R/runBSM_v1.R
In nmatzke/BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
Defines functions
runBSM
# Runs biogeographic stochastic mapping
# (non-stratified, or stratified, versions, read from the
# input res object)
#
# The 'stochastic_mapping_inputs_list' object comes from:
#
# Non-stratified:
#
#
# stochastic_mapping_inputs_list2 = get_inputs_for_stochastic_mapping_stratified(res=resDIVALIKEj)
# wait_before_save = number of iterations of a meaningless for-loop, to
# space-out the saving operations to avoid memory faults in R.app
#
runBSM <- function(res, stochastic_mapping_inputs_list, maxnum_maps_to_try=1, nummaps_goal=maxnum_maps_to_try, maxtries_per_branch=40000, save_after_every_try=TRUE, savedir=getwd(), seedval=as.numeric(Sys.time()), wait_before_save=0.1, master_nodenum_toPrint=0)
{
defaults='
maxnum_maps_to_try=1
nummaps_goal=maxnum_maps_to_try
maxtries_per_branch=40000
save_after_every_try=TRUE
savedir=getwd()
seedval=12345
res; stochastic_mapping_inputs_list=stochastic_mapping_inputs_list; maxnum_maps_to_try=100; nummaps_goal=1; maxtries_per_branch=40000; save_after_every_try=TRUE; savedir=getwd(); seedval=12345; wait_before_save=0.01; master_nodenum_toPrint=0
'
# Necessary default setting to avoid numbers instead of states
options(stringsAsFactors=FALSE)
# Starter
clado_events_tables = list()
ana_events_tables = list()
# 2016-05-05_bug fix
lnum = 0
# Reconcile # of maps to try with nummaps goal
if (nummaps_goal > maxnum_maps_to_try)
{
maxnum_maps_to_try = 2 * nummaps_goal
} # END if (nummaps_goal > maxnum_maps_to_try)
# Set time-stratification
stratified = FALSE
if ((is.numeric(res$inputs$timeperiods))) #&& (length(inputs$timeperiods) > 1))
{
stratified = TRUE
strat_TF = TRUE
} else {
stratified = FALSE
strat_TF = FALSE
}
# Loop through the number of attempts
m=1
for (m in 1:maxnum_maps_to_try)
{
# Initialize
stochastic_mapping_results = NA
clado_events_table = NA
ana_events_table = NA
# Skip loop once you get to nummaps_goal
# (the desired number of successes)
if (lnum >= nummaps_goal)
{
next()
}
startseed = seedval + m
#print(paste0("runBSM startseed = ", startseed))
# Run stratified or non-stratified stochastic mapping
if (strat_TF == FALSE)
{
cmdstr = paste0("stochastic_mapping_results = stochastic_map_given_inputs(stochastic_mapping_inputs=stochastic_mapping_inputs_list, piecenum=NULL, maxtries=", maxtries_per_branch, ", seedval=", startseed, ", include_null_range=res$inputs$include_null_range, master_nodenum_toPrint=master_nodenum_toPrint, allow_null_tips=res$inputs$allow_null_tips)")
} else {
# Stratified
#maxtries=40000; seedval=521; master_nodenum_toPrint=0
# stochastic_mapping_results = stochastic_mapping_on_stratified(res=res, stochastic_mapping_inputs_list=stochastic_mapping_inputs_list, maxtries=40000, seedval=12346, master_nodenum_toPrint=master_nodenum_toPrint)
# stochastic_mapping_inputs_list=stochastic_mapping_inputs_list; maxtries=40000; seedval=12346; master_nodenum_toPrint=9
cmdstr = paste0("stochastic_mapping_results = stochastic_mapping_on_stratified(res=res, stochastic_mapping_inputs_list=stochastic_mapping_inputs_list, maxtries=", maxtries_per_branch, ", seedval=", startseed, ", master_nodenum_toPrint=master_nodenum_toPrint)")
} # END if (strat_TF == FALSE)
#print("AA_stochastic_mapping_on_stratified")
#print(cmdstr)
# Run either of the options
#cat(" ", m, sep="")
#print("try_result:")
# maxtries=40000; seedval=12346; master_nodenum_toPrint=master_nodenum_toPrint
# stochastic_mapping_on_stratified
try_result = try(expr=eval(parse(text=cmdstr)))
#eval(parse(text=cmdstr))
#print(try_result)
#cat("\n")
#print(warnings())
#print(class(try_result))
#cat("\n")
#cat(",", sep="")
# 2016-05-05
# Now that stochastic_mapping_results is initialized to NA each loop, should
# have no weird blank results
#TF2 = ( (length(stochastic_mapping_results)==1) && (is.na(stochastic_mapping_results) == TRUE) )
success_TF = ( class(stochastic_mapping_results) == "data.frame" )
#if ( (class(try_result) != "try-error") && TF2==FALSE )
if ( (class(try_result) == "try-error") && (success_TF == FALSE) )
