Fitting occupancy models with flocker

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Jacob Socolar & Simon Mills

2023-10-20

flocker is an R package for fitting occupancy models that incorporate sophisticated effects structures using simple formula-based syntax. flocker is built on R package brms, which in turn is a front-end for Stan.

This vignette is intended as a companion to Socolar & Mills 2023, where we provide details of the models and post-processing functionality available in flocker in greater detail. Here, we provide illustrative R code for several types of model, demonstrating data simulation, model fitting, and model post-processing. We also showcase the brms syntax that flocker can use to fit a variety of sophisticated effect structures.

Terms and definitions

Socolar & Mills (2023) introduce several terms that figure importantly in this vignette, including:

closure-unit: The groupings of observations over which closure is assumed. In single-species models, a closure-unit corresponds to a “site” or “point”. In multi-species models, a closure-unit is a species-site combination. In dynamic (multi-season) models, a closure-unit is a site-season combination (or species-site-season in a multi-species dynamic model).
rep-constant, rep-varying: We refer to models that assume constant detection probabilities across repeat visits within closure-units as rep-constant models, as contrasted with rep-varying models that incorporate event-specific detection covariates. It turns out that rep-constant models enable a more efficient parametrization of the likelihood than rep-varying models.
unit covariates, event covariates: We refer to any covariate that does not vary across sampling events within closure-units as a “unit covariate”. This includes covariates that are intrinsically properties of single closure-units (e.g. the elevations of sites in a single-species model), covariates that are intrinsically properties of groups of closure units (e.g. elevations of sites in a multi-species model), and covariates that are intrinsically properties of sampling events but happen to be constant within all closure-units (e.g. observer in a sampling design where every site is visited by exactly one observer). We refer to any covariate that varies across sampling events within covariates as an “event covariate”. Note that while unit covariates may appear in either the occupancy or the detection formula, event covariates are restricted to the detection formula. Models that incorporate event covariates are rep-varying (see above); those that do not are rep-constant.

Installation and feedback

Installation instructions are available here. To request features or report bugs (much appreciated!), please open an issue on GitHub.

To make flocker and brms functions globally available within an R session run:

library(flocker)
library(brms)
set.seed(1)

Data simulation

General purpose data simulation is provided via simulate_flocker_data(), which by default will simulate a dataset with 30 species sampled at 50 sites using four replicate surveys (i.e. a single-season multi-species dataset). Non-default arguments will simulate example data for other likelihoods, including multi-season and data-augmented occupancy models.

d <- simulate_flocker_data()

The simulated data d are in list form, with elements for the detection/non-detection observations d$obs, unit covariates d$unit_covs, and event covariates d$event_covs. d$obs is a matrix where rows are species-site combinations, columns are replicate visits, and entries are 1 (detection), 0 (nondetection), or NA (no visit). d$unit_covs is a dataframe containing covariates that vary across the rows of obs (i.e. by closure-unit) but not across the columns within any given row (i.e. do not vary across replicate visits). event_covs is a named list of matrices, with each matrix having the same dimensions as the observation matrix. Each list element corresponds to a covariate that varies across the columns of d$obs (i.e. varies between replicate visits).

Data formatting

flock(), the main function in flocker for fitting occupancy models, expects a highly specific data format that we describe more fully here. The function make_flocker_data() formats data for use with flock() automatically. For single-season models, make_flocker_data() takes as input a matrix or dataframe of detection/non-detection data. Rows represent closure-units, columns represent repeated sampling events within closure-units, and entries must be 0 (nondetection), 1 (detection), or NA (no corresponding sampling event). The data must be formatted so that all NAs are trailing within their rows. For example, if some units were sampled four times and other three times, the three sampling events must be treated as events 1, 2, and 3 (with the fourth event NA) rather than as events 1, 3, and 4 (with the second event NA) or any other combination.

Many occupancy models also include covariates that influence occupancy or detection probabilities. Unit covariates (see Terms and definitions) can be passed to make_flocker_data() as a dataframe with the same number of rows as the observation matrix and data in the same order as the rows of the observation matrix. Columns are covariates, and we recommend using informative column names. Event covariates (see Terms and definitions) can be passed as a named list of matrices whose elements [i, j] are the covariate values for the sampling event represented by the corresponding position of the observation matrix. Again, we recommend using informative names for the list elements. If the corresponding observation is NA, then the value of the event covariate does not matter.

