Package: MGDrivE2 1.0.1

Sean L. Wu

MGDrivE2: Mosquito Gene Drive Explorer 2

A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.

Authors:Sean L. Wu [aut, cre], Jared B. Bennett [aut], Héctor Manuel Sánchez Castellanos [ctb], Tomás M. León [ctb], Andrew J. Dolgert [ctb], John M. Marshall [aut]

MGDrivE2_1.0.1.tar.gz
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MGDrivE2_1.0.1.tgz(r-4.4-any)MGDrivE2_1.0.1.tgz(r-4.3-any)
MGDrivE2_1.0.1.tar.gz(r-4.5-noble)MGDrivE2_1.0.1.tar.gz(r-4.4-noble)
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MGDrivE2.pdf |MGDrivE2.html✨
MGDrivE2/json (API)
NEWS

# Install 'MGDrivE2' in R:
install.packages('MGDrivE2', repos = c('https://marshalllab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marshalllab/mgdrive/issues

Datasets:
  • mu_ts - Mosquito Death Rates, Comoros Islands

On CRAN:

6.16 score 4 stars 30 scripts 158 downloads 1 mentions 36 exports 3 dependencies

Last updated 4 years agofrom:bcd714a107. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxNOTENov 05 2024
R-4.4-winNOTENov 05 2024
R-4.4-macNOTENov 05 2024
R-4.3-winOKNov 05 2024
R-4.3-macOKNov 05 2024

Exports:calc_move_rateequilibrium_lifeycleequilibrium_SEI_SEIRequilibrium_SEI_SISmovement_prob2ratesim_trajectory_CSVsim_trajectory_Rsolve_muAquasplit_aggregate_CSVspn_hazardsspn_P_epiSEIR_networkspn_P_epiSEIR_nodespn_P_epiSIS_networkspn_P_epiSIS_nodespn_P_lifecycle_networkspn_P_lifecycle_nodespn_Sspn_T_epiSEIR_networkspn_T_epiSEIR_nodespn_T_epiSIS_networkspn_T_epiSIS_nodespn_T_lifecycle_networkspn_T_lifecycle_nodesummarize_eggs_genosummarize_eggs_stagesummarize_femalessummarize_females_episummarize_humans_epiSEIRsummarize_humans_epiSISsummarize_larvae_genosummarize_larvae_stagesummarize_malessummarize_pupae_genosummarize_pupae_stagesummarize_stats_CSVtrack_hinf

Dependencies:deSolvelatticeMatrix

MGDrivE2: Advanced Topics

Rendered fromadvanced_topics.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: Data Storage and Analysis

Rendered fromoutput-storage.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-17
Started: 2020-10-17

MGDrivE2: Metapopulation Network Epidemiological Dynamics

Rendered fromepi-network.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: One Node Epidemiological Dynamics

Rendered fromepi-node.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: Simulation of Time-inhomogeneous Stochastic Processes (Seasonality)

Rendered frominhomogeneous.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: Metapopulation Network Lifecycle Dynamics

Rendered fromlifecycle-network.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: One Node Lifecycle Dynamics

Rendered fromlifecycle-node.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

MGDrivE2: SEIR Epidemiological Dynamics

Rendered fromepi-SEIR.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2020-10-08
Started: 2020-10-06