{
# FAILURE!
cat("\nFailure on stochastic mapping attempt #", m, "/", maxnum_maps_to_try, " tries. Holding at success #", lnum, "/", nummaps_goal, ".", sep="")
cat("\n")
print(try_result)
# END if (class(try_result) != "try-error")
} else {
# SUCCESS!
# Non-stratified:
if (strat_TF == FALSE)
{
##########################################
# For NON-stratified stochastic mapping
##########################################
clado_events_table = stochastic_mapping_results
#print(clado_events_table[20,])
# Error check, for no anagenetic events
TF1 = stochastic_mapping_results$anagenetic_events_txt_below_node == "none"
TF2 = is.na(stochastic_mapping_results$anagenetic_events_txt_below_node)
TF3 = stochastic_mapping_results$anagenetic_events_txt_below_node == "NA"
TF4 = stochastic_mapping_results$anagenetic_events_txt_below_node == ""
TFall = (TF1 + TF2 + TF3 + TF4)
TF = TFall == 0
if (sum(TF, na.rm=TRUE) > 0)
{
# Some anagenetic events, make table
#print("here1")
ana_events_table = events_txt_list_into_events_table(events_txt_list=clado_events_table$anagenetic_events_txt_below_node, trtable=clado_events_table, recalc_abs_ages=TRUE)
#print("here2")
} else {
# No anagenetic events
ana_events_table = NA
}
} else {
####################################daughter_nds
# For STRATIFIED stochastic mapping
####################################
#clado_colnames = c("node", "node.type", "edge.length", "time_bp", "stratum", "piecenum", "piececlass", "SUBnode", "SUBnode.type", "SUBedge.length", "clado_event_type", "clado_event_txt", "clado_dispersal_to", "sampled_states_AT_nodes", "sampled_states_AT_brbots", "left_desc_nodes", "right_desc_nodes", "samp_LEFT_dcorner", "samp_RIGHT_dcorner", "anagenetic_events_txt_below_node")
clado_colnames = c("node", "node.type", "parent_br", "edge.length", "ancestor", "daughter_nds", "time_bp", "fossils", "label", "stratum", "time_top", "time_bot", "reltimept", "piecenum", "piececlass", "SUBnode", "SUBnode.type", "SUBparent_br", "SUBedge.length", "SUBancestor", "SUBdaughter_nds" , "SUBtime_bp", "SUBfossils", "SUBlabel", "clado_event_type", "clado_event_txt", "clado_dispersal_to", "sampled_states_AT_nodes", "sampled_states_AT_brbots", "left_desc_nodes", "right_desc_nodes", "samp_LEFT_dcorner", "samp_RIGHT_dcorner", "anagenetic_events_txt_below_node")
#rowsTF = stochastic_mapping_results$master_table_cladogenetic_events$node.type != "tip"
clado_events_table = stochastic_mapping_results$master_table_cladogenetic_events[, clado_colnames]
ana_events_table = stochastic_mapping_results$table_w_anagenetic_events
} # END if (strat_TF == FALSE)
# Print update
lnum = lnum+1
cat("\nSuccess #", lnum, "/", nummaps_goal, " on stochastic mapping attempt #", m, "/", maxnum_maps_to_try, " tries.", sep="")
# Wait a second or two, every 100 successes
# -- attempting to avoid segmentation faults during
# rapid stochastic mapping
if (FALSE)
{
Sys.sleep(wait_before_save)
}
if (TRUE)
{
if (lnum/50 == round(lnum/50))
{
Sys.sleep(wait_before_save * 3)
} # END if (lnum/100 == round(lnum/100))
}
# Store results
clado_events_tables[[lnum]] = clado_events_table
# Error trap -- if no anagenetic events, put NA
# 2016-05-05 bug: is.na(ana_events_table) is flagging yes when whole
# row is NAs
#if (suppressWarnings((length(ana_events_table) > 1) && (is.na(ana_events_table)==TRUE)))
# if (check_for_ana_events_table(ana_events_table) == TRUE)
# {
# error_msg = "STOP ERROR in runBSM(): your anagenetic events table seems to have row(s) that have multiple NAs. This could be due to an out of date 'BioGeoBEARS_stochastic_mapping_v1.R' file, missing this bug fix: '# NJM 2016-05-05 bug fix: add 'as.numeric' rownums_in_trtable = as.numeric(tmptable_rows$nodenum_at_top_of_branch)'"
# cat("\n\n")
# cat(error_msg)
# cat("\n\n")
# stop(error_msg)
# }
#
if ( check_for_ana_events_table(ana_events_table) == TRUE )
{
ana_events_tables[[lnum]] = ana_events_table
} else {
cat("\nNOTE: 'ana_events_table' for this BSM was null, NA or length <1 or >1; this suggests no anagenetic events in this BSM. Replacing with 'NA'.")