To pass data to flocker, we first pass the output from simulate_flocker_data() to make_flocker_data(), which will repackage data and apply the necessary formatting:

fd_rep_varying <- make_flocker_data(
  obs = d$obs, 
  unit_covs = d$unit_covs, 
  event_covs = d$event_covs
  )
#> Formatting data for a single-season occupancy model. For details, see make_flocker_data_static. All warnings and error messages should be interpreted in the context of make_flocker_data_static

The function make_flocker_data() outputs an object of class flocker_data that we can pass to flocker’s model fitting function flock(). Note that this is the general workflow users will need to follow with real data. Alternative inputs to make_flocker_data() and flock() enable the user to readily fit multi-season models as well as multi-species models with data augmentation (see below).

Model fitting

The single-season rep-varying model

To fit a model, in this case a single-season multi-species occupancy model, we use the function flock(). By supplying different arguments to this function, all flavors of occupancy model available in flocker can be fitted. Formulas for the different distributional parameters in the model (occupancy, detection, colonization, extinction, and autologistic terms as applicable) are provided as one-sided formulas to the relevant arguments of flock() (f_occ, f_det, f_col, f_ex, and f_auto as applicable).

rep_varying <- flock(
  f_occ = ~ uc1 + (1 + uc1 | species),
  f_det = ~ uc1 + ec1 + (1 + uc1 + ec1 | species),
  flocker_data = fd_rep_varying,
  cores = 4,
  silent = 2,
  refresh = 0
  )

Arguments supplied to flock() define formulas using brms syntax for the occupancy (f_occ) and detection (f_det) components, and also provide the formatted data. At this stage, the full flexibility and power of brms formula syntax are available to the user (see following sections for some examples). rep_varying is a brmsfit object from package brms and also a flockerfit object from package flocker. Post-processing functions from brms will typically not work with this object and are instead replaced by flocker equivalents.

The single-season rep-constant model

make_flocker_data() will automatically format the data for a rep-constant model when event_covs = NULL and the desired model is a single-season model without data augmentation. To take advantage of the efficiency gains and post-processing functionality of the rep-constant model, it is necessary to supply event_covs = NULL to make_flocker_data() at the moment of data formatting; it is insufficient to omit event covariates from the detection formula supplied to flock() after formatting the data for a rep-varying model.

fd_rep_constant <- make_flocker_data(
  obs = d$obs, 
  unit_covs = d$unit_covs
  )
#> Formatting data for a single-season occupancy model. For details, see make_flocker_data_static. All warnings and error messages should be interpreted in the context of make_flocker_data_static
rep_constant <- flock(
  f_occ = ~ uc1 + (1 + uc1 | species),
  f_det = ~ uc1 + (1 + uc1 | species),
  flocker_data = fd_rep_constant,
  save_pars = save_pars(all = TRUE), # for loo with moment matching
  silent = 2,
  refresh = 0,
  cores = 4
  )

Note that within-chain parallelization is available (uniquely so) for the rep-constant mode:

rep_constant <- flock(
  f_occ = ~ uc1 + (1 + uc1 | species),
  f_det = ~ uc1 + (1 + uc1 | species),
  flocker_data = fd_rep_constant,
  silent = 2,
  refresh = 0,
  chains = 2,
  cores = 2,
  threads = 2
  )

Multi-season models

Here we provide code examples to complement the companion publication. For a more complete vignette on multi-season models in flocker, see the multiseason models vignette.

