Package: SEEPS 0.0.2

Michael Kupperman

SEEPS: An Agent-Based Simulator for Infectious Disease Phylodynamics

A modular, modern simulation suite and toolkit for simulating transmission networks, phylogenies, and evolutionary pairwise distance matrices under different models and assumptions for viral/sequence evolution. While intially developed for HIV, SEEPS offers modular utilities for custom workflows for extension beyond HIV.

Authors:Michael Kupperman [aut, cre], Ruian Ke [aut], Erik Lundgren [aut]

SEEPS_0.0.2.tar.gz
SEEPS_0.0.2.zip(r-4.5)SEEPS_0.0.2.zip(r-4.4)SEEPS_0.0.2.zip(r-4.3)
SEEPS_0.0.2.tgz(r-4.4-any)SEEPS_0.0.2.tgz(r-4.3-any)
SEEPS_0.0.2.tar.gz(r-4.5-noble)SEEPS_0.0.2.tar.gz(r-4.4-noble)
SEEPS_0.0.2.tgz(r-4.4-emscripten)SEEPS_0.0.2.tgz(r-4.3-emscripten)
SEEPS.pdf |SEEPS.html✨
SEEPS/json (API)

# Install 'SEEPS' in R:
install.packages('SEEPS', repos = c('https://molevolepid.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/molevolepid/seeps/issues

On CRAN:

biological-sequencesepidemiologyevolutionhivsimulation-framework

2.18 score 1 stars 48 exports 15 dependencies

Last updated 2 months agofrom:6473bd5f01. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winWARNINGOct 25 2024
R-4.5-linuxWARNINGOct 25 2024
R-4.4-winWARNINGOct 25 2024
R-4.4-macWARNINGOct 25 2024
R-4.3-winWARNINGOct 25 2024
R-4.3-macWARNINGOct 25 2024

Exports:add_root_to_newickbiphasic_HIV_ratebuild_distance_matrix_from_dfclean_upcontact_traced_uniform_idscontact_traced_uniform_restarts_idscontact_tracing_enginefasta_string_to_dataframegen_const_phasegen_exp_phasegen_transmission_history_balanced_treegen_transmission_history_exponential_constantgen_transmission_history_exponential_constant_classicgeneology_to_distance_matrixgeneology_to_distance_matrix_classicgeneology_to_phylogeny_bpbgenerate_rate_modelgenerate_sequencesget_biphasic_HIV_rateget_biphasic_HIV_rate_functionget_Kphasic_hiv_rate_functionget_p17_rate_modelget_V3_rate_modelinitializekeep_sampleslookup_sequence_by_namenever_terminate_early_factoryphylogeny_to_newickrandom_fixed_size_idsrandom_prop_idsreduce_large_matrixreduce_transmission_historyreduce_transmission_history_bpbreduce_transmission_history_bpb2reduce_transmission_history_mtremove_samplesshow_available_regionsshow_available_sequencessimulate_all_paradigms_HIV_V3simulate_classic_HIVsimulate_modern_HIVsimulate_sequences_HIV_V3stepstochastify_transmission_historysufficient_data_data_factoryuniform_discovery_factoryvalidate_statewrap_parameters

Dependencies:apeclidigestgluelatticelifecyclemagrittrnlmephyclustRcpprlangrngtoolsstringistringrvctrs