ana_events_table = NA
ana_events_tables[[lnum]] = ana_events_table
}
if (save_after_every_try == TRUE)
{
# Sometimes it looks like saving happens too fast and R crashes
if (is.null(wait_before_save) == FALSE)
{
# Wait this long before saving
Sys.sleep(wait_before_save)
} # END if (is.null(wait_before_save) == FALSE)
# Archive every round
RES_clado_events_tables = clado_events_tables
RES_ana_events_tables = ana_events_tables
RES_clado_events_tables_fn = slashslash(paste0(savedir, "/", "RES_clado_events_tables_PARTIAL.Rdata"))
RES_ana_events_tables_fn = slashslash(paste0(savedir, "/", "RES_ana_events_tables_PARTIAL.Rdata"))
# Message about saving
cat("...saving to RES_clado_events_tables_PARTIAL.Rdata")
cmdstr = "save(RES_clado_events_tables, file=RES_clado_events_tables_fn)"
savetry = try(expr=cmdstr)
if (class(savetry) == "try-error")
{
cat("...save FAILED for 'RES_clado_events_tables_PARTIAL.Rdata' for some reason, sometimes rapid saves seem to crash on some systems.\n")
} else {
cat("...saved 'RES_clado_events_tables_PARTIAL.Rdata'\n")
}
#print(RES_ana_events_tables)
cmdstr = "save(RES_ana_events_tables, file=RES_ana_events_tables_fn)"
savetry = try(expr=eval(parse(text=cmdstr)))
if (class(savetry) == "try-error")
{
cat("...save FAILED for 'RES_ana_events_tables_PARTIAL.Rdata' for some reason, sometimes rapid saves seem to crash on some systems.\n")
} else {
cat("...saved 'RES_ana_events_tables_PARTIAL.Rdata'")
}
} # END if (save_after_every_try == TRUE)
} # END if ( (class(try_result) == "try-error") && (success_TF == FALSE) )
} # END for (m in 1:maxnum_maps_to_try)
# Archive at the end
RES_clado_events_tables = clado_events_tables
RES_ana_events_tables = ana_events_tables
RES_clado_events_tables_fn = slashslash(paste0(savedir, "/", "RES_clado_events_tables.Rdata"))
RES_ana_events_tables_fn = slashslash(paste0(savedir, "/", "RES_ana_events_tables.Rdata"))
# Print results
cat("\n\n\n=============================================\nBiogeographic Stochastic Mapping is finished.\n\n")
txt = paste0("Saving cladogenetic and anagenetic events tables. ")
cat(txt)
txt2 = paste0("The commands:\n\nload(file=", RES_clado_events_tables_fn, ")\n\nload(file=", RES_ana_events_tables_fn, ")\n\n...will load them to objects RES_clado_events_tables and RES_ana_events_tables.")
cat(txt2)
cat("\n\n")
save(RES_clado_events_tables, file=RES_clado_events_tables_fn)
save(RES_ana_events_tables, file=RES_ana_events_tables_fn)
cat("Now returning to console 'BSM_output', which contains:\n")
cat("BSM_output$RES_clado_events_tables")
cat("\n")
cat("BSM_output$RES_ana_events_tables")
cat("\n=============================================")
cat("\n")
cat("\n")
BSM_output = NULL
BSM_output$RES_clado_events_tables = RES_clado_events_tables
BSM_output$RES_ana_events_tables = RES_ana_events_tables
extract='
clado_events_tables = BSM_output$RES_clado_events_tables
ana_events_tables = BSM_output$RES_ana_events_tables
'
return(BSM_output)
} # END runBSM()
nmatzke/BioGeoBEARS documentation built on July 1, 2024, 12:45 p.m.