First, we simulate some data that are valid for use with multi-season models. Here, we will simulate data for three seasons with one unit covariate and one event covariate. The data will be simulated under a colonization-extinction model with explicit inits, but we will be able to fit other models (autologistic, equilibrium inits) to the same data (note that simulate_flocker_data() can also simulate directly from these other model types).

multi_data <- simulate_flocker_data(
  n_season = 3,
  n_pt = 300,
  n_sp = 1,
  multiseason = "colex", 
  multi_init = "explicit",
  seed = 1
  )

fd_multi <- make_flocker_data(
  multi_data$obs, 
  multi_data$unit_covs, 
  multi_data$event_covs, 
  type = "multi",
  quiet = TRUE
  )

Below, we fit the colonization-extinction model with an explicit model for occupancy in the first timestep. Depending on hardware, fitting this model might take several minutes.

multi_colex <- flock(
  f_occ = ~ uc1,
  f_det = ~ uc1 + ec1,
  f_col = ~ uc1,
  f_ex = ~ uc1,
  flocker_data = fd_multi,
  multiseason = "colex",
  multi_init = "explicit",
  cores = 4,
  silent = 2,
  refresh = 0
)

Here is the colonization-extinction model using equilibrium occupancy probabilities in the first timestep:

multi_colex_eq <- flock(
  f_det = ~ uc1 + ec1,
  f_col = ~ uc1,
  f_ex = ~ uc1,
  flocker_data = fd_multi,
  multiseason = "colex",
  multi_init = "equilibrium",
  cores = 4,
  silent = 2,
  refresh = 0
  )

Here is the autologistic model with explicit occupancy probabilities in the first timestep. To reflect the stereotypical autologistic model with a constant logit-scale offset separating colonization and persistence probabilities, we use the formula f_auto = ~ 1, but it is fine to relax this constraint and use, e.g. f_auto = ~ uc1.

multi_auto <- flock(
  f_occ = ~ uc1,
  f_det = ~ uc1 + ec1,
  f_col = ~ uc1,
  f_auto = ~ 1,
  flocker_data = fd_multi,
  multiseason = "autologistic",
  multi_init = "explicit",
  cores = 4,
  silent = 2,
  refresh = 0
  )

And the autologistic model with equilibrium occupancy probabilities in the first timestep:

multi_auto_eq <- flock(
  f_det = ~ uc1 + ec1,
  f_col = ~ uc1,
  f_auto = ~ 1,
  flocker_data = fd_multi,
  multiseason = "autologistic",
  multi_init = "equilibrium",
  cores = 4,
  silent = 2,
  refresh = 0
)

Data-augmented multi-species models

Here we provide a simple example of code for a data augmented model. For a more complete unified vignette on data-augmented models in flocker, see the data-augmented models vignette.

Fitting the data-augmented model in flocker requires passing the observed data as a three-dimensional array with sites along the first dimension, visits along the second, and species along the third. Additionally, we must supply the n_aug argument to make_flocker_data(), specifying how many all-zero pseudospecies to augment the data with.

augmented_data <- simulate_flocker_data(
    augmented = TRUE
    )
fd_augmented <- make_flocker_data(
  augmented_data$obs, augmented_data$unit_covs, augmented_data$event_covs,
  type = "augmented", n_aug = 100,
  quiet = TRUE
  )
augmented <- flock(
  f_occ = ~ (1 | ff_species),
  f_det = ~ uc1 + ec1 + (1 + uc1 + ec1 | ff_species),
  augmented = TRUE,
  flocker_data = fd_augmented,
  cores = 4,
  silent = 2,
  refresh = 0
  )
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#bulk-ess

Here, the random effect of species is specified using the special grouping keyword ff_species (names beginning with ff_ are reserved in flocker and are not allowed as names for user-supplied covariates).

Post-processing

flocker provides functions for four main types of bespoke post-processing for occupancy models. fitted_flocker() computes (and optionally summarizes) posterior distributions of fitted values at the locations of the data used in model fitting or of new data. get_Z() provides the posterior distribution for the latent occupancy state. predict_flocker() provides posterior predictions at the observed points (e.g. for use in posterior predictive checking) or for new data. loo_flocker() and loo_compare_flocker() both provide functionality for model comparison. See below for details on all four types of post-processing. Both posterior predictions and model comparison rely on subtle aspects of the occupancy model likelihood that we explain in more detail here.

brms-native post-processing

All post-processing functions from brms work on single-season rep-constant models, but do not work on any other model types. For example:

predictions_rep_constant <- brms::posterior_predict(rep_constant)
loo_rep_constant <- brms::loo(rep_constant, moment_match = TRUE)
brms::conditional_effects(rep_constant)

The following functions work on all model types available in flocker.

