plot_traits_vs_rates_on_phylogeny_over_time: Plot multiple mapped phylogenies of trait/range evolution vs....
In deepSTRAPP: Test for Differences in Diversification Rates over Time
plot_traits_vs_rates_on_phylogeny_over_time R Documentation
Plot multiple mapped phylogenies of trait/range evolution vs. diversification rates and regime shifts over time-steps
Description
Plot two mapped phylogenies with evolutionary data with branches cut off for each time-step.
Main input = output of a deepSTRAPP run over time using run_deepSTRAPP_over_time()).
Left facet: plot the evolution of trait data/geographic ranges on the left time-calibrated phylogeny.
For continuous data: Each branch is colored according to the estimates value of the traits.
For categorical and biogeographic data: Each branch is colored according to the posterior probability
of being in a given state/range. Color for each state/range are overlaid using transparency
to produce a single plot for all states/ranges.
Right facet: plot the evolution of diversification rates and location of regime shits estimated from a BAMM
(Bayesian Analysis of Macroevolutionary Mixtures).
Each branch is colored according to the estimated rates of speciation, extinction, or net diversification
stored in an object of class bammdata. Rates can vary along time, thus colors evolved along individual branches.
This function is a wrapper of run_deepSTRAPP_for_focal_time() used to plot mapped phylogenies for
a unique given focal_time.
Returns one plot per focal time in $time_steps.
If a PDF file path is provided in PDF_file_path, the plots will be saved directly in a PDF file,
with one page per focal time in $time_steps.
Usage
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs,
color_scale = NULL,
colors_per_levels = NULL,
add_ACE_pies = TRUE,
cex_pies = 0.5,
rate_type = "net_diversification",
keep_initial_colorbreaks = FALSE,
add_regime_shifts = TRUE,
configuration_type = "MAP",
sample_index = 1,
adjust_size_to_prob = TRUE,
regimes_fill = "grey",
regimes_size = 1,
regimes_pch = 21,
regimes_border_col = "black",
regimes_border_width = 1,
...,
display_plot = TRUE,
PDF_file_path = NULL
)
Arguments
deepSTRAPP_outputs
List of elements generated with run_deepSTRAPP_over_time(),
that summarize the results of a STRAPP run over multiple time-steps in the past.
color_scale
Vector of character string. List of colors to use to build the color scale with grDevices::colorRampPalette()
showing the evolution of a continuous trait. From lowest values to highest values. (For continuous trait data only)
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), the color scale provided densityMaps will be used. (For categorical and biogeographic data only)
add_ACE_pies
Logical. Whether to add pies of posterior probabilities of states/ranges at internal nodes on the mapped phylogeny. Default = TRUE.
cex_pies
Numerical. To adjust the size of the ACE pies. Default = 0.5.
rate_type
A character string specifying the type of diversification rates to plot.
Must be one of 'speciation', 'extinction' or 'net_diversification' (default).
keep_initial_colorbreaks
Logical. Whether to keep the same color breaks as used for the most recent focal time. Typically, the current time (t = 0). Default = FALSE.
add_regime_shifts
Logical. Whether to add the location of regime shifts on the phylogeny (Step 2). Default is TRUE.
configuration_type
A character string specifying how to select the location of regime shifts across posterior samples.
-
configuration_type = "MAP": Use the average locations recorded in posterior samples with the Maximum A Posteriori probability (MAP) configuration.
This regime shift configuration is the most frequent configuration among the posterior samples (See BAMMtools::getBestShiftConfiguration()).
This is the default option.
-
configuration_type = "MSC": Use the average locations recorded in posterior samples with the Maximum Shift Credibility (MSC) configuration.
This regime shift configuration has the highest product of marginal probabilities across branches (See BAMMtools::maximumShiftCredibility()).
-
configuration_type = "index": Use the configuration of a unique posterior sample those index is provided in sample_index.
sample_index
Integer. Index of the posterior samples to use to plot the location of regime shifts.
Used only if configuration_type = index. Default = 1.
adjust_size_to_prob
Logical. Whether to scale the size of the symbols showing the location of regime shifts according to
the marginal shift probability of the shift happening on each location/branch. This will only works if there is an $MSP_tree element
summarizing the marginal shift probabilities across branches in the BAMM_object. Default is TRUE.
regimes_fill
Character string. Set the color of the background of the symbols showing the location of regime shifts.
