Comparing the caribouMetrics Beta model to bboutools models
Source:vignettes/compare-bayesian-models.Rmd
compare-bayesian-models.RmdSimilaries and differences between the caribouMetrics Beta model and the bboutools model
Hughes et al. 2025 described a Beta model with disturbance covariates and informative priors for analysis of a single boreal caribou population with survival data aggregated by year and only cows and calves reported in the composition survey. To align with and allow comparison to the models implemented in bboutools Dalgarno et al. 2025 we extended the Hughes et al. 2025 models as follows:
- Allow analysis of composition survey data in bboutools form that includes Yearlings, Bulls, and UnknownAdults. See Analytic Methods for Estimation of Boreal Caribou Survival, Recruitment and Population Growth for details.
- Allow analysis of monthly survival data in bboutools form
(e.g.
bboudata::bbousurv_a). - Allow for calculation of population growth rate without initial population size information. See Analytic Methods for Estimation of Boreal Caribou Survival, Recruitment and Population Growth for details.
- Allow for analysis of groups of populations with shared interannual variation. TO DO: add link to bboutools documentation when it exists.
Note that bboutools includes a number of different model variants. Throughout this document we compare to the Bayesian model with a random effect of year and no annual trend. For brevity, we refer to that as the “bbou” model.
Key remaining differences between the caribouMetrics Beta model and the bbou model include:
- The Beta model includes anthropogenic and fire disturbance covariates.
- The Beta model intercept and disturbance covariate slope parameters are informed by national demographic-disturbance relationships.
- The distribution of interannual variation differs between the models.
- The bbou model allows for variation in survival among months.
Example data
We compare the Beta and bbou models using three examples derived from
the bboudata::bbousurv_a and
bboudata::bbourecruit_a data sets:
- No local data: used to examine and compare prior predictions from the models.
- Informative local data: Observations from 2010 to 2016.
- Limited local data: Observations from 2014 to 2016.
To examine and compare predictions for unobserved years (2018 to 2021) we add missing data.
library(caribouMetrics)
#> Loading required package: nimble
#> nimble version 1.3.0 is loaded.
#> For more information on NIMBLE and a User Manual,
#> please visit https://R-nimble.org.
#>
#> Note for advanced users who have written their own MCMC samplers:
#> As of version 0.13.0, NIMBLE's protocol for handling posterior
#> predictive nodes has changed in a way that could affect user-defined
#> samplers in some situations. Please see Section 15.5.1 of the User Manual.
#>
#> Attaching package: 'nimble'
#> The following object is masked from 'package:stats':
#>
#> simulate
#> The following object is masked from 'package:base':
#>
#> declare
# use local version on local and installed on GH
if(requireNamespace("devtools", quietly = TRUE)) devtools::load_all()
library(bboudata)
library(bboutools)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(ggplot2)
figWidth = 8
figHeight = 4
useSaved <- T #option to skip slow step of fitting bboutools model
bbouInformativeFile <- here::here("results/vignetteBbbouExample.rds")
bbouLimitedFile <- here::here("results/vignetteBbbouExample2.rds")
bbouPriorFile <- here::here("results/vignetteBbbouExample1.rds")
bbouPriorNationalFile <- here::here("results/vignetteBbbouExample1p.rds")
surv_data = bboudata::bbousurv_a %>% filter(Year > 2010)
surv_data_add = expand.grid(Year=seq(2017,2022),Month=seq(1:12),PopulationName=unique(surv_data$PopulationName))
surv_data=merge(surv_data,surv_data_add,all.x=T,all.y=T)
surv_data$StartTotal[is.na(surv_data$StartTotal)]=1
recruit_data=bboudata::bbourecruit_a %>% filter(Year > 2010)
recruit_data_add = expand.grid(Year=seq(2017,2022),PopulationName=unique(recruit_data$PopulationName))
recruit_data=merge(recruit_data,recruit_data_add,all.x=T,all.y=T)
recruit_data$Month[is.na(recruit_data$Month)]=3;recruit_data$Day[is.na(recruit_data$Day)]=15
surv_dataNone <- surv_data %>% filter(Year > 2017)
recruit_dataNone <- recruit_data %>% filter(Year > 2017)
surv_dataLimited <- surv_data %>% filter(Year > 2014)
recruit_dataLimited <- recruit_data %>% filter(Year > 2014)Comparison of the Beta and national models
As shown by Hughes et al. 2025 the prior means and 95% prior predictive intervals from the Beta model are similar to the means and ranges between the 2.5% and 97.5% quantiles of 3000 simulated survival and recruitment trajectories from the national model.
disturbance = data.frame(Year=unique(surv_data$Year),Anthro=5,fire_excl_anthro=1)
betaPrior <- caribouBayesianPM(surv_dataNone,recruit_dataNone,disturbance)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 0
#> Unobserved stochastic nodes: 65
#> Total graph size: 297
#>
#> Initializing model
#>
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 4
#> Unobserved stochastic nodes: 20
#> Total graph size: 106
#>
#> Initializing model
simNational <-getSimsInitial(disturbance)
#> Warning: Setting expected survival S_bar to be between l_S and h_S.
out_tbls <- getOutputTables(betaPrior, simInitial = simNational)
typeLabs = c("Beta","National")
95% prior predictive intervals from Beta model with 5% anthropogenic disturbance, default priors, and no local data compared to simulations from the national model.