Fitted values

Fitted values for any of the distributional parameter (one or more of occupancy, detection, colonization, extinction, autologistic, and/or Omega, the fitted probability that a given (pseudo)species occurs in the metacommunity) are available via fitted_flocker. For example:

fitted_flocker(rep_constant)
fitted_flocker(rep_varying)
fitted_flocker(multi_colex)
fitted_flocker(augmented)

fitted_flocker provides a replacement for brms::posterior_linpred(). While the brms-native function executes on any flocker model, it returns in an opaque shape related to the flocker data format. fitted_flocker() returns in the shape of the observations passed to make_flocker_data(), with posterior iterations stacked along its final dimension.

The posterior occupancy state

The function get_Z() returns the posterior distribution of occupancy probabilities across the closure-units. The shape of the output depends on the class of model, and is an array in the shape of the first visit in obs as passed to make_flocker_data, with posterior iterations stacked along the final dimension. Thus, for a single-season rep-varying model, the output is a matrix where rows are posterior iterations, columns are closure-units, and values are draws from the posterior distribution of occupancy probabilities:

get_Z(rep_varying)

For all model types, get_Z() accepts an optional new_data argument. Leaving the default new_data = NULL supplies the posterior for the true occupancy state at the locations of the data used to fit the model. Otherwise, the posterior is computed over the new data. For single-season models, new_data can be supplied as a dataframe of unit covariate values or as a flocker_data object. For multi-season models, only a flocker_data object is allowed. Note that if predictions are desired at sites without observations, it is acceptable to pass an array of dummy observations (e.g. all zeros) to make_flocker_data() and then to set history_condition = FALSE in the call to get_Z().

get_Z() accepts several additional arguments that control the way that posterior is obtained and the values returned. See the companion paper and ?get_Z for details.

Posterior prediction

The function predict_flocker() provides posterior predictions. By default, predictions are provided for the covariate data to which the model were fit, but predictions to new data are also possible via the new_data argument. The output differs by model type. For single-season rep-constant models, the return is a matrix where rows are iterations, columns are units, and values are the number of detections. For single-season rep-varying models, the return is an array whose first dimension is units, second dimension is sampling events, third dimension is iterations, and values are 1, 0, or NA, representing detection, nondetection, and no corresponding sampling event. For example:

predict_flocker(rep_varying)

predict_flocker() accepts several additional arguments that control the way that posterior is obtained and the values of returned. See the companion paper and ?predict_flocker for details.

Model comparison

The most straightforward way to compare models fit with flocker is the function loo_compare_flocker(). This function takes a list of flocker_fit objects as its argument and returns a model comparison table based on the difference in the expected log predictive density (elpd) between models. This table is a compare.loo object from loo::loo_compare(). The “leave-one-out” holdouts consist of entire closure-units (single-season models), series (multi-season models), or species (augmented models), not single sampling events (see the companion paper and here for details of why).

loo_compare_flocker() accepts as input a list of flockerfit objects and outputs a model comparison table. For example, we can compare the rep-constant and rep-varying models that we fit to the same initial data. Recall that the data were simulated with event-covariate effects on detection, and as expected the rep-varying model performs best. Note that we ensure that these comparisons between rep-constant and rep-varying models are valid by omitting the binomial coefficient when computing the log-likelihood for the rep-constant model.

loo_compare_flocker(
  list(rep_constant, rep_varying)
)
#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.

#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
#>        elpd_diff se_diff
#> model2    0.0       0.0 
#> model1 -171.1      17.2

Likewise, we can compare the four flavors of multi-season model that we fit above. Recall that the data were simulated under colonization-extinction dynamics (rather than autologistic) and under explicit initial occupancy probabilities (rather than equilibrium). As expected, the multi_colex model performs best:

loo_compare_flocker(
  list(multi_colex, multi_colex_eq, multi_auto, multi_auto_eq)
)
#>        elpd_diff se_diff
#> model1   0.0       0.0  
#> model3  -7.8       4.1  
#> model2 -27.1       7.2  
#> model4 -32.9       7.9

Flocker also provides the function loo_flocker() to return a table of elpd_loo, p_loo, and looic estimates from loo::loo() or brms::loo() (the latter for single-season rep-constant models only).