Equivalent to the bg argument in BAMMtools::addBAMMshifts(). Default is "grey".
regimes_size
Numerical. Set the size of the symbols showing the location of regime shifts.
Equivalent to the cex argument in BAMMtools::addBAMMshifts(). Default is 1.
regimes_pch
Integer. Set the shape of the symbols showing the location of regime shifts.
Equivalent to the pch argument in BAMMtools::addBAMMshifts(). Default is 21.
regimes_border_col
Character string. Set the color of the border of the symbols showing the location of regime shifts.
Equivalent to the col argument in BAMMtools::addBAMMshifts(). Default is "black".
regimes_border_width
Numerical. Set the width of the border of the symbols showing the location of regime shifts.
Equivalent to the lwd argument in BAMMtools::addBAMMshifts(). Default is 1.
...
Additional graphical arguments to pass down to phytools::plot.contMap(), phytools::plot.simmap(),
plot_densityMaps_overlay(), BAMMtools::plot.bammdata(), BAMMtools::addBAMMshifts(), and par().
display_plot
Logical. Whether to display the plot generated in the R console. Default is TRUE.
PDF_file_path
Character string. If provided, the plot will be saved in a PDF file following the path provided here. The path must end with ".pdf".
Details
The main input deepSTRAPP_outputs is the typical output of run_deepSTRAPP_over_time().
It provides information on results of a STRAPP run performed over multiple time-steps, and can also encompass
updated phylogenies with mapped trait evolution and diversification rates and regimes shifts if appropriate arguments are set.
-
return_updated_trait_data_with_Map must be set to TRUE so that the trait data extracted for the given $time_steps
and the list of updated versions of mapped phylogenies (contMap/densityMaps) is returned among the outputs under $updated_trait_data_with_Map_over_time.
The updated contMap/densityMaps consist in cutting off branches and mappings that are younger than the successive $time_steps.
-
return_updated_BAMM_object must be set to TRUE so that the list of updated_BAMM_object with phylogenies and mapped diversification rates
cut-off at the successive $time_steps are returned among the outputs under $updated_BAMM_objects_over_time.
$MAP_BAMM_object and $MSC_BAMM_object elements are required in the elements of $updated_BAMM_objects_over_time to plot regime shift locations
following the "MAP" or "MSC" configuration_type respectively.
A $MSP_tree element is required to scale the size of the symbols showing the location of regime shifts according marginal shift probabilities.
(If adjust_size_to_prob = TRUE).
Alternatively, the main input deepSTRAPP_outputs can be the output of run_deepSTRAPP_over_time(),
providing results of STRAPP tests over multiple time-steps. In this case, you must provide a focal_time to select the
unique time-step used for plotting.
-
return_updated_trait_data_with_Map must be set to TRUE so that the trait data extracted and
the updated version of mapped phylogenies (contMap/densityMaps) are returned among the outputs under $updated_trait_data_with_Map_over_time.
-
return_updated_BAMM_object must be set to TRUE so that the BAMM_objects with phylogeny and mapped diversification rates
cut-off at the specified time-steps are returned among the outputs under $updated_BAMM_objects_over_time.
For plotting a single time-step (i.e., $focal_time) at once, see plot_traits_vs_rates_on_phylogeny_for_focal_time().
Value
If display_plot = TRUE, the function displays the successive plots with two facets in the R console:
(Left) A time-calibrated phylogeny displaying the evolution of trait/biogeographic data.
(Right) A time-calibrated phylogeny displaying diversification rates and regime shifts.
A plot per time-steps is generated and displayed successively in the console.
If PDF_file_path is provided, the plots will be exported in a unique PDF file with one page per time-step.