Readme and manuals

Help Manual

Help pageTopics
Base Aquatic Function for Genotype Summarybase_aquatic_geno
Base Aquatic Function for Erlang-Stage Summarybase_aquatic_stage
Base Summary of Erlang Stages for Aquatic Life Stagesbase_erlang
Base Summary of Erlang Stages for Adult Femalesbase_erlang_F
Base Summary for Eggs, Larvae, Pupae, Susceptible Females, and Infectious Femalesbase_gen
Base Summary for Latent Femalesbase_gen_FE
Base Summary Functionbase_MQ
Base Summary for Males, Unmated Females, and Humansbase_MUH
Base Summary of Erlang Stages for Adult Femalesbase_sum_F
Base Function for Human Summarybase_summarize_humans
Calculate Outbound Movement Ratecalc_move_rate
Calculate Equilibrium for Lifecycle Model (Logistic or Lotka-Volterra)equilibrium_lifeycle
Calculate Equilibrium for Mosquito SEI - Human SEIR Modelequilibrium_SEI_SEIR
Calculate Equilibrium for Mosquito SEI - Human SIS Modelequilibrium_SEI_SIS
Rate Matrix (Q) for Adult Mosquito SEI Dynamicsmake_Q_SEI
Convert Stochastic Matrix to Rate Matrixmovement_prob2rate
Mosquito Death Rates, Comoros Islandsmu_ts
Simulate Trajectory From one SPN Modelsim_trajectory_base_CSV
Simulate Trajectory From one SPN Modelsim_trajectory_base_R
Simulate Trajectory From a SPN Modelsim_trajectory_CSV
Simulate Trajectory From a SPN Modelsim_trajectory_R
Solve for Constant Aquatic Mortalitysolve_muAqua
Split CSV output by Patch and Aggregate by Mate or Dwell-Stagesplit_aggregate_CSV
Make Hazards (Lambda) For a MGDrivE2: Node and Network Simulationsspn_hazards
Make Places (P) For a Network (SEI Mosquitoes - SEIR Humans)spn_P_epiSEIR_network
Make Places (P) For a Node (SEI Mosquitoes - SEIR Humans)spn_P_epiSEIR_node
Make Places (P) For a Network (SEI Mosquitoes - SIS Humans)spn_P_epiSIS_network
Make Places (P) For a Node (SEI Mosquitoes - SIS Humans)spn_P_epiSIS_node
Make Places (P) For a Network (Mosquitoes only)spn_P_lifecycle_network
Make Places (P) For a Node (Mosquitoes only)spn_P_lifecycle_node
Make Post Matrix For a Petri Netspn_Post
Make Pre Matrix For a Petri Netspn_Pre
Make stoichiometry Matrix For a Petri Netspn_S
Make Transitions (T) For a Network (SEI Mosquitoes - SEIR Humans)spn_T_epiSEIR_network
Make Transitions (T) For a Node (SEI Mosquitoes - SEIR Humans)spn_T_epiSEIR_node
Make Transitions (T) For a Network (SEI Mosquitoes - SIS Humans)spn_T_epiSIS_network
Make Transitions (T) For a Node (SEI Mosquitoes - SIS Humans)spn_T_epiSIS_node
Make Transitions (T) For a Network (Mosquitoes only)spn_T_lifecycle_network
Make Transitions (T) For a Node (Mosquitoes only)spn_T_lifecycle_node
Make Chemical Langevin (CLE) Sampler for a SPN modelstep_CLE
Make Gillespie's Direct Method (DM) Sampler for a SPN modelstep_DM
Make Mean-field Approximation (ODE) Numerical Integrator for a SPN Modelstep_ODE
Make Poisson Time-Step (PTS) Sampler for a SPN Modelstep_PTS
Summarize Eggs by Genotypesummarize_eggs_geno
Summarize Eggs by Erlang-Stagesummarize_eggs_stage
Summarize Adult Females (One Node or Metapopulation Network, Lifecycle Model)summarize_females
Summarize Adult Females (One Node or Metapopulation Network, SEI Mosquitoes)summarize_females_epi
Summarize Humans (One Node or Metapopulation Network, SEI Mosquitoes - SEIR Humans)summarize_humans_epiSEIR
Summarize Humans (One Node or Metapopulation Network, SEI Mosquitoes - SIS Humans)summarize_humans_epiSIS
Summarize Larvae by Genotypesummarize_larvae_geno
Summarize Larval by Erlang-Stagesummarize_larvae_stage
Summarize Adult Males (One Node or Metapopulation Network)summarize_males
Summarize Pupal by Genotypesummarize_pupae_geno
Summarize Pupal by Erlang-Stagesummarize_pupae_stage
Summary Statistics for MGDrivE2summarize_stats_CSV
Make tracking matrix for human infection eventstrack_hinf