assumed these values would be close to zero due to prior trends. These values were obtained using the R code MVN_analysis_figure5.
The values given in this file are Hatch (hatch date, where 1 = 27 June), S16 (estimated survival to 15 days), var (variance), L95, and U95.
R_code: this folder contains R code files for analyses including:1) MVN_analysis_figure3: this file provides annotated R code to estimate daily survival rates of Dunlin chicks as a function of invertebrate biomass for chick ages (2 and 7 days) and average hatch date for initial (3 July) and replacement (15 July) nests. Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). This code requires input files ‘beta.csv’, ‘vcov.csv’, and ‘predictions_figure3.csv’. It creates output file ‘plot_data_figure3.csv’.
2) MVN_analysis_figure4: this file provides annotated R code to estimate daily survival rates of Dunlin chicks as a function of invertebrate biomass for chick ages (2 and 7 days) and average hatch date for initial (3 July) and replacement (15 July) nests. Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). This code requires input files ‘beta.csv’, ‘vcov.csv’, and ‘predictions_figure4.csv’. It creates output file ‘plot_data_figure4.csv’.
3) MVN_analysis_figure5: this file provides annotated R code to estimate daily survival rates of Dunlin chicks as a function of invertebrate biomass for chick ages (2 and 7 days) and average hatch date for initial (3 July) and replacement (15 July) nests. Daily survival rates and associated SDs were estimated using 10,000 simulations of the beta estimates assuming a multivariate normal distribution and the variance-covariance matrix from the top-ranked model (HD x age2 + I). This code requires input files ‘beta.csv’, ‘vcov.csv’, and ‘predictions_figure5.csv’. It creates output file ‘plot_data_figure5.csv’.
program_mark_files: this folder contains Program MARK files used in analyses including:1) dunl_brood_survival.inp: this file was used to import data into Program MARK to estimated brood survival using ‘nest survival models’. The data are divided into two groups based on year (2008 and 2009). When entered into Program MARK: Occassions=34, Groups=2, Indiv Cov=34.
Variables are separated by spaces and include:
year-chick ID: chick id. Year followed by ‘-‘, nest number, and group
day hatched: ordinal hatch date, where 1 = 27 June
last alive: ordinal date chick was last seen alive. Day 1 = 27 June
last checked: ordinal date chick was last checked. Day 1 = 27 June. Last alive and last check dates are the same for chicks that fledged
fate_code: fate of nest. Categorical (‘0’ = fledged, ‘1’ = died)
number: number of chicks with this encounter history. Always 1
age day 1: age of chick on day 1 (27 June). Age = 0 for dates prior to chick hatching or after age 16
age day 2: age of chick on day 2 (28 June). Age = 0 for dates prior to chick hatching or after age 16
age day 3: age of chick on day 3 (29 June). Age = 0 for dates prior to chick hatching or after age 16
age day 4: age of chick on day 4 (30 June). Age = 0 for dates prior to chick hatching or after age 16
age day 5: age of chick on day 5 (1 July). Age = 0 for dates prior to chick hatching or after age 16
age day 6: age of chick on day 6 (2 July). Age = 0 for dates prior to chick hatching or after age 16
age day 7: age of chick on day 7 (3 July). Age = 0 for dates prior to chick hatching or after age 16
age day 8: age of chick on day 8 (4 July). Age = 0 for dates prior to chick hatching or after age 16
age day 9: age of chick on day 9 (5 July). Age = 0 for dates prior to chick hatching or after age 16
age day 10: age of chick on day 10 (6 July). Age = 0 for dates prior to chick hatching or after age 16
age day 11: age of chick on day 11 (7 July). Age = 0 for dates prior to chick hatching or after age 16
age day 12: age of chick on day 12 (8 July). Age = 0 for dates prior to chick hatching or after age 16
age day 13: age of chick on day 13 (9 July). Age = 0 for dates prior to chick hatching or after age 16
age day 14: age of chick on day 14 (10 July). Age = 0 for dates prior to chick hatching or after age 16
age day 15: age of chick on day 15 (11 July). Age = 0 for dates prior to chick hatching or after age 16
age day 16: age of chick on day 16 (12 July). Age = 0 for dates prior to chick hatching or after age 16
age day 17: age of chick on day 17 (13 July). Age = 0 for dates prior to chick hatching or after age 16
age day 18: age of chick on day 18 (14 July). Age = 0 for dates prior to chick hatching or after age 16.
age day 19: age of chick on day 19 (15 July). Age = 0 for dates prior to chick hatching or after age 16
age day 20: age of chick on day 20 (16 July). Age = 0 for dates prior to chick hatching or after age 16
age day 21: age of chick on day 21 (17 July). Age = 0 for dates prior to chick hatching or after age 16
age day 22: age of chick on day 22 (18 July). Age = 0 for dates prior to chick hatching or after age 16
age day 23: age of chick on day 23 (19 July). Age = 0 for dates prior to chick hatching or after age 16
age day 24: age of chick on day 24 (20 July). Age = 0 for dates prior to chick hatching or after age 16
age day 25: age of chick on day 25 (21 July). Age = 0 for dates prior to chick hatching or after age 16
age day 26: age of chick on day 26 (22 July). Age = 0 for dates prior to chick hatching or after age 16
age day 27: age of chick on day 27 (23 July). Age = 0 for dates prior to chick hatching or after age 16
age day 28: age of chick on day 28 (24 July). Age = 0 for dates prior to chick hatching or after age 16
age day 29: age of chick on day 29 (25 July). Age = 0 for dates prior to chick hatching or after age 16
age day 30: age of chick on day 30 (26 July). Age = 0 for dates prior to chick hatching or after age 16
age day 31: age of chick on day 31 (27 July). Age = 0 for dates prior to chick hatching or after age 16
age day 32: age of chick on day 32 (28 July). Age = 0 for dates prior to chick hatching or after age 16
age day 33: age of chick on day 33 (29 July). Age = 0 for dates prior to chick hatching or after age 16
age day 34: age of chick on day 34 (30 July). Age = 0 for dates prior to chick hatching or after age 16
hatch_date_ordinal: ordinal hatch date, where 1 = 27 June
2) DUNL_BROOD_SURVIVAL.DBF: this file was created by Program MARK, and is needed to open models and results in Program MARK.
3) DUNL_BROOD_SURVIVAL.FPT: this file was created by Program MARK, and is needed to open models and results in Program MARK.
figure_files: this folder contains an ArcGIS map package used to create figure 1 (a map of the study area), sigma plot files for creation of figures 2-5, and final high-qulaity jpgs for all figures.