Author(s)
Maël Doré
See Also
plot_contMap() phytools::plot.densityMap() plot_densityMaps_overlay() plot_BAMM_rates()
Function in deepSTRAPP needed to produce the deepSTRAPP_outputs as input: run_deepSTRAPP_over_time()
Function in deepSTRAPP to a single time-step at once: plot_traits_vs_rates_on_phylogeny_for_focal_time()
Examples
if (deepSTRAPP::is_dev_version())
{
# ----- Example 1: Continuous trait ----- #
## Load data
# Load trait df
data(Ponerinae_trait_tip_data, package = "deepSTRAPP")
# Load phylogeny with old calibration
data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
# Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Prepare trait data
# Extract continuous trait data as a named vector
Ponerinae_cont_tip_data <- setNames(object = Ponerinae_trait_tip_data$fake_cont_tip_data,
nm = Ponerinae_trait_tip_data$Taxa)
# Select a color scheme from lowest to highest values
color_scale = c("darkgreen", "limegreen", "orange", "red")
# Get Ancestral Character Estimates based on a Brownian Motion model
# To obtain values at internal nodes
Ponerinae_ACE <- phytools::fastAnc(tree = Ponerinae_tree_old_calib, x = Ponerinae_cont_tip_data)
# (May take several minutes to run)
# Run a Stochastic Mapping based on a Brownian Motion model
# to interpolate values along branches and obtain a "contMap" object
Ponerinae_contMap <- phytools::contMap(Ponerinae_tree, x = Ponerinae_cont_tip_data,
res = 100, # Number of time steps
plot = FALSE)
# Plot contMap = stochastic mapping of continuous trait
plot_contMap(contMap = Ponerinae_contMap,
color_scale = color_scale)
## Set for time steps of 5 My. Will generate deepSTRAPP workflows for 0 to 40 Mya.
# nb_time_steps <- 5
time_step_duration <- 5
time_range <- c(0, 40)
## Run deepSTRAPP on net diversification rates
Ponerinae_deepSTRAPP_cont_old_calib_0_40 <- run_deepSTRAPP_over_time(
contMap = Ponerinae_contMap,
ace = Ponerinae_ACE,
tip_data = Ponerinae_cont_tip_data,
trait_data_type = "continuous",
BAMM_object = Ponerinae_BAMM_object_old_calib,
# nb_time_steps = nb_time_steps,
time_range = time_range,
time_step_duration = time_step_duration,
return_perm_data = TRUE,
extract_trait_data_melted_df = TRUE,
extract_diversification_data_melted_df = TRUE,
return_STRAPP_results = TRUE,
return_updated_trait_data_with_Map = TRUE,
return_updated_BAMM_object = TRUE,
verbose = TRUE,
verbose_extended = TRUE)
## Load directly trait data output
data(Ponerinae_deepSTRAPP_cont_old_calib_0_40, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Plot updated contMap vs. updated diversification rates
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
# To use the same color breaks as for t = 0 My in all BAMM plots
keep_initial_colorbreaks = TRUE,
color_scale = c("limegreen", "orange", "red"), # Adjust color scale on contMap
legend = TRUE, labels = TRUE, # Show legend and label on BAMM plot
cex = 0.7) # Adjust label size on contMap
# PDF_file_path = "Updated_maps_cont_old_calib_0_40My.pdf")
# ----- Example 2: Biogeographic data ----- #
## Load data
# Load phylogeny
data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
# Load trait df
data(Ponerinae_binary_range_table, package = "deepSTRAPP")
# Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Prepare range data for Old World vs. New World
# No overlap in ranges
table(Ponerinae_binary_range_table$Old_World, Ponerinae_binary_range_table$New_World)
Ponerinae_NO_data <- stats::setNames(object = Ponerinae_binary_range_table$Old_World,
nm = Ponerinae_binary_range_table$Taxa)
Ponerinae_NO_data <- as.character(Ponerinae_NO_data)
Ponerinae_NO_data[Ponerinae_NO_data == "TRUE"] <- "O" # O = Old World
Ponerinae_NO_data[Ponerinae_NO_data == "FALSE"] <- "N" # N = New World
names(Ponerinae_NO_data) <- Ponerinae_binary_range_table$Taxa
table(Ponerinae_NO_data)
colors_per_levels <- c("mediumpurple2", "peachpuff2")
names(colors_per_levels) <- c("N", "O")
# (May take several minutes to run)
## Run evolutionary models
Ponerinae_biogeo_data <- prepare_trait_data(
tip_data = Ponerinae_NO_data,
trait_data_type = "biogeographic",
phylo = Ponerinae_tree_old_calib,
evolutionary_models = "DEC+J", # Default = "DEC" for biogeographic
BioGeoBEARS_directory_path = tempdir(), # Ex: "./BioGeoBEARS_directory/"
keep_BioGeoBEARS_files = FALSE,
prefix_for_files = "Ponerinae_old_calib",
max_range_size = 2,
split_multi_area_ranges = TRUE, # Set to TRUE to use only unique areas "A" and "B"
nb_simulations = 100, # Reduce to save time (Default = '1000')
colors_per_levels = colors_per_levels,
return_model_selection_df = TRUE,
verbose = TRUE)
# Load directly output
data(Ponerinae_biogeo_data_old_calib, package = "deepSTRAPP")
