Function for Fitting Latent Factor Multi-Species Hierarchical Distance Sampling Models

Function for fitting latent factor multi-species hierarchical distance sampling models.

Usage

lfMsDS(abund.formula, det.formula, data, inits, priors,  
       tuning, n.factors, n.batch, batch.length, accept.rate = 0.43, 
       family = 'Poisson', transect = 'line', det.func = 'halfnormal', 
       n.omp.threads = 1, verbose = TRUE, n.report = 100, 
       n.burn = round(.10 * n.batch * batch.length), n.thin = 1, 
       n.chains = 1, ...)

Arguments

abund.formula: a symbolic description of the model to be fit for the abundance portion of the model using R's model syntax. Only right-hand side of formula is specified. See example below. Random intercepts and slopes are allowed using lme4 syntax (Bates et al. 2015).
det.formula: a symbolic description of the model to be fit for the detection portion of the model using R's model syntax. Only right-hand side of formula is specified. See example below. Random intercepts and slopes are allowed using lme4 syntax (Bates et al. 2015).
data: a list containing data necessary for model fitting. Valid tags are y, covs, coords, dist.breaks, and offset. y is a three-dimensional array of observed count data with first dimension equal to the number of species, second dimension equal to the number of sites, and third dimension equal to the maximum number of replicates at a given site. covs is a matrix or data frame containing the variables used in the abundance and/or the detection portion of the model, with \(J\) rows for each column (variable). dist.breaks is a vector of distances that denote the breakpoints of the distance bands. dist.breaks should have length equal to the third dimension of y plus one. offset is an offset that can be used to scale estimates from abundance per transect to density per some desired unit of measure. This can be either a single value or a vector with an offset value for each site (e.g., if transects differ in length). coords is a matrix or data frame with two columns that contain the spatial coordinates of each site. Note that spAbundance assumes coordinates are specified in a projected coordinate system.
inits: a list with each tag corresponding to a parameter name. Valid tags are alpha.comm, beta.comm, beta, alpha, tau.sq.beta, tau.sq.alpha, sigma.sq.mu, sigma.sq.p, kappa, N, lambda, w. sigma.sq.mu and sigma.sq.p are only relevant when including random effects in the abundance and detection portion of the model, respectively. kappa is only relevant when family = 'NB'. The value portion of each tag is the parameter's initial value. See priors description for definition of each parameter name. Additionally, the tag fix can be set to TRUE to fix the starting values across all chains. If fix is not specified (the default), starting values are varied randomly across chains.
priors: a list with each tag corresponding to a parameter name. Valid tags are beta.comm.normal, alpha.comm.normal, tau.sq.beta.ig, tau.sq.alpha.ig, sigma.sq.mu.ig, sigma.sq.p.ig, and kappa.unif. Community-level abundance (beta.comm) and detection (alpha.comm) regression coefficients are assumed to follow a normal distribution. The hyperparameters of the normal distribution are passed as a list of length two with the first and second elements corresponding to the mean and variance of the normal distribution, which are each specified as vectors of length equal to the number of coefficients to be estimated or of length one if priors are the same for all coefficients. If not specified, prior means are set to 0 and prior variances are set to 100. Community-level variance parameters for abundance (tau.sq.beta) and detection (tau.sq.alpha) are assumed to follow an inverse Gamma distribution. The hyperparameters of the inverse gamma distribution are passed as a list of length two with the first and second elements corresponding to the shape and scale parameters, which are each specified as vectors of length equal to the number of coefficients to be estimated or a single value if all parameters are assigned the same prior. If not specified, prior shape and scale parameters are set to 0.1. sigma.sq.mu and sigma.sq.p are the random effect variances for any abundance or detection random effects, respectively, and are assumed to follow an inverse Gamma distribution. The hyperparameters of the inverse-Gamma distribution are passed as a list of length two with first and second elements corresponding to the shape and scale parameters, respectively, which are each specified as vectors of length equal to the number of random intercepts or of length one if priors are the same for all random effect variances. kappa is the negative binomial dispersion parameter for each species and is assumed to follow a uniform distribution. The hyperparameters of the uniform distribution are passed as a list of length two with first and second elements corresponding to the lower and upper bounds of the uniform distribution, respectively, which are each specified as vectors of length equal to the number of species or of length one if priors are the same for all species-specific dispersion parameters.
tuning: a list with each tag corresponding to a parameter name, whose value defines the initial variance of the adaptive sampler. Valid tags are beta, alpha, lambda (the latent factor loadings), w (the latent factors), beta.star (the abundance random effect values), alpha.star (the detection random effect values), and kappa. See Roberts and Rosenthal (2009) for details.
n.factors: the number of factors to use in the latent factor model approach. Typically, the number of factors is set to be small (e.g., 4-5) relative to the total number of species in the community, which will lead to substantial decreases in computation time. However, the value can be anywhere between 1 and N (the number of species in the community).
n.batch: the number of MCMC batches in each chain to run for the Adaptive MCMC sampler. See Roberts and Rosenthal (2009) for details.
batch.length: the length of each MCMC batch in each chain to run for the Adaptive MCMC sampler. See Roberts and Rosenthal (2009) for details.
accept.rate: target acceptance rate for Adaptive MCMC. Default is 0.43. See Roberts and Rosenthal (2009) for details.
family: the distribution to use for the latent abundance process. Currently supports 'NB' (negative binomial) and 'Poisson'.
transect: the type of transect. Currently supports line transects ('line') or circular transects (i.e., point counts; 'point').
det.func: the detection model used to describe how detection probability varies with distance. In other software, this is often referred to as the key function. Currently supports two functions: half normal ('halfnormal') and negative exponential ('negexp').
n.omp.threads: a positive integer indicating the number of threads to use for SMP parallel processing. The package must be compiled for OpenMP support. For most Intel-based machines, we recommend setting n.omp.threads up to the number of hypterthreaded cores. Note, n.omp.threads > 1 might not work on some systems. Currently only relevant for spatial models.
verbose: if TRUE, messages about data preparation, model specification, and progress of the sampler are printed to the screen. Otherwise, no messages are printed.
n.report: the interval to report MCMC progress.
n.burn: the number of samples out of the total n.samples to discard as burn-in for each chain. By default, the first 10% of samples is discarded.
n.thin: the thinning interval for collection of MCMC samples. The thinning occurs after the n.burn samples are discarded. Default value is set to 1.
n.chains: the number of chains to run in sequence.
...: currently no additional arguments

