Data from: A hierarchical population model for the estimation of latent prey abundance and demographic rates of a nomadic predator
Data files
Jun 23, 2025 version files 13.70 MB
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input.RData
14.30 KB
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README.md
4.41 KB
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sim_results_250sims.RData
13.68 MB
Abstract
Linking the demographic parameters underlying population change to environmental conditions is a central goal of population demography. However, multicollinearity among processes in ecological studies can complicate parameter estimation and inference. We sought to demonstrate the use of structural equation modelling, a technique for estimating hypothesized causal pathways among collinear observed and unobserved variables, in the context of integrated population models. We monitored a population of Tengmalm's owls (Aegolius funereus) breeding in the Jura Mountains of northwestern Switzerland and eastern France for 31 years (1990-2020) and collected data on captured prey items. We use concepts central to structural equation models (i.e., latent variables) and integrated population models to estimate the effects of latent prey abundance on Tengmalm's owl demographic parameters. We observed strong positive effects of latent prey abundance during time t on clutch size, fledging probability, and immigration rates into the breeding population, and strong effects of positive changes in latent prey abundance from time t to t+1 on first-year and adult survival. We also observed long-term declines in immigration into the study area. Our work provides a straightforward example of incorporating concepts central to structural equation models (e.g., latent variables) to model environmental processes underlying demographic rates in integrated population models, and has interesting implications for metapopulation ecology of Tengmalm's owl populations in Europe.
Dataset DOI: https://doi.org/10.5061/dryad.0rxwdbsbv
Description of the data and file structure
Files and variables
File: input.RData
Description: These are the input data used to run the model that estimates Tengmalm's owl demographic parameters and abundance. Brief descriptions of
ch: capture-history
marr.a: a multinomial array (marr) used to summarize adult (a) capture-recapture data
marr.j: a multinomial array used to summarize juvenile (j) capture-recapture data
band: list of unique marks (rings) applied to birds)
brood.age: a covariate for reproductive success (and clutch size) denoting whether each brood was tended by an SY (first-time breeder) or ASY (adult) female
brood.year: denotes which year each brood was hatched in (brood year == 1 denotes the year 1990)
c: clutch size of each observed nest
date: initiation or laying date of each observed nest
f: number of fledglings (must be <= c)
known.age: a vector denoting which broods had a known age female
known.c: a vector denoting which nests had a known clutch size
known.d: a vector denoting which nests had a known initiation or laying date
mouse: number of mouse remains observed in nest bowls of sampled nests
n: number of marked adult owls
n.years: number of years
prey.year: denotes which years nests sampled for prey remains were sampled in (prey.year == 1 denotes the year 1990)
rel.a: a vector of releases (rel) of adults (a) during each year of the study
rel.j: a vector of releases (rel) of juveniles (j) during each year of the study
start: first year of the study (1990)
territory: territory each nest sampled for prey remains was located in
vole: number of vole remains observed in nest bowls of sampled nests
x = vole + mouse
y.nests = number of nests discovered per year with equivalent effort
zB: z-standardized nests
zT: z-standardized year
File: sim_results_250sims.RData
Description: Summarized output from the simulation
ch: a simulated capture history from the last (nSims) simulation
jags.data: data supplied to JAGS
kappa.est: a storage array used to store model output across simulations
m: model output
marr: a summarized multistate multinomial array
phi: simulated survival parameters
r: number of releases of each age class
z: true latent states of simulated owls from the last (nSims) simulation
zI/zJ: used to simulate data
A: number of adults
alpha: parameter values used to simulate the data
alpha.est: a storage array used to store model output across simulations
beta: parameter values used to simulate the data
beta.est: a storage array used to store model output across simulations
c: clutches of simulated observed nests
d: initiation dates of simulated observed nests
delta: simulated mean initiation dates
eta: simulated random variation in rodent abundance
i,I,j,J: values used in data simulation, see script for more details
kappa: decrease in immigration over time
loop/n: vectors used to loop when simulating data
N: abundance of simulated population
nb,nc,ni,nt: MCMC settings for JAGS
ns: number of states (2; 1 = juvenile, 2 = adult)
nSims: number of simulations to run
nu: simulated mean prey capture rates
omega: simulated expected number of immigrants
p: age-specific detection, set equivalent for both age-classes at 0.4
parameters: parameter names
pi: juvenile sex ratio
psi: egg-to-fledging probability for last simulation
q: 1 - p
rel: number of releases (corresponds to m-array; see Kery and Schaub 2021 for more details)
S/t/tmp: values used during data simulation, see script for more details
x: observed rodent remains at simulated nests
xi: expected clutch sizes during each year
y: observed counts
zeta: factor loadings for SEM
zeta.est: a storage array used to store model output across simulations
zT: z-standardized time
Code/software
Program R is required to view the data and run the associated code.
model.R is the model file used to estimate Tengmalm owl demographic rates and abundance via the IPM described in the manuscript
simulation.R is the script used to simulate data, recover simulated parameter estimates, and summarize model results across multiple simulations.
See the manuscript (Riecke et al. 2025, Ecological Modelling) and other cited research within for full details of data collection.