## Set for time steps of 5 My. Will generate deepSTRAPP workflows from 0 to 40 Mya.
time_range <- c(0, 40)
time_step_duration <- 5
# (May take several minutes to run)
## Run deepSTRAPP on net diversification rates for time-steps = 0 to 40 Mya.
Ponerinae_deepSTRAPP_biogeo_old_calib_0_40 <- run_deepSTRAPP_over_time(
densityMaps = Ponerinae_biogeo_data_old_calib$densityMaps,
ace = Ponerinae_biogeo_data_old_calib$ace,
tip_data = Ponerinae_ON_tip_data,
trait_data_type = "biogeographic",
BAMM_object = Ponerinae_BAMM_object_old_calib,
time_range = time_range,
time_step_duration = time_step_duration,
seed = 1234, # Set seed for reproducibility
alpha = 0.10, # Select a generous level of significance for the sake of the example
rate_type = "net_diversification",
return_perm_data = TRUE,
extract_trait_data_melted_df = TRUE,
extract_diversification_data_melted_df = TRUE,
return_STRAPP_results = TRUE,
return_updated_trait_data_with_Map = TRUE,
return_updated_BAMM_object = TRUE,
verbose = TRUE,
verbose_extended = TRUE)
## Load directly output
data(Ponerinae_deepSTRAPP_biogeo_old_calib_0_40, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Explore output
str(Ponerinae_deepSTRAPP_biogeo_old_calib_0_40, max.level = 1)
## Plot updated contMap vs. updated diversification rates
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs = Ponerinae_deepSTRAPP_biogeo_old_calib_0_40,
# Adjust colors on densityMaps
colors_per_levels = c("N" = "dodgerblue2", "O" = "orange"),
legend = TRUE, labels = TRUE, # Show legend and label on BAMM plot
cex_pies = 0.2, # Adjust size of ACE pies on densityMaps
cex = 0.7) # Adjust label size on contMap
# PDF_file_path = "Updated_maps_biogeo_old_calib_0_40My.pdf")
}
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| plot_traits_vs_rates_on_phylogeny_over_time | R Documentation |
Plot multiple mapped phylogenies of trait/range evolution vs. diversification rates and regime shifts over time-steps
Description
Plot two mapped phylogenies with evolutionary data with branches cut off for each time-step.
Main input = output of a deepSTRAPP run over time using run_deepSTRAPP_over_time()).
Left facet: plot the evolution of trait data/geographic ranges on the left time-calibrated phylogeny.
For continuous data: Each branch is colored according to the estimates value of the traits.
For categorical and biogeographic data: Each branch is colored according to the posterior probability of being in a given state/range. Color for each state/range are overlaid using transparency to produce a single plot for all states/ranges.
Right facet: plot the evolution of diversification rates and location of regime shits estimated from a BAMM (Bayesian Analysis of Macroevolutionary Mixtures). Each branch is colored according to the estimated rates of speciation, extinction, or net diversification stored in an object of class
bammdata. Rates can vary along time, thus colors evolved along individual branches.
This function is a wrapper of run_deepSTRAPP_for_focal_time() used to plot mapped phylogenies for
a unique given focal_time.
Returns one plot per focal time in $time_steps.
If a PDF file path is provided in PDF_file_path, the plots will be saved directly in a PDF file,
with one page per focal time in $time_steps.