References

Bates, Douglas, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48. doi:10.18637/jss.v067.i01 .

Royle, J. A. (2004). N‐mixture models for estimating population size from spatially replicated counts. Biometrics, 60(1), 108-115.

Sollmann, R., Gardner, B., Williams, K. A., Gilbert, A. T., & Veit, R. R. (2016). A hierarchical distance sampling model to estimate abundance and covariate associations of species and communities. Methods in Ecology and Evolution, 7(5), 529-537.

Author

Jeffrey W. Doser doserjef@msu.edu,

Value

An object of class lfMsDS that is a list comprised of:

beta.comm.samples: a coda object of posterior samples for the community level abundance regression coefficients.
alpha.comm.samples: a coda object of posterior samples for the community level detection regression coefficients.
tau.sq.beta.samples: a coda object of posterior samples for the abundance community variance parameters.
tau.sq.alpha.samples: a coda object of posterior samples for the detection community variance parameters.
beta.samples: a coda object of posterior samples for the species level abundance regression coefficients.
alpha.samples: a coda object of posterior samples for the species level detection regression coefficients.
kappa.samples: a coda object of posterior samples for the species level abundance dispersion parameters. Only included when family = 'NB'.
lambda.samples: a coda object of posterior samples for the latent factor loadings.
w.samples: a three-dimensional array of posterior samples for the latent effects for each latent factor.
N.samples: a three-dimensional array of posterior samples for the latent abundance values for each species. Note that these values always represent transect-level abundance, even when an offset is supplied. Array dimensions correspond to MCMC sample, species, and site.
mu.samples: a three-dimensional array of posterior samples for the latent expected abundance values for each species. When an offset is supplied in the data object, these correspond to expected abundance per unit area (i.e., density). Array dimensions correspond to MCMC sample, species, and site.
sigma.sq.mu.samples: a coda object of posterior samples for variances of random effects included in the abundance portion of the model. Only included if random effects are specified in abund.formula.
sigma.sq.p.samples: a coda object of posterior samples for variances of random effects included in the detection portion of the model. Only included if random effects are specified in det.formula.
beta.star.samples: a coda object of posterior samples for the abundance random effects. Only included if random effects are specified in abund.formula.
alpha.star.samples: a coda object of posterior samples for the detection random effects. Only included if random effects are specified in det.formula.
y.rep.samples: a four-dimensional array of fitted values. Array dimensions correspond to MCMC samples, species, sites, and distance band.
pi.samples: a four-dimensional array of cell-specific detection probabilities. Array dimensions correspond to MCMC samples, species, sites, and distance band.
rhat: a list of Gelman-Rubin diagnostic values for some of the model parameters.
ESS: a list of effective sample sizes for some of the model parameters.
run.time: MCMC sampler execution time reported using proc.time().