95% prior predictive intervals from Beta model with 5% anthropogenic disturbance, default priors, and no local data compared to simulations from the national model.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0.5,highBound=1.5);plot(lam)
95% prior predictive intervals from Beta model with 5% anthropogenic disturbance, default priors, and no local data compared to simulations from the national model.
Comparison of Beta and bbou prior predictions
The bbou model default priors are less informative than the Beta model default priors.
if(useSaved&file.exists(bbouPriorFile)){
bbouPrior <- readRDS(bbouPriorFile)
}else{
bbouPrior <- bbouMakeSummaryTable(surv_dataNone,recruit_dataNone,return_mcmc=T)
if(dir.exists(dirname(bbouPriorFile))){saveRDS(bbouPrior,bbouPriorFile)}
}
#> Registered S3 methods overwritten by 'mcmcr':
#> method from
#> as.mcmc.nlists nlist
#> as.mcmc.list.mcarray rjags
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
simBbouPrior <-getSimsInitial(bbouPrior)
out_tbls <- getOutputTables(betaPrior, simInitial = simBbouPrior)
typeLabs = c("Beta","Bbou")
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and default priors.
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and default priors.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0,highBound=2);plot(lam)
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and default priors.
The bbou priors can be set to (approximately) match the Beta model priors. When disturbance is constant, the models with informative priors make similar predictions of expected demographic rates.
b0Priors <- getBBNationalInformativePriors(Anthro=unique(disturbance$Anthro),fire_excl_anthro=unique(disturbance$fire_excl_anthro),month=T)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 0
#> Unobserved stochastic nodes: 78
#> Total graph size: 349
#>
#> Initializing model
#>
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 5
#> Unobserved stochastic nodes: 24
#> Total graph size: 120
#>
#> Initializing model
if(useSaved&file.exists(bbouPriorNationalFile)){
bbouPriorNational <- readRDS(bbouPriorNationalFile)
}else{
bbouPriorNational <- bbouMakeSummaryTable(surv_dataNone,recruit_dataNone,return_mcmc=T,priors=b0Priors)
if(dir.exists(dirname(bbouPriorNationalFile))){saveRDS(bbouPriorNational,bbouPriorNationalFile)}
}
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[1]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[2]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[1]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[2]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[1]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[2]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[1]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[2]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[1]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[1]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[2]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[2]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
simBbouPriorNational <-getSimsInitial(bbouPriorNational)
out_tbls <- getOutputTables(betaPrior, simInitial = simBbouPriorNational)
typeLabs = c("Beta","Bbou National")
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
lamBar = plotRes(out_tbls, "Expected growth rate",typeLabels=typeLabs,lowBound=0,highBound=2);plot(lamBar)
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0,highBound=2);plot(lam)
Prior means and 95% predictive intervals from Beta and bbou models with 5% anthropogenic disturbance and priors informed by national demographic-disturbance relationships.
Comparison of Beta and bbou models with informative local data
With more informative data, the Beta model with constant disturbance covariates and informative priors often gives results that are comparable to the bbou model with default (less informative) priors.
betaInformative <- caribouBayesianPM(surv_data,recruit_data,disturbance)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 61
#> Unobserved stochastic nodes: 95
#> Total graph size: 661
#>
#> Initializing model
#>
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 16
#> Unobserved stochastic nodes: 43
#> Total graph size: 204
#>
#> Initializing model
if(useSaved&file.exists(bbouInformativeFile)){
bbouInformative <- readRDS(bbouInformativeFile)
}else{
bbouInformative <- bbouMakeSummaryTable(surv_data,recruit_data,return_mcmc=T)
if(dir.exists(dirname(bbouInformativeFile))){saveRDS(bbouInformative,bbouInformativeFile)}
}
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
simBbouInformative <-getSimsInitial(bbouInformative)
out_tbls <- getOutputTables(betaInformative, simInitial = simBbouInformative)
typeLabs = c("Beta","Bbou")
Posterior means and 95% posterior predictive intervals from Beta and bbou models with 5% anthropogenic disturbance, default priors, and informative local data.
Posterior means and 95% posterior predictive intervals from Beta and bbou models with 5% anthropogenic disturbance, default priors, and informative local data.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0.5,highBound=1.5);plot(lam)
Posterior means and 95% posterior predictive intervals from Beta and bbou models with 5% anthropogenic disturbance, default priors, and informative local data.