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Defines functions runBSM
# Runs biogeographic stochastic mapping
# (non-stratified, or stratified, versions, read from the
# input res object)
#
# The 'stochastic_mapping_inputs_list' object comes from:
#
# Non-stratified:
#
#
# stochastic_mapping_inputs_list2 = get_inputs_for_stochastic_mapping_stratified(res=resDIVALIKEj)
# wait_before_save = number of iterations of a meaningless for-loop, to
# space-out the saving operations to avoid memory faults in R.app
#
runBSM <- function(res, stochastic_mapping_inputs_list, maxnum_maps_to_try=1, nummaps_goal=maxnum_maps_to_try, maxtries_per_branch=40000, save_after_every_try=TRUE, savedir=getwd(), seedval=as.numeric(Sys.time()), wait_before_save=0.1, master_nodenum_toPrint=0)
{
defaults='
maxnum_maps_to_try=1
nummaps_goal=maxnum_maps_to_try
maxtries_per_branch=40000
save_after_every_try=TRUE
savedir=getwd()
seedval=12345
res; stochastic_mapping_inputs_list=stochastic_mapping_inputs_list; maxnum_maps_to_try=100; nummaps_goal=1; maxtries_per_branch=40000; save_after_every_try=TRUE; savedir=getwd(); seedval=12345; wait_before_save=0.01; master_nodenum_toPrint=0
'
# Necessary default setting to avoid numbers instead of states
options(stringsAsFactors=FALSE)
# Starter
clado_events_tables = list()
ana_events_tables = list()
# 2016-05-05_bug fix
lnum = 0
# Reconcile # of maps to try with nummaps goal
if (nummaps_goal > maxnum_maps_to_try)
{
maxnum_maps_to_try = 2 * nummaps_goal
} # END if (nummaps_goal > maxnum_maps_to_try)
# Set time-stratification
stratified = FALSE
if ((is.numeric(res$inputs$timeperiods))) #&& (length(inputs$timeperiods) > 1))
{
stratified = TRUE
strat_TF = TRUE
} else {
stratified = FALSE
strat_TF = FALSE
}
# Loop through the number of attempts
m=1
for (m in 1:maxnum_maps_to_try)
{
# Initialize
stochastic_mapping_results = NA
clado_events_table = NA
ana_events_table = NA
# Skip loop once you get to nummaps_goal
# (the desired number of successes)
if (lnum >= nummaps_goal)
{
next()
}
startseed = seedval + m
#print(paste0("runBSM startseed = ", startseed))
# Run stratified or non-stratified stochastic mapping
if (strat_TF == FALSE)
{
cmdstr = paste0("stochastic_mapping_results = stochastic_map_given_inputs(stochastic_mapping_inputs=stochastic_mapping_inputs_list, piecenum=NULL, maxtries=", maxtries_per_branch, ", seedval=", startseed, ", include_null_range=res$inputs$include_null_range, master_nodenum_toPrint=master_nodenum_toPrint, allow_null_tips=res$inputs$allow_null_tips)")
} else {
# Stratified
#maxtries=40000; seedval=521; master_nodenum_toPrint=0
# stochastic_mapping_results = stochastic_mapping_on_stratified(res=res, stochastic_mapping_inputs_list=stochastic_mapping_inputs_list, maxtries=40000, seedval=12346, master_nodenum_toPrint=master_nodenum_toPrint)
# stochastic_mapping_inputs_list=stochastic_mapping_inputs_list; maxtries=40000; seedval=12346; master_nodenum_toPrint=9
cmdstr = paste0("stochastic_mapping_results = stochastic_mapping_on_stratified(res=res, stochastic_mapping_inputs_list=stochastic_mapping_inputs_list, maxtries=", maxtries_per_branch, ", seedval=", startseed, ", master_nodenum_toPrint=master_nodenum_toPrint)")
} # END if (strat_TF == FALSE)
#print("AA_stochastic_mapping_on_stratified")
#print(cmdstr)
# Run either of the options
#cat(" ", m, sep="")
#print("try_result:")
# maxtries=40000; seedval=12346; master_nodenum_toPrint=master_nodenum_toPrint
# stochastic_mapping_on_stratified
try_result = try(expr=eval(parse(text=cmdstr)))
#eval(parse(text=cmdstr))
#print(try_result)
#cat("\n")
#print(warnings())
#print(class(try_result))
#cat("\n")
#cat(",", sep="")
# 2016-05-05
# Now that stochastic_mapping_results is initialized to NA each loop, should
# have no weird blank results
#TF2 = ( (length(stochastic_mapping_results)==1) && (is.na(stochastic_mapping_results) == TRUE) )
success_TF = ( class(stochastic_mapping_results) == "data.frame" )
#if ( (class(try_result) != "try-error") && TF2==FALSE )
if ( (class(try_result) == "try-error") && (success_TF == FALSE) )