The return object will include additional objects used for subsequent prediction and/or model fit evaluation.

Examples

set.seed(210)
J.x <- 10
J.y <- 10 
J <- J.x * J.y
# Number of distance bins from which to simulate data. 
n.bins <- 5
# Length of each bin. This should be of length n.bins
bin.width <- c(.10, .10, .20, .3, .1)
# Number of species
n.sp <- 5
# Community-level abundance coefficients
beta.mean <- c(-1, 0.2, 0.3, -0.2)
p.abund <- length(beta.mean)
tau.sq.beta <- c(0.2, 0.3, 0.5, 0.4)
# Detection coefficients
alpha.mean <- c(-1.0, -0.3)
p.det <- length(alpha.mean)
tau.sq.alpha <- c(0.1, 0.2)
# Detection decay function
det.func <- 'halfnormal'
mu.RE <- list()
p.RE <- list()
# Draw species-level effects from community means.
beta <- matrix(NA, nrow = n.sp, ncol = p.abund)
alpha <- matrix(NA, nrow = n.sp, ncol = p.det)
for (i in 1:p.abund) {
  beta[, i] <- rnorm(n.sp, beta.mean[i], sqrt(tau.sq.beta[i]))
}
for (i in 1:p.det) {
  alpha[, i] <- rnorm(n.sp, alpha.mean[i], sqrt(tau.sq.alpha[i]))
}
sp <- FALSE 
family <- 'Poisson'
kappa <- runif(n.sp, 0.3, 3) 
offset <- pi * .8^2
transect <- 'line'
factor.model <- TRUE
n.factors <- 3

dat <- simMsDS(J.x = J.x, J.y = J.y, n.bins = n.bins, bin.width = bin.width,
               n.sp = n.sp, beta = beta, alpha = alpha, det.func = det.func, kappa = kappa, 
               mu.RE = mu.RE, p.RE = p.RE, sp = sp, cov.model = cov.model,
               sigma.sq = sigma.sq, phi = phi, nu = nu, family = family, 
               offset = offset, transect = transect, factor.model = factor.model, 
               n.factors = n.factors)
#> overdispersion parameter (kappa) is ignored when family == 'Poisson'

y <- dat$y
X <- dat$X
X.p <- dat$X.p
coords <- dat$coords
dist.breaks <- dat$dist.breaks

covs <- cbind(X, X.p)
colnames(covs) <- c('int.abund', 'abund.cov.1', 'abund.cov.2', 'abund.cov.3', 
                    'int.det', 'det.cov.1')

data.list <- list(y = y, 
                  covs = covs,
                  dist.breaks = dist.breaks, 
                  coords = coords,
                  offset = offset)

# Priors
prior.list <- list(beta.comm.normal = list(mean = 0, var = 10),
                   alpha.comm.normal = list(mean = 0, var = 10), 
                   kappa.unif = list(0, 100), 
                   tau.sq.beta.ig = list(a = 0.1, b = 0.1),
                   tau.sq.alpha.ig = list(a = 0.1, b = 0.1)) 
# Starting values
inits.list <- list(alpha.comm = 0, beta.comm = 0, beta = 0,
                   alpha = 0, kappa = 1)

tuning <- list(beta = 0.1, alpha = 0.1, beta.star = 0.3, alpha.star = 0.1, 
               kappa = 0.8, lambda = 1, w = 1) 