The bboutools models do not include disturbance covariates, so we expect the models to project different outcomes in a case where disturbance changes over time.
disturbance = data.frame(Year=seq(2011,2051),Anthro=seq(20,2*40+20,length.out=41),fire_excl_anthro=1)
betaAnthroChange <- caribouBayesianPM(surv_data,recruit_data,disturbance)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 61
#> Unobserved stochastic nodes: 472
#> Total graph size: 3129
#>
#> Initializing model
#>
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 45
#> Unobserved stochastic nodes: 159
#> Total graph size: 1429
#>
#> Initializing model
if(useSaved&file.exists(bbouInformativeFile)){
bbouInformative <- readRDS(bbouInformativeFile)
}else{
bbouInformative <- bbouMakeSummaryTable(surv_data,recruit_data,return_mcmc=T)
if(dir.exists(dirname(bbouInformativeFile))){saveRDS(bbouInformative,bbouInformativeFile)}
}
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[9]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[10]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[11]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[12]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[9]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[10]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[11]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[12]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[9]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[10]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[11]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[12]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[9]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[10]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[11]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[12]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[9]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[9]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[10]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[10]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[11]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[11]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[12]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[12]: logProb is NA or NaN.
simBbouInformative <-getSimsInitial(bbouInformative)
out_tbls <- getOutputTables(betaAnthroChange, simInitial = simBbouInformative)
typeLabs = c("Beta","Bbou")
Posterior means and 95% posterior predictive intervals from Beta and bbou models with default priors, informative local data, and anthropogenic disturbance increasing from 20 to 100% over 40 years.
Posterior means and 95% posterior predictive intervals from Beta and bbou models with default priors, informative local data, and anthropogenic disturbance increasing from 20 to 100% over 40 years.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0.5,highBound=1.5);plot(lam)
Posterior means and 95% posterior predictive intervals from Beta and bbou models with default priors, informative local data, and anthropogenic disturbance increasing from 20 to 100% over 40 years.
Comparison of Beta and bbou models with limited local data
If local data is limited the bbou model with default (less informative) priors and the Beta model with disturbance covariates and informative priors may also give different results, particularly if observations are inconsistent with expectations from the observed distribution of outcomes across the country.
disturbance = data.frame(Year=unique(surv_data$Year),Anthro=90,fire_excl_anthro=5)
betaLimited <- caribouBayesianPM(surv_dataLimited,recruit_dataLimited,disturbance)
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 13
#> Unobserved stochastic nodes: 91
#> Total graph size: 453
#>
#> Initializing model
#>
#> Compiling model graph
#> Resolving undeclared variables
#> Allocating nodes
#> Graph information:
#> Observed stochastic nodes: 8
#> Unobserved stochastic nodes: 31
#> Total graph size: 148
#>
#> Initializing model
if(useSaved&file.exists(bbouLimitedFile)){
bbouLimited <- readRDS(bbouLimitedFile)
}else{
bbouLimited <- bbouMakeSummaryTable(surv_dataLimited,recruit_dataLimited,return_mcmc=T)
if(dir.exists(dirname(bbouLimitedFile))){saveRDS(bbouLimited,bbouLimitedFile)}
}
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[6]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[6]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[6]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[6]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[6]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[6]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[6]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[6]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[6]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[6]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[3]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[4]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[5]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[6]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[7]: logProb is NA or NaN.
#> warning: value of stochastic node FemaleYearlings[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node FemaleYearlings[8]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[3]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[4]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[5]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[6]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[7]: logProb is NA or NaN.
#> warning: value of stochastic node Cows[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Cows[8]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[3]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[4]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[5]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[6]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[7]: logProb is NA or NaN.
#> warning: value of stochastic node OtherAdultsFemales[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node OtherAdultsFemales[8]: logProb is NA or NaN.
#> warning: value of deterministic node AdultsFemales[3]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[4]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[5]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[6]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[7]: value is NA or NaN even after trying to calculate.
#> warning: value of deterministic node AdultsFemales[8]: value is NA or NaN even after trying to calculate.
#> warning: value of stochastic node Calves[3]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[3]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[4]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[4]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[5]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[5]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[6]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[6]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[7]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[7]: logProb is NA or NaN.
#> warning: value of stochastic node Calves[8]: value is NA or NaN even after trying to simulate.
#> warning: problem initializing stochastic node Calves[8]: logProb is NA or NaN.
simBbouLimited <-getSimsInitial(bbouLimited)
out_tbls <- getOutputTables(betaLimited, simInitial = simBbouLimited)
typeLabs = c("Beta","Bbou")
Posterior means and 95% predictive intervals from Beta and bbou models with 90% anthropogenic disturbance, default priors, and limited local data.
Posterior means and 95% predictive intervals from Beta and bbou models with 90% anthropogenic disturbance, default priors, and limited local data.
lam = plotRes(out_tbls, "Population growth rate",typeLabels=typeLabs,lowBound=0.5,highBound=1.5);plot(lam)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_ribbon()`).
Posterior means and 95% predictive intervals from Beta and bbou models with 90% anthropogenic disturbance, default priors, and limited local data.
References
Dalgarno S, Boulanger J, Pearson A, et al (2025) bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data. Journal of Open Source Software 10:7997. https://doi.org/10.21105/joss.07997
Hughes J, Endicott S, Calvert AM, Johnson CA (2025) Integration of national demographic-disturbance relationships and local data can improve caribou population viability projections and inform monitoring decisions. Ecological Informatics 87:103095. https://doi.org/10.1016/j.ecoinf.2025.103095