PyRate
PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
파일 탐색기
최종 버전 다운로드 (.zip)- Athyridida5_lz0.txt
- Athyridida5_lz1.txt
- Athyridida5_lz2.txt
- ADE-NN.py
- pretrainedADENN
- variables.data-00000-of-00001
- variables.index
- saved_model.pb
- ADE-NN2.py
- ADE-NN3.py
- README.md
- Feliformia.py
- Feliformia.tre
- Ferns_BDCskyline_mcmc.log
- Ferns_BDCskyline_rates.pdf
- Ferns_Independent_skyline_mcmc.log
- Ursidae.py
- Ursidae.tre
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc.pkl
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Amphicyonidae_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Borophagus_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Canidae_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_coefficient_of_rate_variation.csv
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.r
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Eurasia_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_ex_predictor_influence.csv
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_ex_rates.log
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_ex_shap_per_species.csv
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Less10kg_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_mcmc.log
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_Musteloidea_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_PDP.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_per_species_rates.log
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_RTT.pdf
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_sp_predictor_influence.csv
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_sp_rates.log
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_sp_shap_per_species.csv
- Carnivora_occs_1_G_BDS_BDNN_16_8TVc_sum.txt
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc.pkl
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_coefficient_of_rate_variation.csv
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.pdf
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.r
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_ex_predictor_influence.csv
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_ex_rates.log
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_ex_shap_per_species.csv
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_mcmc.log
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_PDP.pdf
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_per_species_rates.log
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_RTT.pdf
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_sp_predictor_influence.csv
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_sp_rates.log
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_sp_shap_per_species.csv
- Carnivora_occs_1_taxon_time_tables_G_BDS_BDNN_16_8TVc_sum.txt
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc.pkl
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_coefficient_of_rate_variation.csv
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.pdf
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_contribution_per_species_rates.r
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_ex_predictor_influence.csv
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_ex_rates.log
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_ex_shap_per_species.csv
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_mcmc.log
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_PDP.pdf
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_per_species_rates.log
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_RTT.pdf
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_sp_predictor_influence.csv
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_sp_rates.log
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_sp_shap_per_species.csv
- Carnivora_occs_1_time_windows_G_BDS_BDNN_16_8TVc_sum.txt
- 01.txt
- 02.txt
- 03.txt
- 04.txt
- 05.txt
- 06.txt
- 07.txt
- 08.txt
- 09.txt
- 10.txt
- 11.txt
- 12.txt
- 01.txt
- 02.txt
- 03.txt
- 04.txt
- 05.txt
- 06.txt
- 07.txt
- 08.txt
- 09.txt
- 10.txt
- 11.txt
- 12.txt
- Backscale_custom_tables.txt