{
# FAILURE!
cat("\nFailure on stochastic mapping attempt #", m, "/", maxnum_maps_to_try, " tries. Holding at success #", lnum, "/", nummaps_goal, ".", sep="")
cat("\n")
print(try_result)
# END if (class(try_result) != "try-error")
} else {
# SUCCESS!
# Non-stratified:
if (strat_TF == FALSE)
{
##########################################
# For NON-stratified stochastic mapping
##########################################
clado_events_table = stochastic_mapping_results
#print(clado_events_table[20,])
# Error check, for no anagenetic events
TF1 = stochastic_mapping_results$anagenetic_events_txt_below_node == "none"
TF2 = is.na(stochastic_mapping_results$anagenetic_events_txt_below_node)
TF3 = stochastic_mapping_results$anagenetic_events_txt_below_node == "NA"
TF4 = stochastic_mapping_results$anagenetic_events_txt_below_node == ""
TFall = (TF1 + TF2 + TF3 + TF4)
TF = TFall == 0
if (sum(TF, na.rm=TRUE) > 0)
{
# Some anagenetic events, make table
#print("here1")
ana_events_table = events_txt_list_into_events_table(events_txt_list=clado_events_table$anagenetic_events_txt_below_node, trtable=clado_events_table, recalc_abs_ages=TRUE)
#print("here2")
} else {
# No anagenetic events
ana_events_table = NA
}
} else {
####################################daughter_nds
# For STRATIFIED stochastic mapping
####################################
#clado_colnames = c("node", "node.type", "edge.length", "time_bp", "stratum", "piecenum", "piececlass", "SUBnode", "SUBnode.type", "SUBedge.length", "clado_event_type", "clado_event_txt", "clado_dispersal_to", "sampled_states_AT_nodes", "sampled_states_AT_brbots", "left_desc_nodes", "right_desc_nodes", "samp_LEFT_dcorner", "samp_RIGHT_dcorner", "anagenetic_events_txt_below_node")
clado_colnames = c("node", "node.type", "parent_br", "edge.length", "ancestor", "daughter_nds", "time_bp", "fossils", "label", "stratum", "time_top", "time_bot", "reltimept", "piecenum", "piececlass", "SUBnode", "SUBnode.type", "SUBparent_br", "SUBedge.length", "SUBancestor", "SUBdaughter_nds" , "SUBtime_bp", "SUBfossils", "SUBlabel", "clado_event_type", "clado_event_txt", "clado_dispersal_to", "sampled_states_AT_nodes", "sampled_states_AT_brbots", "left_desc_nodes", "right_desc_nodes", "samp_LEFT_dcorner", "samp_RIGHT_dcorner", "anagenetic_events_txt_below_node")
#rowsTF = stochastic_mapping_results$master_table_cladogenetic_events$node.type != "tip"
clado_events_table = stochastic_mapping_results$master_table_cladogenetic_events[, clado_colnames]
ana_events_table = stochastic_mapping_results$table_w_anagenetic_events
} # END if (strat_TF == FALSE)
# Print update
lnum = lnum+1
cat("\nSuccess #", lnum, "/", nummaps_goal, " on stochastic mapping attempt #", m, "/", maxnum_maps_to_try, " tries.", sep="")
# Wait a second or two, every 100 successes
# -- attempting to avoid segmentation faults during
# rapid stochastic mapping
if (FALSE)
{
Sys.sleep(wait_before_save)
}
if (TRUE)
{
if (lnum/50 == round(lnum/50))
{
Sys.sleep(wait_before_save * 3)
} # END if (lnum/100 == round(lnum/100))
}
# Store results
clado_events_tables[[lnum]] = clado_events_table
# Error trap -- if no anagenetic events, put NA
# 2016-05-05 bug: is.na(ana_events_table) is flagging yes when whole
# row is NAs
#if (suppressWarnings((length(ana_events_table) > 1) && (is.na(ana_events_table)==TRUE)))
# if (check_for_ana_events_table(ana_events_table) == TRUE)
# {
# error_msg = "STOP ERROR in runBSM(): your anagenetic events table seems to have row(s) that have multiple NAs. This could be due to an out of date 'BioGeoBEARS_stochastic_mapping_v1.R' file, missing this bug fix: '# NJM 2016-05-05 bug fix: add 'as.numeric' rownums_in_trtable = as.numeric(tmptable_rows$nodenum_at_top_of_branch)'"
# cat("\n\n")
# cat(error_msg)
# cat("\n\n")
# stop(error_msg)
# }
#
if ( check_for_ana_events_table(ana_events_table) == TRUE )
{
ana_events_tables[[lnum]] = ana_events_table
} else {
cat("\nNOTE: 'ana_events_table' for this BSM was null, NA or length <1 or >1; this suggests no anagenetic events in this BSM. Replacing with 'NA'.")
