Palaoro_2022_data_and_code.zip
biology_root_D_test_dated
BEAST_MCC_dated_tree.nex
21.3 kB
DD_info_dated_females.rds
297 Bytes
DD_info_dated_males.rds
363 Bytes
Dtest_function_informed_root.R
16.9 kB
Prepare_dated_tree.R
1.7 kB
Read_Dtest_results.R
4.4 kB
informed.dated.Q.mcmc.care.females.rds
18.4 kB
informed.dated.Q.mcmc.care.males.rds
18.6 kB
informed.dated.Q.mcmc.precursor.females.rds
32.3 kB
informed.dated.Q.mcmc.precursor.males.rds
76.6 kB
informed.dated.simmap.mcmc.care.females.rds
11.2 MB
informed.dated.simmap.mcmc.care.males.rds
11.5 MB
informed.dated.simmap.mcmc.precursor.females.rds
11.5 MB
informed.dated.simmap.mcmc.precursor.males.rds
18.9 MB
make_DD_test_females_informed_root.R
3.2 kB
make_DD_test_males_informed_root.R
3.3 kB
miss_rps_male.rds
345 Bytes
missing_reps_make_DD_test_males_informed_root.R
3.7 kB
run_pipeline.R
431 Bytes
run_simmap_mcmc_care_females.R
3.0 kB
run_simmap_mcmc_care_males.R
3.1 kB
run_simmap_mcmc_precursor_females.R
3.5 kB
run_simmap_mcmc_precursor_males.R
4.3 kB
biology_root_D_test_unit_branch_length
DD_info_unit_females.rds
281 Bytes
DD_info_unit_males.rds
370 Bytes
Dtest_function_informed_root.R
16.8 kB
Read_Dtest_results.R
4.4 kB
Unit_tree.pdf
14.3 kB
informed.unit.Q.mcmc.care.females.rds
18.7 kB
informed.unit.Q.mcmc.care.males.rds
19.2 kB
informed.unit.Q.mcmc.precursor.females.rds
52.6 kB
informed.unit.Q.mcmc.precursor.males.rds
97.8 kB
informed.unit.simmap.mcmc.care.females.rds
8.2 MB
informed.unit.simmap.mcmc.care.males.rds
8.3 MB
informed.unit.simmap.mcmc.precursor.females.rds
8.5 MB
informed.unit.simmap.mcmc.precursor.males.rds
9.4 MB
make_DD_test_females_informed_root.R
3.3 kB
make_DD_test_males_informed_root.R
3.3 kB
prepare_tree.R
509 Bytes
run_pipeline.R
327 Bytes
run_simmap_mcmc_care_females.R
3.1 kB
run_simmap_mcmc_care_males.R
3.0 kB
run_simmap_mcmc_precursor_females.R
3.3 kB
run_simmap_mcmc_precursor_males.R
4.2 kB
tree_unit_solved.tre
7.4 kB
compute_marginal_asr_prec
female_prec_asr.R
2.5 kB
male_prec_asr.R
2.8 kB
data
BEAST_calibration_results
BEAST_calibration_solved.xml
181.0 kB
BEAST_calibration_solved.xml.state
17.2 kB
empty_matrix.fasta
36.2 kB
empty_matrix.log
31.2 MB
empty_matrix.trees
615.4 MB
start_calib_tree_solved.tre
12.7 kB
empty_matrix_MCC.tree
248.1 kB
get_calibrated_starting_tree
.~lock.calibration_table_complete.csv#
102 Bytes
Precursors_Database_10-05-22_data.csv
8.9 kB
calibration_info_BEAST.txt
98.7 kB
calibration_table_complete.csv
2.7 kB
empty_matrix.fasta
36.2 kB
generate_BEAST_calibration_block.R
4.2 kB
generate_empty_data_matrix.R
620 Bytes
get_chronos_calibration.R
2.9 kB
phylo_chronos_ages.pdf
15.6 kB
phylo_chronos_ages_solved.pdf
16.9 kB
precursors2.trees.nex
9.8 kB
ref_calibration_priors_info_BEAST.txt
1.0 kB
start_calib_tree.tre
11.8 kB
start_calib_tree_solved.tre
12.7 kB
precursors2.trees.nex
9.8 kB
free_root_D_test_dated
BEAST_MCC_dated_tree.nex
21.3 kB
DD_info_dated_females.rds
307 Bytes
DD_info_dated_males.rds
346 Bytes
Dtest_function_informed_root.R
19.6 kB
Prepare_dated_tree.R
1.7 kB
Read_Dtest_results.R
4.4 kB
informed.dated.Q.mcmc.care.females.rds
18.5 kB
informed.dated.Q.mcmc.care.males.rds
18.3 kB
informed.dated.Q.mcmc.precursor.females.rds
31.9 kB
informed.dated.Q.mcmc.precursor.males.rds
63.9 kB
informed.dated.simmap.mcmc.care.females.rds
11.4 MB
informed.dated.simmap.mcmc.care.males.rds
11.6 MB
informed.dated.simmap.mcmc.precursor.females.rds
11.5 MB
informed.dated.simmap.mcmc.precursor.males.rds
14.9 MB
make_DD_test_females_informed_root.R
3.4 kB
make_DD_test_males_informed_root.R
3.5 kB
missing_reps_make_DD_test_males_informed_root.R
3.7 kB
run_pipeline.R
431 Bytes
run_simmap_mcmc_care_females.R
3.2 kB
run_simmap_mcmc_care_males.R
3.3 kB
run_simmap_mcmc_precursor_females.R
3.7 kB
run_simmap_mcmc_precursor_males.R
4.5 kB
free_root_D_test_unit_branch_length
DD_info_unit_females.rds
290 Bytes
DD_info_unit_males.rds
365 Bytes
Dtest_function_informed_root.R
19.6 kB
Read_Dtest_results.R
4.4 kB
informed.unit.Q.mcmc.care.females.rds
18.7 kB
informed.unit.Q.mcmc.care.males.rds
19.3 kB
informed.unit.Q.mcmc.precursor.females.rds
51.4 kB
informed.unit.Q.mcmc.precursor.males.rds
96.7 kB
informed.unit.simmap.mcmc.care.females.rds
8.2 MB
informed.unit.simmap.mcmc.care.males.rds
8.3 MB
informed.unit.simmap.mcmc.precursor.females.rds
8.5 MB
informed.unit.simmap.mcmc.precursor.males.rds
9.5 MB
make_DD_test_females_informed_root.R
3.4 kB
make_DD_test_males_informed_root.R
3.5 kB
prepare_tree.R
509 Bytes
run_pipeline.R
327 Bytes
run_simmap_mcmc_care_females.R
3.3 kB
run_simmap_mcmc_care_males.R
3.1 kB
run_simmap_mcmc_precursor_females.R
3.5 kB
run_simmap_mcmc_precursor_males.R
4.4 kB
tree_unit_solved.tre
7.4 kB