n.batch <- 4 
batch.length <- 25
n.burn <- 0
n.thin <- 1
n.chains <- 1

out <- lfMsDS(abund.formula = ~ abund.cov.1 + abund.cov.2 + abund.cov.3,
        det.formula = ~ det.cov.1,
        data = data.list, 
        n.batch = n.batch, 
        batch.length = batch.length, 
        inits = inits.list, 
        family = 'Poisson',
        det.func = 'halfnormal', 
        transect = transect, 
        tuning = tuning,
        n.factors = n.factors,
        priors = prior.list, 
        accept.rate = 0.43, 
        n.omp.threads = 1, 
        verbose = TRUE, 
        n.report = 10,
        n.burn = n.burn,
        n.thin = n.thin,
        n.chains = n.chains) 
#> ----------------------------------------
#> 	Preparing to run the model
#> ----------------------------------------
#> N is not specified in initial values.
#> Setting initial values based on observed data
#> tau.sq.beta is not specified in initial values.
#> Setting initial values to random values between 0.05 and 1
#> tau.sq.alpha is not specified in initial values.
#> Setting to initial values to random values between 0.05 and 1
#> lambda is not specified in initial values.
#> Setting initial values of the lower triangle to 0
#> w is not specified in initial values.
#> Setting initial value to 0
#> ----------------------------------------
#> 	Model description
#> ----------------------------------------
#> Latent Factor Multi-species Poisson HDS model with 100 sites and 5 species.
#> 
#> Samples per Chain: 100 (4 batches of length 25)
#> Burn-in: 0 
#> Thinning Rate: 1 
#> Number of Chains: 1 
#> Total Posterior Samples: 100 
#> 
#> Using 3 latent factors.
#> 
#> Source compiled with OpenMP support and model fit using 1 thread(s).
#> 
#> Adaptive Metropolis with target acceptance rate: 43.0
#> ----------------------------------------
#> 	Chain 1
#> ----------------------------------------
#> Sampling ... 
#> Batch: 4 of 4, 100.00%
summary(out, level = 'community')
#> 
#> Call:
#> lfMsDS(abund.formula = ~abund.cov.1 + abund.cov.2 + abund.cov.3, 
#>     det.formula = ~det.cov.1, data = data.list, inits = inits.list, 
#>     priors = prior.list, tuning = tuning, n.factors = n.factors, 
#>     n.batch = n.batch, batch.length = batch.length, accept.rate = 0.43, 
#>     family = "Poisson", transect = transect, det.func = "halfnormal", 
#>     n.omp.threads = 1, verbose = TRUE, n.report = 10, n.burn = n.burn, 
#>     n.thin = n.thin, n.chains = n.chains)
#> 
#> Samples per Chain: 100
#> Burn-in: 0
#> Thinning Rate: 1
#> Number of Chains: 1
#> Total Posterior Samples: 100
#> Run Time (min): 0.0064
#> 
#> ----------------------------------------
#> 	Community Level
#> ----------------------------------------
#> Abundance Means (log scale): 
#>                Mean     SD    2.5%     50%  97.5% Rhat ESS
#> (Intercept) -0.6701 0.3613 -1.2136 -0.7109 0.1036   NA   5
#> abund.cov.1  0.2566 0.2648 -0.2142  0.2591 0.6807   NA 181
#> abund.cov.2  0.3706 0.3294 -0.1922  0.3848 1.0010   NA 100
#> abund.cov.3 -0.0752 0.3404 -0.6489 -0.0629 0.6510   NA 100
#> 
#> Abundance Variances (log scale): 
#>               Mean     SD   2.5%    50%  97.5% Rhat ESS
#> (Intercept) 0.2857 0.4185 0.0302 0.1938 0.8073   NA  54
#> abund.cov.1 0.4026 0.4289 0.0530 0.2602 1.9691   NA  55
#> abund.cov.2 0.5502 0.9141 0.0428 0.2710 2.8077   NA  52
#> abund.cov.3 0.5033 0.5880 0.0609 0.3612 1.8817   NA  53
#> 
#> Detection Means (log scale): 
#>                Mean     SD    2.5%     50%  97.5% Rhat ESS
#> (Intercept) -0.6515 0.4056 -1.2345 -0.7566 0.0889   NA   3
#> det.cov.1   -0.2839 0.2873 -0.8234 -0.3032 0.2277   NA  11
#> 
#> Detection Variances (log scale): 
#>               Mean     SD   2.5%    50%  97.5% Rhat ESS
#> (Intercept) 0.2077 0.2602 0.0365 0.1302 1.1004   NA  34
#> det.cov.1   0.2400 0.2236 0.0375 0.1586 0.8450   NA  47