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update: scripts.filemerge

scripts.md ## this file

LabTemplate.R ## Use this to structure other labs

Tutorials

ICI3D_RTutorial_0.R ICI3D_RTutorial_1.R ICI3D_RTutorial_2.R ICI3D_RTutorial_3.R ICI3D_RTutorial_4.R ICI3D_RTutorial_5_DataCleaning.R

Examples

ICI3D_Example_binomialDistribution.R ICI3D_Example_chainBinom.R ICI3D_Example_StochasticSpillover_functions.R ICI3D_Example_StochasticSpillover.R

Labs

ICI3D_Lab_EpiStudyDesign.R

  • ICI3D_Lab_EpiStudyDesign.answers.R

ICI3D_Lab_Heterogeneity.R ## Old heterogeneity (stochastic) ICI3D_Lab_Heterogeneous_Groups.R ## new deterministic

  • ICI3D_Heterogeneous_Groups.R ## a service file
  • git log -- labNow.R ## a presentation file from 2025, gone now

ICI3D_Lab_introLikelihood.R ICI3D_Lab_LikelihoodPlusRejectionP.R ICI3D_Lab_MCMC-Binomial.R ICI3D_Lab_MCMC-SI_HIV.R ICI3D_Lab_MLE_HIVmodel.R ICI3D_Lab_ODEmodels.R ICI3D_Lab_RCT.R ICI3D_Lab_SampDistrVariability.R

Live

First SIR implementation; this version introduced 2026, should look for predecessors

  • ICI3D_Live_Intro_Implementation.R

Participatory

This is a fairly random sample and randomly named. Other participatory coding is elsewhere, still working on this particCodingDynMod2016.R particCoding_Rabies2017.R participatoryCoding2016.R participatory_coding_2024.R participatoryCoding_HIVTB.R participatoryCoding_IRSmalaria2014.R participatoryCoding_MalariaITN_2017.R participatoryDesign2021.R ParticipatoryDynamicModel_TB.R participatoryDynamics2025.R

macpan (under development, maybe a bit out of date?)

mpLabCompartmental.R mpLabFitting.R mpNotesCompartmental.R

Unsorted

ICI3D_previous_VisualizingData.R ICI3D_spillover_introductions.R binomialDistribution.R boxcars.R DerivExponential.R dynamicalFeverModelScript.R dynamicalFeverScript.R hetero_play.R hetSIRfxnMASTER.R hivAndFertilityExtension.R hivAndFertility.R introBayes.R librariesNeeded.R LikelihoodExamples.R seir_cumInc.R seir.R seir.w.seasonal.R

Temporary (clear out?)

tempLCfuns.R tempLC.R

md

batch.md issue.md README.md

These are service files and can be deleted once we're happy with the naming change of 2026

names.txt migrate.txt