Usage
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs,
color_scale = NULL,
colors_per_levels = NULL,
add_ACE_pies = TRUE,
cex_pies = 0.5,
rate_type = "net_diversification",
keep_initial_colorbreaks = FALSE,
add_regime_shifts = TRUE,
configuration_type = "MAP",
sample_index = 1,
adjust_size_to_prob = TRUE,
regimes_fill = "grey",
regimes_size = 1,
regimes_pch = 21,
regimes_border_col = "black",
regimes_border_width = 1,
...,
display_plot = TRUE,
PDF_file_path = NULL
)
Arguments
deepSTRAPP_outputs |
List of elements generated with |
color_scale |
Vector of character string. List of colors to use to build the color scale with |
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 |
add_ACE_pies |
Logical. Whether to add pies of posterior probabilities of states/ranges at internal nodes on the mapped phylogeny. Default = |
cex_pies |
Numerical. To adjust the size of the ACE pies. Default = |
rate_type |
A character string specifying the type of diversification rates to plot. Must be one of 'speciation', 'extinction' or 'net_diversification' (default). |
keep_initial_colorbreaks |
Logical. Whether to keep the same color breaks as used for the most recent focal time. Typically, the current time (t = 0). Default = |
add_regime_shifts |
Logical. Whether to add the location of regime shifts on the phylogeny (Step 2). Default is |
configuration_type |
A character string specifying how to select the location of regime shifts across posterior samples.
|
sample_index |
Integer. Index of the posterior samples to use to plot the location of regime shifts.
Used only if |
adjust_size_to_prob |
Logical. Whether to scale the size of the symbols showing the location of regime shifts according to
the marginal shift probability of the shift happening on each location/branch. This will only works if there is an |
regimes_fill |
Character string. Set the color of the background of the symbols showing the location of regime shifts.
Equivalent to the |
regimes_size |
Numerical. Set the size of the symbols showing the location of regime shifts.
Equivalent to the |
regimes_pch |
Integer. Set the shape of the symbols showing the location of regime shifts.
Equivalent to the |
regimes_border_col |
Character string. Set the color of the border of the symbols showing the location of regime shifts.
Equivalent to the |
regimes_border_width |
Numerical. Set the width of the border of the symbols showing the location of regime shifts.
Equivalent to the |
... |
Additional graphical arguments to pass down to |
display_plot |
Logical. Whether to display the plot generated in the R console. Default is |
PDF_file_path |
Character string. If provided, the plot will be saved in a PDF file following the path provided here. The path must end with ".pdf". |
Details
The main input deepSTRAPP_outputs is the typical output of run_deepSTRAPP_over_time().
It provides information on results of a STRAPP run performed over multiple time-steps, and can also encompass
updated phylogenies with mapped trait evolution and diversification rates and regimes shifts if appropriate arguments are set.
-
return_updated_trait_data_with_Mapmust be set toTRUEso that the trait data extracted for the given$time_stepsand the list of updated versions of mapped phylogenies (contMap/densityMaps) is returned among the outputs under$updated_trait_data_with_Map_over_time. The updatedcontMap/densityMapsconsist in cutting off branches and mappings that are younger than the successive$time_steps. -
return_updated_BAMM_objectmust be set toTRUEso that the list ofupdated_BAMM_objectwith phylogenies and mapped diversification rates cut-off at the successive$time_stepsare returned among the outputs under$updated_BAMM_objects_over_time.
$MAP_BAMM_object and $MSC_BAMM_object elements are required in the elements of $updated_BAMM_objects_over_time to plot regime shift locations
following the "MAP" or "MSC" configuration_type respectively.
A $MSP_tree element is required to scale the size of the symbols showing the location of regime shifts according marginal shift probabilities.
(If adjust_size_to_prob = TRUE).
Alternatively, the main input deepSTRAPP_outputs can be the output of run_deepSTRAPP_over_time(),
providing results of STRAPP tests over multiple time-steps. In this case, you must provide a focal_time to select the
unique time-step used for plotting.