`brms` tips and tricks

Mastering advanced occupancy modeling via flocker is mostly a matter of mastering the syntax available in brms. Here are some useful pieces of syntax:

Priors

Priors can be implemented as they would with any brms model. Priors can be specified using set_prior(), with priors specified for groups of parameters (via class) or individual parameters (via coef). The priors used for a particular model can be retrieved using brms::prior_summary(), and the names of the parameters and their default priors can be displayed prior to model fitting using get_flocker_prior() which is a drop-in replacement for brms::get_prior().

get_flocker_prior(
  f_occ = ~ uc1 + (1 + uc1 | species),
  f_det = ~ uc1 + ec1 + (1 + uc1 + ec1 | species),
  flocker_data = fd_rep_varying
  )
#>                 prior     class      coef   group resp dpar nlpar lb ub       source
#>                (flat)         b                                              default
#>                (flat)         b       ec1                               (vectorized)
#>                (flat)         b       uc1                               (vectorized)
#>                lkj(1)       cor                                              default
#>                lkj(1)       cor           species                       (vectorized)
#>  student_t(3, 0, 2.5) Intercept                                              default
#>  student_t(3, 0, 2.5)        sd                                    0         default
#>  student_t(3, 0, 2.5)        sd           species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       ec1 species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd Intercept species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       uc1 species                  0    (vectorized)
#>                (flat)         b                         occ                  default
#>                (flat)         b       uc1               occ             (vectorized)
#>                (flat) Intercept                         occ                  default
#>  student_t(3, 0, 2.5)        sd                         occ        0         default
#>  student_t(3, 0, 2.5)        sd           species       occ        0    (vectorized)
#>  student_t(3, 0, 2.5)        sd Intercept species       occ        0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       uc1 species       occ        0    (vectorized)
brms::prior_summary(rep_varying)
#>                 prior     class      coef   group resp dpar nlpar lb ub       source
#>                (flat)         b                                              default
#>                (flat)         b       ec1                               (vectorized)
#>                (flat)         b       uc1                               (vectorized)
#>                (flat)         b                         occ                  default
#>                (flat)         b       uc1               occ             (vectorized)
#>  student_t(3, 0, 2.5) Intercept                                              default
#>                (flat) Intercept                         occ                  default
#>  lkj_corr_cholesky(1)         L                                              default
#>  lkj_corr_cholesky(1)         L           species                       (vectorized)
#>  student_t(3, 0, 2.5)        sd                                    0         default
#>  student_t(3, 0, 2.5)        sd                         occ        0         default
#>  student_t(3, 0, 2.5)        sd           species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       ec1 species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd Intercept species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       uc1 species                  0    (vectorized)
#>  student_t(3, 0, 2.5)        sd           species       occ        0    (vectorized)
#>  student_t(3, 0, 2.5)        sd Intercept species       occ        0    (vectorized)
#>  student_t(3, 0, 2.5)        sd       uc1 species       occ        0    (vectorized)

Note that in examples like the above, with covariates shared between both the occupancy and detection model formulas (uc1 in this example), then the prior table will contain two entries associated with the covariate, one for the parameter governing occupancy and one for the parameter governing detection. Specifying priors for parameters in formulas other than detection can be done with reference to the dpar column, e.g.:

user_prior <- c(brms::set_prior("normal(0, 1)", coef = "uc1"), 
                brms::set_prior("normal(0, 3)", coef = "uc1", dpar = "occ"))

where the uc1 parameter in the occupancy component is specified by the addition of the dpar argument, and the uc1 parameter in the detection component is specified without reference to dpar.

For more on priors in brms, see ?brms::set_prior.