- Paleotemperature_humans.txt
- Paleotemperature_nohumans.txt
- RTT_groups.csv
- Time_windows.txt
- Backscale.txt
- Carnivora_occs.py
- Paleotemperature.txt
- Stages.txt
- Traits.txt
- Canis_pbdb_data.csv
- Canis_pbdb_data.txt
- Canis_pbdb_data_PyRate.py
- Canis_pbdb_data_TaxonList.txt
- epochs_q.txt
- fossil_occs.txt
- mammals.txt
- occs.py
- README.md
- sealevel.txt
- temperature.csv
- temperature.txt
- temperature.csv
- Body_mass_1.txt
- Body_mass_2.txt
- Body_mass_3.txt
- Carnivora_1.txt
- Carnivora_2.txt
- Carnivora_3.txt
- CarnivoraFossils.txt
- CarnivoraFossilsSite.txt
- CarnivoraRecent.txt
- FamilyGenera.txt
- Example1_DES_in_rep1.txt
- Example1_DES_in_rep2.txt
- Example1_DES_in_rep3.txt
- Example2_out_rep1.txt
- Example2_out_rep2.txt
- Example2_out_rep3.txt
- Example_1_minimum_data.txt
- Example_1_recent_distributions.txt
- Example_2_coordinates.txt
- Example_2_recent_coordinates.txt
- Example_regions.cpg
- Example_regions.dbf
- Example_regions.prj
- Example_regions.qpj
- Example_regions.shp
- Example_regions.shx
- red.txt
- plants_cenozoic_DES.txt
- pyrate_DES_input_example_script.R
- pyrate_DES_utilities.R
- Carnivora_BDNN_backtransformation.png
- Carnivora_BDNN_family_speciation.png
- Carnivora_BDNN_humans.png
- Carnivora_BDNN_RTT.png
- Carnivora_BDNN_RTT_Borophagus.png
- Carnivora_BDNN_temp_extinction.png
- DES_bodymass_dispersal.png
- DES_observed_diversity.png
- DES_rate_shifts_through_time.png
- DES_temperature_extinction.png
- Ferns_MBD_short_run.png
- Lagged_model.png
- LandPlants_RTT.png
- RTT_plot_RJMCMC.png
- angiosperm_px
- arid_px
- boreal_px
- CO2_px
- cold_px
- gymnosperm_px
- magmatism_px
- mountain_px
- oxygen_px
- scatter_px
- sealevel_px
- selenium_px
- sporeplant_px
- temperate_px
- temperature_px
- tropical_px
- Ammonoidea.csv
- Ammonoidea.py
- Ammonoidea_bound_se.txt
- Carnivores_MCDD.txt
- epochs.txt
- epochs_q.txt
- Example_data_MTE.txt
- example_species_list.txt
- example_species_list_scores.txt
- Felids_twoTraits.py
- Ferns_SE.txt
- PhanerozoicTempSmooth.txt
- Rhinocerotidae_PyRate.py
- stages.txt
- temperature.txt
- Ursidae.txt
- Ursidae_bm.txt
- Ursidae_discrete.txt
- Ursidae_PyRate.py
- Ursidae_SE.txt
- Ursidae_TaxonList.txt
- ADE_slice.py
- bd_sampling.py
- fossil_sampler_from_tree_loop.py
- fossil_sampler_sim.py
- fossil_sampler_sim_multi_q_scale.py
- plot_BDNN.py
- plot_MTE_results.R
- PyRateContinuousShift_plotHR.py
- PyRateDES2.py
- PyRateMTET.py
- summarize_BDNN_results.py
- Rhinos_Grj_ex_rates.log
- Rhinos_Grj_mcmc.log
- Rhinos_Grj_sp_rates.log
- Rhinos_Grj_sum.txt
- epochs_q.txt
- Rhinos.py
- Rhinos_mcmcdiv.log
- mcmcDivE.py
- plot_mcmcDivE_results.R
- README.md
- _FastPyRateC.so
- _FastPyRateC.so
- FastPyRateC.cpp
- FastPyRateC.h
- FastPyRateC.i
- install.sh
- make.sh
- setup.py
- _FastPyRateC.so
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- _FastPyRateC.pyd
- README.md
- bdnn_lib.py
- birthdeath_simulator.py
- calculate_marginal_rates_shift_model.py
- check_species_names.py
- des_mcmc_lib.py
- des_model_lib.py
- fastPyRateC.zip
- lib_DD_likelihood.py
- lib_updates_priors.py
- lib_utilities.py
- phylo_bds_likelihood.py
- plot_PyRatePhylo.R
- plotDESmarginal_rates.R
- PPmodeltest.py
- PyRate_logo1024.png
- PyRate_logo1024lr.png
- rtt_plot_bds.py
- pyrate_tutorial_0.md
- pyrate_tutorial_1.md
- pyrate_tutorial_2.md
- pyrate_tutorial_3.md
- pyrate_tutorial_4.md
- pyrate_tutorial_5.md
- pyrate_tutorial_6.md
- pyrate_tutorial_bdnn.md
- README.md
- LICENSE
- plot_functions_BDC_model.R
- PyRate.py
- pyrate_utilities.r
- PyRateContinuous.py
- PyRateDES.py
- PyRateMBD.py
- PyRateMCDD.py
- PyRateMTE.py
- README.md
- requirements.txt
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/dsilvestro/PyRate
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd PyRate
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. Python
쉬움 추천사전 준비물
pip install -r requirements.txt
requirements.txt 등에 명시된 파이썬 라이브러리를 설치합니다.
python <실행할 파일명>.py # README에서 정확한 실행 파일명을 확인하세요
파이썬 스크립트(또는 모듈)를 실행합니다.
에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.
// repository documentation
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