-
return_updated_trait_data_with_Mapmust be set toTRUEso that the trait data extracted and the updated version of mapped phylogenies (contMap/densityMaps) are returned among the outputs under$updated_trait_data_with_Map_over_time. -
return_updated_BAMM_objectmust be set toTRUEso that theBAMM_objectswith phylogeny and mapped diversification rates cut-off at the specified time-steps are returned among the outputs under$updated_BAMM_objects_over_time.
For plotting a single time-step (i.e., $focal_time) at once, see plot_traits_vs_rates_on_phylogeny_for_focal_time().
Value
If display_plot = TRUE, the function displays the successive plots with two facets in the R console:
(Left) A time-calibrated phylogeny displaying the evolution of trait/biogeographic data.
(Right) A time-calibrated phylogeny displaying diversification rates and regime shifts. A plot per time-steps is generated and displayed successively in the console.
If PDF_file_path is provided, the plots will be exported in a unique PDF file with one page per time-step.
Author(s)
Maël Doré
See Also
plot_contMap() phytools::plot.densityMap() plot_densityMaps_overlay() plot_BAMM_rates()
Function in deepSTRAPP needed to produce the deepSTRAPP_outputs as input: run_deepSTRAPP_over_time()
Function in deepSTRAPP to a single time-step at once: plot_traits_vs_rates_on_phylogeny_for_focal_time()
Examples
if (deepSTRAPP::is_dev_version())
{
# ----- Example 1: Continuous trait ----- #
## Load data
# Load trait df
data(Ponerinae_trait_tip_data, package = "deepSTRAPP")
# Load phylogeny with old calibration
data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
# Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Prepare trait data
# Extract continuous trait data as a named vector
Ponerinae_cont_tip_data <- setNames(object = Ponerinae_trait_tip_data$fake_cont_tip_data,
nm = Ponerinae_trait_tip_data$Taxa)
# Select a color scheme from lowest to highest values
color_scale = c("darkgreen", "limegreen", "orange", "red")
# Get Ancestral Character Estimates based on a Brownian Motion model
# To obtain values at internal nodes
Ponerinae_ACE <- phytools::fastAnc(tree = Ponerinae_tree_old_calib, x = Ponerinae_cont_tip_data)
# (May take several minutes to run)
# Run a Stochastic Mapping based on a Brownian Motion model
# to interpolate values along branches and obtain a "contMap" object
Ponerinae_contMap <- phytools::contMap(Ponerinae_tree, x = Ponerinae_cont_tip_data,
res = 100, # Number of time steps
plot = FALSE)
# Plot contMap = stochastic mapping of continuous trait
plot_contMap(contMap = Ponerinae_contMap,
color_scale = color_scale)
## Set for time steps of 5 My. Will generate deepSTRAPP workflows for 0 to 40 Mya.
# nb_time_steps <- 5
time_step_duration <- 5
time_range <- c(0, 40)
## Run deepSTRAPP on net diversification rates
Ponerinae_deepSTRAPP_cont_old_calib_0_40 <- run_deepSTRAPP_over_time(
contMap = Ponerinae_contMap,
ace = Ponerinae_ACE,
tip_data = Ponerinae_cont_tip_data,
trait_data_type = "continuous",
BAMM_object = Ponerinae_BAMM_object_old_calib,
# nb_time_steps = nb_time_steps,
time_range = time_range,
time_step_duration = time_step_duration,
return_perm_data = TRUE,
extract_trait_data_melted_df = TRUE,
extract_diversification_data_melted_df = TRUE,
return_STRAPP_results = TRUE,
return_updated_trait_data_with_Map = TRUE,
return_updated_BAMM_object = TRUE,
verbose = TRUE,
verbose_extended = TRUE)
## Load directly trait data output
data(Ponerinae_deepSTRAPP_cont_old_calib_0_40, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Plot updated contMap vs. updated diversification rates
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
# To use the same color breaks as for t = 0 My in all BAMM plots
keep_initial_colorbreaks = TRUE,
