Convert simmaps into densityMaps suitable for deepSTRAPP
Source:R/convert_simmaps_to_densityMaps.R
convert_simmaps_to_densityMaps.RdConvert simmaps representing independent simulations of evolutionary history
into a densityMaps object suitable to use as input for a deepSTRAPP run.
simmaps are mapping discrete character/geographic evolutionary history as
transitions in character states/geographic ranges across nodes and branches of a phylogeny.
densityMaps are recording the posterior probability/frequencies of being in a given state/range along branches.
In deepSTRAPP format, densityMaps is a list of objects of class "densityMap" where each object corresponds to
the frequency of presence/absence of a state/range.
Usage
convert_simmaps_to_densityMaps(
simmaps,
colors_per_levels = NULL,
tol = 1e-05,
verbose = TRUE
)Arguments
- simmaps
List of objects of class
"simmap", typically generated withprepare_trait_data()orphytools::make.simmap(), that represent discrete character/geographic evolutionary history (i.e., transitions in character states/geographic ranges) mapped along branches.- colors_per_levels
Named character string. To set the colors to use to map each state/range posterior probabilities. Names = states/ranges; values = colors. If
NULL(default), therainbow()color scale will be used.- tol
Positive numeric. To set the tolerance used to match node ages and time steps (i.e., consider them equal). Default = 1e-5.
- verbose
Logical. Whether to display progress every 100 edges. Default =
TRUE.
Value
The function returns a densityMaps as a list of objects of class "densityMap",
where each object is mapping the frequency of presence/absence of a state/range.
The number of objects depends on the number of states/ranges observed across the simmaps provided for conversion.
Each densityMap is named as "Density_map_X" with X being each of the state/range recorded across the simmaps.
Each densityMap is a list of three elements:
$treeList of classes"simmap"and"phylo"that contains the phylogeny in ape format and the mapping of states/ranges frequencies along branches in$tree$maps.$colsNamed character strings. Colors mapped to the 0 to 1000 scale used to record frequencies in$tree$maps.$statesCharacter string with two values. First entry is the absence of the state/range recorded as "Not X". Second entry is the presence of the state/range recorded as "X", X being the state/range name.
Details
The function is a wrapper of the original phytools::densityMap() by Liam Revell.
However, it does not produce a single densityMap for binary states,
but rather can handle simmaps mapping any number of states/ranges, and produce a densityMaps list
that summarizes the frequency of presence/absence of each state/range in subsequent densityMap objects.
Both simmaps and densityMaps objects can be used as inputs for a deepSTRAPP run
with run_deepSTRAPP_for_focal_time() or run_deepSTRAPP_over_time().
simmaps retain the identity of each simulated history,
allowing deepSTRAPP to keep track of which simulation generated each set of trait values (i.e., states/ranges).
However, retaining all simulated histories can require substantial RAM, particularly for large phylogenies or many simulations.
Alternatively, densityMaps summarize the frequency of states/ranges across simulations.
They require substantially less RAM and can be used to visualize the overall uncertainty
in trait evolution with plot_densityMaps_overlay().
The trade-off is that densityMaps discard the identity of individual simulations and
therefore cannot be used to track which simulated history generated a given set of trait values.
Examples
## Load data
# Load trait df
data(Ponerinae_trait_tip_data, package = "deepSTRAPP")
# Load phylogeny
data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
# Extract categorical data with 3-levels
Ponerinae_cat_3lvl_tip_data <- setNames(object = Ponerinae_trait_tip_data$fake_cat_3lvl_tip_data,
nm = Ponerinae_trait_tip_data$Taxa)
table(Ponerinae_cat_3lvl_tip_data)
#> Ponerinae_cat_3lvl_tip_data
#> arboreal subterranean terricolous
#> 193 953 388
# Select color scheme for states
colors_per_states <- c("forestgreen", "sienna", "goldenrod")
names(colors_per_states) <- c("arboreal", "subterranean", "terricolous")
# (May take several minutes to run)
## Produce densityMaps using stochastic character mapping based on an ER Mk model
Ponerinae_cat_3lvl_data_old_calib <- prepare_trait_data(
tip_data = Ponerinae_cat_3lvl_tip_data,
phylo = Ponerinae_tree_old_calib,
trait_data_type = "categorical",
colors_per_levels = colors_per_states,
evolutionary_models = "ER", # Use ER model
run_stochastic_maps = TRUE,
nb_simulations = 100, # Reduce number of simulations to save time
seed = 1234, # Set seed for reproducibility
return_simmaps = TRUE, # Return simmaps in the output
plot_map = FALSE)
#> Warning: Entries in 'tip_data' were reordered to match 'phylo$tip.label.
#>
#> 2026-10-30 00:59:07.09644 - Fit 1 evolutionary model(s): ER.