Users should understand the implications of the default brms behavior to internally center the design matrix, which affects how the prior on the intercept gets set (see ?brms::set_prior). Here is an example, based on a single-season rep-varying model, wherein we set a logistic prior on the value of the intercepts (flat on the probability scale) when all predictors are held at their means and a moderately regularizing prior on the coefficients:

rep_varying_prior1 <- flock(
  f_occ = ~ uc1,
  f_det = ~ ec1,
  flocker_data = fd_rep_varying,
  prior = 
    brms::set_prior("logistic(0,1)", class = "Intercept") +
    brms::set_prior("logistic(0,1)", class = "Intercept", dpar = "occ") +
    brms::set_prior("normal(0,2)", class = "b") +
    brms::set_prior("normal(0,2)", class = "b", dpar = "occ"),
  cores = 4,
  silent = 2,
  refresh = 0
  )
brms::prior_summary(rep_varying_prior1)
#>          prior     class coef group resp dpar nlpar lb ub       source
#>    normal(0,2)         b                                          user
#>    normal(0,2)         b  ec1                             (vectorized)
#>    normal(0,2)         b                  occ                     user
#>    normal(0,2)         b  uc1             occ             (vectorized)
#>  logistic(0,1) Intercept                                          user
#>  logistic(0,1) Intercept                  occ                     user

Here is an example where we set informative priors on the intercepts when all covariates are fixed to zero and the same moderately regularizing prior on the coefficients:

rep_varying_prior2 <- flock(
  f_occ = ~ 0 + Intercept + uc1,
  f_det = ~ 0 + Intercept + ec1,
  flocker_data = fd_rep_varying,
  prior = 
    brms::set_prior("normal(0,2)", class = "b") +
    brms::set_prior("normal(0,2)", class = "b", dpar = "occ") +
    brms::set_prior("normal(1, 1)", class = "b", coef = "Intercept") +
    brms::set_prior("normal(-1, 1)", class = "b", coef = "Intercept", dpar = "occ"),
  cores = 4,
  silent = 2,
  refresh = 0
  )
brms::prior_summary(rep_varying_prior2)
#>          prior class      coef group resp dpar nlpar lb ub       source
#>    normal(0,2)     b                                               user
#>    normal(0,2)     b       ec1                             (vectorized)
#>   normal(1, 1)     b Intercept                                     user
#>    normal(0,2)     b                       occ                     user
#>  normal(-1, 1)     b Intercept             occ                     user
#>    normal(0,2)     b       uc1             occ             (vectorized)

Model formulas

Simple formulas follow the same syntax as R’s lm() function. For example:

mod1 <- flock(
  f_occ = ~ uc1 + (1|species), 
  f_det = ~ 1, 
  flocker_data = fd_rep_constant
  )

Random effects

Simple random effects follow lme4 syntax, including advanced lme4 syntax like || for uncorrelated effects and / and : for expansion of multiple grouping terms. Here’s a simple example:

mod2 <- flock(
  f_occ = ~ uc1 + (1|species), 
  f_det = ~ 1, 
  flocker_data = fd_rep_constant
  )

When a model includes multiple random effects with the same grouping term, by default they are modeled as correlated within the occupancy or detection formulas, but as uncorrelated between formulas. For example, the code below estimates a single correlation for the intercept and slope in the occupancy sub-model.

mod3 <- flock(
  f_occ = ~ uc1 + (1 + uc1 | species), 
  f_det = ~ ec1 + (1 | species), 
  flocker_data = fd_rep_varying
  )

However, this assumption can easily be relaxed using the |<ID>| syntax from brms. The <ID> is an arbitrary character string representing a group of terms to model as correlated. The below code, for example, models correlated intercepts in the occupancy and detection sub-models, and correlated effects of sc1 on occupancy and vc1 on detection, but no correlations between the intercepts and the slopes in either sub-model:

mod4 <- flock(
  f_occ = ~ uc1 + (1 |g1| species) + (0 + uc1 |g2| species), 
  f_det = ~ ec1 + (1 |g1| species) + (0 + ec1 |g2| species), 
  flocker_data = fd_rep_varying
  )

For more on brms syntax for random effects syntax, see the documentation here.