color_scale = c("limegreen", "orange", "red"), # Adjust color scale on contMap
legend = TRUE, labels = TRUE, # Show legend and label on BAMM plot
cex = 0.7) # Adjust label size on contMap
# PDF_file_path = "Updated_maps_cont_old_calib_0_40My.pdf")
# ----- Example 2: Biogeographic data ----- #
## Load data
# Load phylogeny
data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
# Load trait df
data(Ponerinae_binary_range_table, package = "deepSTRAPP")
# Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Prepare range data for Old World vs. New World
# No overlap in ranges
table(Ponerinae_binary_range_table$Old_World, Ponerinae_binary_range_table$New_World)
Ponerinae_NO_data <- stats::setNames(object = Ponerinae_binary_range_table$Old_World,
nm = Ponerinae_binary_range_table$Taxa)
Ponerinae_NO_data <- as.character(Ponerinae_NO_data)
Ponerinae_NO_data[Ponerinae_NO_data == "TRUE"] <- "O" # O = Old World
Ponerinae_NO_data[Ponerinae_NO_data == "FALSE"] <- "N" # N = New World
names(Ponerinae_NO_data) <- Ponerinae_binary_range_table$Taxa
table(Ponerinae_NO_data)
colors_per_levels <- c("mediumpurple2", "peachpuff2")
names(colors_per_levels) <- c("N", "O")
# (May take several minutes to run)
## Run evolutionary models
Ponerinae_biogeo_data <- prepare_trait_data(
tip_data = Ponerinae_NO_data,
trait_data_type = "biogeographic",
phylo = Ponerinae_tree_old_calib,
evolutionary_models = "DEC+J", # Default = "DEC" for biogeographic
BioGeoBEARS_directory_path = tempdir(), # Ex: "./BioGeoBEARS_directory/"
keep_BioGeoBEARS_files = FALSE,
prefix_for_files = "Ponerinae_old_calib",
max_range_size = 2,
split_multi_area_ranges = TRUE, # Set to TRUE to use only unique areas "A" and "B"
nb_simulations = 100, # Reduce to save time (Default = '1000')
colors_per_levels = colors_per_levels,
return_model_selection_df = TRUE,
verbose = TRUE)
# Load directly output
data(Ponerinae_biogeo_data_old_calib, package = "deepSTRAPP")
## Set for time steps of 5 My. Will generate deepSTRAPP workflows from 0 to 40 Mya.
time_range <- c(0, 40)
time_step_duration <- 5
# (May take several minutes to run)
## Run deepSTRAPP on net diversification rates for time-steps = 0 to 40 Mya.
Ponerinae_deepSTRAPP_biogeo_old_calib_0_40 <- run_deepSTRAPP_over_time(
densityMaps = Ponerinae_biogeo_data_old_calib$densityMaps,
ace = Ponerinae_biogeo_data_old_calib$ace,
tip_data = Ponerinae_ON_tip_data,
trait_data_type = "biogeographic",
BAMM_object = Ponerinae_BAMM_object_old_calib,
time_range = time_range,
time_step_duration = time_step_duration,
seed = 1234, # Set seed for reproducibility
alpha = 0.10, # Select a generous level of significance for the sake of the example
rate_type = "net_diversification",
return_perm_data = TRUE,
extract_trait_data_melted_df = TRUE,
extract_diversification_data_melted_df = TRUE,
return_STRAPP_results = TRUE,
return_updated_trait_data_with_Map = TRUE,
return_updated_BAMM_object = TRUE,
verbose = TRUE,
verbose_extended = TRUE)
## Load directly output
data(Ponerinae_deepSTRAPP_biogeo_old_calib_0_40, package = "deepSTRAPP")
## This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.
## Explore output
str(Ponerinae_deepSTRAPP_biogeo_old_calib_0_40, max.level = 1)
## Plot updated contMap vs. updated diversification rates
plot_traits_vs_rates_on_phylogeny_over_time(
deepSTRAPP_outputs = Ponerinae_deepSTRAPP_biogeo_old_calib_0_40,
# Adjust colors on densityMaps
colors_per_levels = c("N" = "dodgerblue2", "O" = "orange"),
legend = TRUE, labels = TRUE, # Show legend and label on BAMM plot
cex_pies = 0.2, # Adjust size of ACE pies on densityMaps
cex = 0.7) # Adjust label size on contMap
# PDF_file_path = "Updated_maps_biogeo_old_calib_0_40My.pdf")
}
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