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.
#>
#> 2026-09-28 01:40:28.330905 - 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
#>
#> 2026-09-28 01:40:33.79655 - 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
#> 2026-09-28 01:40:33.798517 - 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.
#> 2026-09-28 01:42:58.448015 - Extract ACE as posterior sampling from stochastic mapping.
#> 2026-09-28 01:43:02.214246 - Create densityMaps by summarizing simulations of evolutionary history (simmaps).
#>
#> 2026-09-28 01:43:06.180632 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:43:07.313563 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:43:08.636192 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:43:11.076743 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:43:12.507233 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:43:12.864481 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:43:13.276652 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:43:13.621381 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:43:14.016594 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:43:14.423379 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:43:14.822193 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:43:15.56529 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:43:16.277666 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:43:17.380056 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:43:18.09632 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:43:19.336086 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:43:20.500756 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:43:21.362501 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:43:22.026097 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:43:22.602274 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:43:23.354496 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:43:24.248366 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:43:25.341809 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:43:26.09528 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:43:26.809629 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:43:27.680887 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:43:28.928619 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:43:30.891268 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:43:33.142416 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:43:35.090992 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:43:36.283999 - Posterior probabilities computed for State = arboreal - n°1/3
#> 2026-09-28 01:43:39.635772 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:43:40.596251 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:43:41.721395 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:43:43.933572 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:43:44.721925 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:43:45.052556 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:43:45.479064 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:43:45.82737 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:43:46.224133 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:43:46.63806 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:43:47.033875 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:43:47.774749 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:43:48.478605 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:43:49.611864 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:43:50.331156 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:43:51.619987 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:43:52.828955 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:43:53.707122 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:43:54.401175 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:43:55.594211 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:43:56.333791 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:43:57.190616 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:43:58.259118 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:43:59.014391 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:43:59.706775 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:44:00.552411 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:44:01.758706 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:44:03.6852 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:44:05.937259 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:44:07.878844 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:44:09.071975 - Posterior probabilities computed for State = subterranean - n°2/3
#> 2026-09-28 01:44:12.513708 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:44:13.462003 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:44:14.619982 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:44:16.77134 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:44:17.582145 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:44:17.909274 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:44:18.323384 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:44:18.672501 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:44:19.066262 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:44:19.498611 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:44:19.900604 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:44:20.626495 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:44:21.366598 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:44:22.489086 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:44:23.246728 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:44:24.520467 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:44:25.74046 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:44:26.637864 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:44:27.358994 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:44:27.948501 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:44:28.725261 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:44:29.63577 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:44:30.773366 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:44:31.562227 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:44:32.291981 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:44:33.198155 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:44:34.492429 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:44:37.086702 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:44:39.302542 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:44:41.230862 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:44:42.400728 - 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)
#> 2026-09-28 01:44:45.957977 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:44:46.913798 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:44:48.058867 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:44:50.204713 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:44:51.011895 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:44:51.337569 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:44:51.749041 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:44:52.095516 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:44:52.504903 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:44:52.915961 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:44:53.314625 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:44:54.052 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:44:54.758754 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:44:55.894019 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:44:56.636693 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:44:57.924075 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:44:59.136144 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:45:00.022975 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:45:00.722747 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:45:01.311242 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:45:02.10367 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:45:03.026973 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:45:04.171164 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:45:04.953456 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:45:05.706474 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:45:06.620529 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:45:07.903867 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:45:09.944959 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:45:12.283444 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:45:14.314914 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:45:16.167731 - Posterior probabilities computed for State = arboreal - n°1/3
#> 2026-09-28 01:45:19.486275 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:45:20.461933 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:45:21.603163 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:45:23.873548 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:45:24.675845 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:45:25.005512 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:45:25.441259 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:45:25.792592 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:45:26.187613 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:45:26.606289 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:45:27.030674 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:45:27.759607 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:45:28.492425 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:45:29.623584 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:45:30.371119 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:45:31.651575 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:45:32.874618 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:45:33.76569 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:45:34.486043 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:45:35.075671 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:45:35.866988 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:45:36.777654 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:45:37.928434 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:45:38.721917 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:45:39.456641 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:45:40.364513 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:45:41.669083 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:45:43.702009 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:45:46.04171 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:45:48.070987 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:45:49.317195 - Posterior probabilities computed for State = subterranean - n°2/3
#> 2026-09-28 01:45:52.850163 - Posterior probability computed for edge n°100/3066
#> 2026-09-28 01:45:54.506571 - Posterior probability computed for edge n°200/3066
#> 2026-09-28 01:45:55.575321 - Posterior probability computed for edge n°300/3066
#> 2026-09-28 01:45:57.499608 - Posterior probability computed for edge n°400/3066
#> 2026-09-28 01:45:58.23593 - Posterior probability computed for edge n°500/3066
#> 2026-09-28 01:45:58.542131 - Posterior probability computed for edge n°600/3066
#> 2026-09-28 01:45:58.927786 - Posterior probability computed for edge n°700/3066
#> 2026-09-28 01:45:59.262664 - Posterior probability computed for edge n°800/3066
#> 2026-09-28 01:45:59.632729 - Posterior probability computed for edge n°900/3066
#> 2026-09-28 01:46:00.016554 - Posterior probability computed for edge n°1000/3066
#> 2026-09-28 01:46:00.389774 - Posterior probability computed for edge n°1100/3066
#> 2026-09-28 01:46:01.067408 - Posterior probability computed for edge n°1200/3066
#> 2026-09-28 01:46:01.73156 - Posterior probability computed for edge n°1300/3066
#> 2026-09-28 01:46:02.762953 - Posterior probability computed for edge n°1400/3066
#> 2026-09-28 01:46:03.43755 - Posterior probability computed for edge n°1500/3066
#> 2026-09-28 01:46:04.605816 - Posterior probability computed for edge n°1600/3066
#> 2026-09-28 01:46:05.740077 - Posterior probability computed for edge n°1700/3066
#> 2026-09-28 01:46:06.551006 - Posterior probability computed for edge n°1800/3066
#> 2026-09-28 01:46:07.20026 - Posterior probability computed for edge n°1900/3066
#> 2026-09-28 01:46:07.75062 - Posterior probability computed for edge n°2000/3066
#> 2026-09-28 01:46:08.476572 - Posterior probability computed for edge n°2100/3066
#> 2026-09-28 01:46:09.305784 - Posterior probability computed for edge n°2200/3066
#> 2026-09-28 01:46:10.344781 - Posterior probability computed for edge n°2300/3066
#> 2026-09-28 01:46:11.076006 - Posterior probability computed for edge n°2400/3066
#> 2026-09-28 01:46:11.752783 - Posterior probability computed for edge n°2500/3066
#> 2026-09-28 01:46:12.583944 - Posterior probability computed for edge n°2600/3066
#> 2026-09-28 01:46:13.771114 - Posterior probability computed for edge n°2700/3066
#> 2026-09-28 01:46:15.634364 - Posterior probability computed for edge n°2800/3066
#> 2026-09-28 01:46:17.79391 - Posterior probability computed for edge n°2900/3066
#> 2026-09-28 01:46:19.669865 - Posterior probability computed for edge n°3000/3066
#> 2026-09-28 01:46:20.801189 - 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)