#>
#> ------ ER model ------
#>
#> GEIGER-fitted comparative model of discrete data
#> fitted Q matrix:
#> arboreal subterranean terricolous
#> arboreal -0.0002508455 0.0001254228 0.0001254228
#> subterranean 0.0001254228 -0.0002508455 0.0001254228
#> terricolous 0.0001254228 0.0001254228 -0.0002508455
#>
#> model summary:
#> log-likelihood = -45.665085
#> AIC = 93.330171
#> AICc = 93.332782
#> free parameters = 1
#>
#> Convergence diagnostics:
#> optimization iterations = 100
#> failed iterations = 0
#> number of iterations with same best fit = 100
#> frequency of best fit = 1.000
#>
#> object summary:
#> 'lik' -- likelihood function
#> 'bnd' -- bounds for likelihood search
#> 'res' -- optimization iteration summary
#> 'opt' -- maximum likelihood parameter estimates
#>
#> 2026-10-30 00:59:10.009869 - Compare model fits.
#>
#> model logL k AIC AICc delta_AICc Akaike_weights rank
#> ER ER -45.66509 1 93.33017 93.33278 0 100 1
#> 2026-10-30 00:59:10.011661 - Run simulations for stochastic mapping.
#>
#> make.simmap is sampling character histories conditioned on
#> the transition matrix
#>
#> Q =
#> arboreal subterranean terricolous
#> arboreal -0.0002508455 0.0001254228 0.0001254228
#> subterranean 0.0001254228 -0.0002508455 0.0001254228
#> terricolous 0.0001254228 0.0001254228 -0.0002508455
#> (specified by the user);
#> and (mean) root node prior probabilities
#> pi =
#> arboreal subterranean terricolous
#> 0.3333333 0.3333333 0.3333333
#> Done.
#> 2026-10-30 01:01:27.660177 - Extract ACE as posterior sampling from stochastic mapping.
#> 2026-10-30 01:01:30.963099 - Create densityMaps by summarizing simulations of evolutionary history (simmaps).
#>
#> 2026-10-30 01:01:34.825133 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:01:35.777763 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:01:36.942395 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:01:39.051235 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:01:39.857297 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:01:40.189281 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:01:40.603086 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:01:40.956158 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:01:41.357194 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:01:41.771922 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:01:42.178664 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:01:42.912864 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:01:43.625137 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:01:44.753599 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:01:45.491881 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:01:46.779598 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:01:48.503873 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:01:49.338429 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:01:50.00014 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:01:50.565262 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:01:51.310625 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:01:52.17602 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:01:53.258046 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:01:53.99849 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:01:54.710799 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:01:55.572669 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:01:56.794622 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:01:58.717611 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:02:00.943834 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:02:02.862512 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:02:04.04508 - Posterior probabilities computed for State = arboreal - n°1/3
#> 2026-10-30 01:02:07.437098 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:02:08.366303 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:02:09.48506 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:02:11.525775 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:02:12.304008 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:02:12.622633 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:02:13.032969 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:02:13.371911 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:02:13.76139 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:02:14.16507 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:02:14.562225 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:02:15.26748 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:02:15.960176 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:02:17.054079 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:02:17.769352 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:02:19.004962 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:02:20.183485 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:02:21.040306 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:02:21.721962 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:02:22.868667 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:02:23.577313 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:02:24.409154 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:02:25.445851 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:02:26.157017 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:02:26.826291 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:02:27.654743 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:02:28.820386 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:02:30.701336 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:02:32.852329 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:02:34.718882 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:02:35.876304 - Posterior probabilities computed for State = subterranean - n°2/3
#> 2026-10-30 01:02:39.091194 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:02:40.018603 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:02:41.260596 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:02:43.301849 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:02:44.081375 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:02:44.400788 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:02:44.811776 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:02:45.150471 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:02:45.545448 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:02:45.947295 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:02:46.347671 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:02:47.061274 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:02:47.76277 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:02:48.851162 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:02:49.563916 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:02:50.808735 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:02:51.996631 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:02:52.861786 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:02:53.548386 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:02:54.122455 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:02:54.884246 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:02:56.350233 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:02:57.382193 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:02:58.09416 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:02:58.759367 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:02:59.588267 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:03:00.75437 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:03:02.616084 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:03:04.758669 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:03:06.623703 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:03:07.764261 - Posterior probabilities computed for State = terricolous - n°3/3