Nonlinear models

Via brms, flocker supports Gaussian processes of arbitrary dimensionality (brms::gp()) as well as mgcv syntax for thin-plate regression splines (brms::s()) and tensor product smooths (brms::t2()), and brms syntax for monotonic effects of ordinal factors via brms::mo() (see here). For example:

mod5 <- flock(
  f_occ = ~ s(uc1), 
  f_det = ~ t2(uc1, ec1), 
  flocker_data = fd_rep_varying
  )

mod6 <- flock(
  f_occ = ~ 1, 
  f_det = ~ gp(uc1, ec1), 
  flocker_data = fd_rep_varying
  )

In addition, brms provides the ability to estimate models wherein the predictors (e.g. for occupancy and detection) are parametric nonlinear functions whose parameters have their own covariate-based linear predictors. For more details and an example, see the nonlinear models vignette.

Phylogenetic models

Phylogenetic effects can be included by providing a covariance matrix as a data2 argument and using the brms::gr() function to link species identities in flocker_data with the supplied covariance matrix. Note that phylogenetic effects can be included in either the occupancy component, the detection component, or both! In our experience, it can be computationally tractable to include multiple phylogenetic effects within a single occupancy model (see Mills et al. 2022).

# simulate an example phylogeny
phylogeny <- ape::rtree(30, tip.label = paste0("sp_", 1:30))

# calculate covariance matrix
A <- ape::vcv.phylo(phylogeny)

mod8 <- flock(
  f_occ = ~ 1 + (1|gr(species, cov = A)), 
  f_det = ~  1 + ec1 + (1|species), 
  flocker_data = fd_rep_varying, 
  data2 = list(A = A)
  )

mod9 <- flock(
  f_occ = ~ 1 + (1|gr(species, cov = A)), 
  f_det = ~  1 + ec1 + (1|gr(species, cov = A)), 
  flocker_data = fd_rep_varying, 
  data2 = list(A = A)
  )

See here for further details about specifying phylogenetic effects in brms.

Spatial and autoregressive structures

In addition to spatial Gaussian processes, brms provides a variety of autoregressive structures, both one-dimensional (see brms::ar(), brms::arma()) and two-dimensional (see brms::car(), brms::sar(). See here for details about conditional autoregressive (CAR) models in brms, and note that flock() accepts a data2 argument that it can pass to brms as necessary.

Our principle caution for users is that these autoregressive structures might lead to degenerate models when applied at the visit level (in detection formulas) or at the closure-unit level (in occupancy, colonization, extinction, or autologistic formulas) because observation-level random effects are often degenerate in regressions with Bernoulli responses. Thus we recommend applying autoregressive terms to groupings of multiple visits (detection formula) or multiple closure-units (other formulas). However, we note that flocker does provide a well-identified one-dimensional first-order autoregressive structure for occupancy across closure-units in a single-season model. This is achieved by co-opting the autologistic parameterization of the multi-season model and applying it instead to closure-units arranged along a one-dimensional spatial transect, yielding a one-dimensional analog of a spatial autologistic occupancy model.

A second caution is to remind users that in multi-species models, users will likely want to fit separate spatial terms by species (Doser et al 2022). For Gaussian processes, this can be achieved via the by argument to brms::gp(). For some conditional autoregressive structures (those that allow disconnected islands), this can be achieved by passing a block-diagonal adjacency matrix wherein species are disconnected components.

We note that gaussian process priors for spatially varying coefficients are readily achieved via the nonlinear formula syntax of brms, though they may require large volumes of data to successfully fit. For more details and an example, see the nonlinear models vignette.

Measurement error in covariates

See here for relevant brms documentation.

Additional fitting arguments

flock will pass any relevant parameters forward to brms::brm(), giving the user important control over the algorithmic details of how the model is fit. See ?brms::brm for details. To speed up the execution, we recommend supplying the argument backend = "cmdstanr". This requires the cmdstanr package and a working installation of cmdstan; see here for instructions to get started and further details.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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Fitting occupancy models with flocker

Jacob Socolar & Simon Mills

2023-10-20

Terms and definitions

Installation and feedback

Data simulation

Data formatting

Model fitting

The single-season rep-varying model

The single-season rep-constant model

Multi-season models

Data-augmented multi-species models

Post-processing

brms-native post-processing

Fitted values

The posterior occupancy state

Posterior prediction

Model comparison

brms tips and tricks

Priors

Model formulas

Random effects

Nonlinear models

Phylogenetic models

Spatial and autoregressive structures

Measurement error in covariates

Additional fitting arguments

`brms` tips and tricks