ana_events_table = NA
ana_events_tables[[lnum]] = ana_events_table
}
if (save_after_every_try == TRUE)
{
# Sometimes it looks like saving happens too fast and R crashes
if (is.null(wait_before_save) == FALSE)
{
# Wait this long before saving
Sys.sleep(wait_before_save)
} # END if (is.null(wait_before_save) == FALSE)
# Archive every round
RES_clado_events_tables = clado_events_tables
RES_ana_events_tables = ana_events_tables
RES_clado_events_tables_fn = slashslash(paste0(savedir, "/", "RES_clado_events_tables_PARTIAL.Rdata"))
RES_ana_events_tables_fn = slashslash(paste0(savedir, "/", "RES_ana_events_tables_PARTIAL.Rdata"))
# Message about saving
cat("...saving to RES_clado_events_tables_PARTIAL.Rdata")
cmdstr = "save(RES_clado_events_tables, file=RES_clado_events_tables_fn)"
savetry = try(expr=cmdstr)
if (class(savetry) == "try-error")
{
cat("...save FAILED for 'RES_clado_events_tables_PARTIAL.Rdata' for some reason, sometimes rapid saves seem to crash on some systems.\n")
} else {
cat("...saved 'RES_clado_events_tables_PARTIAL.Rdata'\n")
}
#print(RES_ana_events_tables)
cmdstr = "save(RES_ana_events_tables, file=RES_ana_events_tables_fn)"
savetry = try(expr=eval(parse(text=cmdstr)))
if (class(savetry) == "try-error")
{
cat("...save FAILED for 'RES_ana_events_tables_PARTIAL.Rdata' for some reason, sometimes rapid saves seem to crash on some systems.\n")
} else {
cat("...saved 'RES_ana_events_tables_PARTIAL.Rdata'")
}
} # END if (save_after_every_try == TRUE)
} # END if ( (class(try_result) == "try-error") && (success_TF == FALSE) )
} # END for (m in 1:maxnum_maps_to_try)
# Archive at the end
RES_clado_events_tables = clado_events_tables
RES_ana_events_tables = ana_events_tables
RES_clado_events_tables_fn = slashslash(paste0(savedir, "/", "RES_clado_events_tables.Rdata"))
RES_ana_events_tables_fn = slashslash(paste0(savedir, "/", "RES_ana_events_tables.Rdata"))
# Print results
cat("\n\n\n=============================================\nBiogeographic Stochastic Mapping is finished.\n\n")
txt = paste0("Saving cladogenetic and anagenetic events tables. ")
cat(txt)
txt2 = paste0("The commands:\n\nload(file=", RES_clado_events_tables_fn, ")\n\nload(file=", RES_ana_events_tables_fn, ")\n\n...will load them to objects RES_clado_events_tables and RES_ana_events_tables.")
cat(txt2)
cat("\n\n")
save(RES_clado_events_tables, file=RES_clado_events_tables_fn)
save(RES_ana_events_tables, file=RES_ana_events_tables_fn)
cat("Now returning to console 'BSM_output', which contains:\n")
cat("BSM_output$RES_clado_events_tables")
cat("\n")
cat("BSM_output$RES_ana_events_tables")
cat("\n=============================================")
cat("\n")
cat("\n")
BSM_output = NULL
BSM_output$RES_clado_events_tables = RES_clado_events_tables
BSM_output$RES_ana_events_tables = RES_ana_events_tables
extract='
clado_events_tables = BSM_output$RES_clado_events_tables
ana_events_tables = BSM_output$RES_ana_events_tables
'
return(BSM_output)
} # END runBSM()
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