# Note that densityMaps are already produced by the [deepSTRAPP::prepare_trait_data()] function,
# but for the sake of example, we can convert the simmaps stored in the output into densityMaps,
# using [deepSTRAPP::convert_simmaps_to_densityMaps()].
## Convert simmaps to densityMaps as input format for deepSTRAPP
Ponerinae_densityMaps <- convert_simmaps_to_densityMaps(
simmaps = Ponerinae_cat_3lvl_data_old_calib$simmaps)
#> 2026-10-30 01:03:11.131484 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:03:12.061855 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:03:13.171021 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:03:15.304906 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:03:16.08184 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:03:16.404857 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:03:16.811847 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:03:17.149988 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:03:17.543569 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:03:17.949584 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:03:18.344223 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:03:19.054763 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:03:19.752166 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:03:20.840706 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:03:21.550508 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:03:22.79743 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:03:23.989151 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:03:24.848089 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:03:25.528157 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:03:26.108411 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:03:26.873154 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:03:27.763571 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:03:29.443031 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:03:30.157765 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:03:30.826401 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:03:31.660485 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:03:32.828217 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:03:34.677108 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:03:36.826545 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:03:38.680327 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:03:39.818385 - Posterior probabilities computed for State = arboreal - n°1/3
#> 2026-10-30 01:03:43.043103 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:03:43.975386 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:03:45.094002 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:03:47.244216 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:03:48.023839 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:03:48.349714 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:03:48.759274 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:03:49.104447 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:03:49.493055 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:03:49.902605 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:03:50.295924 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:03:51.011615 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:03:51.714774 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:03:52.814303 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:03:53.529759 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:03:54.782444 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:03:55.975009 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:03:56.84812 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:03:57.539402 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:03:58.116934 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:03:58.879132 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:03:59.778966 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:04:00.893431 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:04:02.247598 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:04:02.921202 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:04:03.756985 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:04:04.936764 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:04:06.804032 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:04:08.957166 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:04:10.809526 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:04:11.958112 - Posterior probabilities computed for State = subterranean - n°2/3
#> 2026-10-30 01:04:15.27533 - Posterior probability computed for edge n°100/3066
#> 2026-10-30 01:04:16.202525 - Posterior probability computed for edge n°200/3066
#> 2026-10-30 01:04:17.307394 - Posterior probability computed for edge n°300/3066
#> 2026-10-30 01:04:19.373539 - Posterior probability computed for edge n°400/3066
#> 2026-10-30 01:04:20.16134 - Posterior probability computed for edge n°500/3066
#> 2026-10-30 01:04:20.482484 - Posterior probability computed for edge n°600/3066
#> 2026-10-30 01:04:20.890759 - Posterior probability computed for edge n°700/3066
#> 2026-10-30 01:04:21.234683 - Posterior probability computed for edge n°800/3066
#> 2026-10-30 01:04:21.622027 - Posterior probability computed for edge n°900/3066
#> 2026-10-30 01:04:22.037463 - Posterior probability computed for edge n°1000/3066
#> 2026-10-30 01:04:22.435152 - Posterior probability computed for edge n°1100/3066
#> 2026-10-30 01:04:23.152138 - Posterior probability computed for edge n°1200/3066
#> 2026-10-30 01:04:23.853238 - Posterior probability computed for edge n°1300/3066
#> 2026-10-30 01:04:24.946291 - Posterior probability computed for edge n°1400/3066
#> 2026-10-30 01:04:25.659451 - Posterior probability computed for edge n°1500/3066
#> 2026-10-30 01:04:26.906688 - Posterior probability computed for edge n°1600/3066
#> 2026-10-30 01:04:28.108743 - Posterior probability computed for edge n°1700/3066
#> 2026-10-30 01:04:28.976084 - Posterior probability computed for edge n°1800/3066
#> 2026-10-30 01:04:29.669441 - Posterior probability computed for edge n°1900/3066
#> 2026-10-30 01:04:30.25296 - Posterior probability computed for edge n°2000/3066
#> 2026-10-30 01:04:31.024027 - Posterior probability computed for edge n°2100/3066
#> 2026-10-30 01:04:31.93247 - Posterior probability computed for edge n°2200/3066
#> 2026-10-30 01:04:33.045087 - Posterior probability computed for edge n°2300/3066
#> 2026-10-30 01:04:34.406492 - Posterior probability computed for edge n°2400/3066
#> 2026-10-30 01:04:35.077412 - Posterior probability computed for edge n°2500/3066
#> 2026-10-30 01:04:35.912967 - Posterior probability computed for edge n°2600/3066
#> 2026-10-30 01:04:37.08554 - Posterior probability computed for edge n°2700/3066
#> 2026-10-30 01:04:38.942529 - Posterior probability computed for edge n°2800/3066
#> 2026-10-30 01:04:41.083087 - Posterior probability computed for edge n°2900/3066
#> 2026-10-30 01:04:42.939564 - Posterior probability computed for edge n°3000/3066
#> 2026-10-30 01:04:44.072361 - Posterior probabilities computed for State = terricolous - n°3/3
# Plot densityMaps one by one
plot(Ponerinae_densityMaps[[1]]) # densityMap for state n°1 ("arboreal")
plot(Ponerinae_densityMaps[[2]]) # densityMap for state n°1 ("subterranean")
plot(Ponerinae_densityMaps[[3]]) # densityMap for state n°1 ("terricolous")
# Plot overlay of all densityMaps
plot_densityMaps_overlay(densityMaps = Ponerinae_densityMaps)
