# Title of Dataset: Data from: Spatial consistency in drivers of population dynamics of a declining migratory bird --- This data archive contains processed model input data and MCMC samples associated with the manuscript: "Spatial consistency in drivers of population dynamics of a declining migratory bird" by ChloƩ R. Nater, Malcolm D. Burgess, Peter Coffey, Bob Harris, Frank Lander, David Price, Mike Reed and Robert A. Robinson ## Description of the data and file structure Two types of data files are provided: processed input data and mcmc samples. ### Processed input data .rds files named XXX_IPMData.rds, one for each of the seven study populations, consisting of a list object that contains all data necessary for fitting the integrated population models from the paper. These list objects constitute the output of the data wrangling pipeline deposited at https://github.com/SPI-Birds/SPI-IPM/blob/main/SPI-IPM_Code/01_Data_Reformatting/DataPrep_PopID.R. The original raw data from which the lists were constructed can be requested from SPI-Birds (https://spibirds.org/). **File list:** - DIN_IPMData.rds (Population Dinas) - EDM_IPMData.rds (Population East Dartmoor) - KAT_IPMData.rds (Population Loch Katrine) - NAG_IPMData.rds (Population Forest of Dean) - NWA_IPMData.rds (Population Denbigh) - OKE_IPMData.rds (Population Okehampton) - TEI_IPMData.rds (Population Teign Valley) The lists contain 37 different objects that can be used as inputs for the integrated population models. **Object definitions:** - y[i,t] = CJS capture history of individual i over all time steps t - CHs[i,t] = multistate capture history of individual i over all time steps t (1 = juvenile, 2 = yearling/adult) - ageclass[i,t] = age class of individual i during time step t (1 = juvenile, 2 = yearling/adult) - first[i] = first capture of individual i - last[i] = last occasion to consider for individual i - y.sum[i,t] = Unique summarized CJS capture history i over all time steps t - CHs.sum[i,t] = Unique summarized multistate capture history i over all time steps t (1 = juvenile, 2 = yearling/adult) - ageclass.sum[i,t] = age class of unique capture history i during time step t (1 = juvenile, 2 = yearling/adult) - first.sum[i] = first capture of unique capture history i - last.sum[i] = last occasion to consider for unique capture history i - CHs.count[i] = number of occurences of unique capture history i - A.marray[t1,t2] = Number of yearlings/adults released at occasion t1 and recaptured at occasion t2 (m-array) - J.marray[t1,t2] = Number of fledglings/juveniles released at occasion t1 and recaptured at occasion t2 (m-array) - NestCount[t] = Total number of active nests in year t - EggNoTot[t] = Total number of eggs laid in year t (summed over all broods) - EggNoSP[t] = Proportion of broods that EggNoTot[t] is based on - ClutchSize[x] = Clutch size for brood x - CS_year[x] = Year of brood x - CS_FAge[x] = Age class of the mother of brood x (1 = yearling, 2 = adult) - FledgedTot[t] = Total number of fledglings produced in year t (summed over all broods) - FledgedSP[t] = Proportion of broods that EggNoTot[t] is based on - Fledged[x] = Number of fledglings from brood x - Laid[x] = Number of eggs laid in brood x - F_year[x] = Year of brood x - F_FAge[x] = Age class of the mother of brood x (1 = yearling, 2 = adult) - anyFledged[x] = Whether any fledglings were produced in brood x - NoFledged[y] = Number of fledglings from successful brood y - NoLaid[y] = Number of eggs laid in successful brood y - NoF_year[y] = Year of successful brood y - NoF_FAge[y] = Age class of the mother of successful brood y (1 = yearling, 2 = adult - ImmNoObs[t] = Total number of immigrants (= unmarked adults) captured in year t - ImmAgeProps[a] = All-time average proportion of known age immigrants in age class a (1 = yearling, 2 = adult) - ImmAgeProps_t[a,t] = Proportion of known age immigrants in age class a (1 = yearling, 2 = adult) in year t - NS_Data[t] = Whether or not any nest data was collected in year t - PropCapBrood[t] = the proportion of nests for which the female was captured in year t - AR_Data[t] = Whether or not any adults were ringed/recaptured in year t - YearIndeces = Table documenting assignment of time indeces to study years Object definitions can also be found in the model setup code deposited at https://github.com/SPI-Birds/SPI-IPM/blob/main/SPI-IPM_Code/02-04_IPM_Setup%26Run/IPMSetup.R ### MCMC samples .rds files named SPI-IPM_XXX.rds, one for each of the seven study populations, consisting of a list object. Each list contains posterior samples for all parameters included in the integrated population models from the paper (= output of model runs, 3 MCMC chains). For definitions of parameters, please refer to the code deposited in the SPI-IPM GitHub repository (https://github.com/SPI-Birds/SPI-IPM/tree/main/SPI-IPM_Code) and the code manual (https://spi-birds.github.io/SPI-IPM/). **File list:** - SPI-IPM_DIN.rds (Population Dinas) - SPI-IPM_EDM.rds (Population East Dartmoor) - SPI-IPM_KAT.rds (Population Loch Katrine) - SPI-IPM_NAG.rds (Population Forest of Dean) - SPI-IPM_NWA.rds (Population Denbigh) - SPI-IPM_OKE.rds (Population Okehampton) - SPI-IPM_TEI.rds (Population Teign Valley) ## Sharing/access Information The original raw data from which the input data was constructed can be requested from SPI-Birds (https://spibirds.org/).