ICI3D R tutorials

This repository contains tutorials for the MMED and DAIDD clinics.

Name		Name	Last commit message	Last commit date
Latest commit History 413 Commits
MMED_2026_PC4		MMED_2026_PC4
SimpleStochastic		SimpleStochastic
dynamicalFeverShiny		dynamicalFeverShiny
gillespie		gillespie
git_push		git_push
outputs		outputs
pipelines		pipelines
sampling_JD		sampling_JD
testing		testing
.Rapp.history		.Rapp.history
.gitignore		.gitignore
DerivExponential.R		DerivExponential.R
HetSIR_functions.Rdata		HetSIR_functions.Rdata
ICI3D_Example_StochasticSpillover.R		ICI3D_Example_StochasticSpillover.R
ICI3D_Example_StochasticSpillover_functions.R		ICI3D_Example_StochasticSpillover_functions.R
ICI3D_Example_binomialDistribution.R		ICI3D_Example_binomialDistribution.R
ICI3D_Example_chainBinom.R		ICI3D_Example_chainBinom.R
ICI3D_Heterogeneous_Groups.R		ICI3D_Heterogeneous_Groups.R
ICI3D_Lab_EpiStudyDesign.R		ICI3D_Lab_EpiStudyDesign.R
ICI3D_Lab_EpiStudyDesign.answers.R		ICI3D_Lab_EpiStudyDesign.answers.R
ICI3D_Lab_HealthEcosModelling.R		ICI3D_Lab_HealthEcosModelling.R
ICI3D_Lab_Heterogeneity.R		ICI3D_Lab_Heterogeneity.R
ICI3D_Lab_Heterogeneous_Groups.R		ICI3D_Lab_Heterogeneous_Groups.R
ICI3D_Lab_LikelihoodPlusRejectionP.R		ICI3D_Lab_LikelihoodPlusRejectionP.R
ICI3D_Lab_MCMC-Binomial.R		ICI3D_Lab_MCMC-Binomial.R
ICI3D_Lab_MCMC-SI_HIV.R		ICI3D_Lab_MCMC-SI_HIV.R
ICI3D_Lab_MLE_HIVmodel.R		ICI3D_Lab_MLE_HIVmodel.R
ICI3D_Lab_ODEmodels.R		ICI3D_Lab_ODEmodels.R
ICI3D_Lab_RCT.R		ICI3D_Lab_RCT.R
ICI3D_Lab_SampDistrVariability.R		ICI3D_Lab_SampDistrVariability.R
ICI3D_Lab_introLikelihood.R		ICI3D_Lab_introLikelihood.R
ICI3D_Lab_introLikelihood.extras.R		ICI3D_Lab_introLikelihood.extras.R
ICI3D_Live_Intro_Implementation.R		ICI3D_Live_Intro_Implementation.R
ICI3D_Participatory_Design_2026_pertussis.R		ICI3D_Participatory_Design_2026_pertussis.R
ICI3D_RTutorial_0.R		ICI3D_RTutorial_0.R
ICI3D_RTutorial_1.R		ICI3D_RTutorial_1.R
ICI3D_RTutorial_2.R		ICI3D_RTutorial_2.R
ICI3D_RTutorial_3.R		ICI3D_RTutorial_3.R
ICI3D_RTutorial_4.R		ICI3D_RTutorial_4.R
ICI3D_RTutorial_5_DataCleaning.R		ICI3D_RTutorial_5_DataCleaning.R
ICI3D_previous_VisualizingData.R		ICI3D_previous_VisualizingData.R
ICI3D_spillover_introductions.R		ICI3D_spillover_introductions.R
LabTemplate.R		LabTemplate.R
LikelihoodExamples.R		LikelihoodExamples.R
MCMC_SI_runs.Rdata		MCMC_SI_runs.Rdata
MMED_2026_PC1.R		MMED_2026_PC1.R
MMED_2026_PC2.R		MMED_2026_PC2.R
Makefile		Makefile
Mutxt.Rdata		Mutxt.Rdata
ParticipatoryDynamicModel_TB.R		ParticipatoryDynamicModel_TB.R
README.md		README.md
RTutorials.Rproj		RTutorials.Rproj
amv.pl		amv.pl
batch.md		batch.md
batch.pl		batch.pl
binomialDistribution.R		binomialDistribution.R
boxcars.R		boxcars.R
content.mk		content.mk
cotrimStudy.R		cotrimStudy.R
cotrimTest.R		cotrimTest.R
dynamicalFever.Rproj		dynamicalFever.Rproj
dynamicalFeverData.Rdata		dynamicalFeverData.Rdata
dynamicalFeverModelScript.R		dynamicalFeverModelScript.R
dynamicalFeverScript.R		dynamicalFeverScript.R
dynamicalFeverSlideset.pdf		dynamicalFeverSlideset.pdf
fluExperiment.R		fluExperiment.R
fluExperiment_again.R		fluExperiment_again.R
fluStudy.R		fluStudy.R
fluTest.R		fluTest.R
hetSIR.Rdata		hetSIR.Rdata
hetSIRfxnMASTER.R		hetSIRfxnMASTER.R
hetero_play.R		hetero_play.R
hivAndFertility.R		hivAndFertility.R
hivAndFertilityExtension.R		hivAndFertilityExtension.R
introBayes.R		introBayes.R
issue.md		issue.md
labNow.R		labNow.R
librariesNeeded.R		librariesNeeded.R
links.pl		links.pl
migrate.txt		migrate.txt
mpLabCompartmental.R		mpLabCompartmental.R
mpLabFitting.R		mpLabFitting.R
mpNotesCompartmental.R		mpNotesCompartmental.R
multistudy.R		multistudy.R
mv.pl		mv.pl
names.txt		names.txt
particCodingDynMod2016.R		particCodingDynMod2016.R
particCoding_Rabies2017.R		particCoding_Rabies2017.R
participatoryCoding2016.R		participatoryCoding2016.R
participatoryCoding_HIVTB.R		participatoryCoding_HIVTB.R
participatoryCoding_IRSmalaria2014.R		participatoryCoding_IRSmalaria2014.R
participatoryCoding_MalariaITN_2017.R		participatoryCoding_MalariaITN_2017.R
participatoryDesign2021.R		participatoryDesign2021.R
participatoryDynamics2025.R		participatoryDynamics2025.R
participatory_coding_2024.R		participatory_coding_2024.R
scripts.md		scripts.md
seir.R		seir.R
seir.w.seasonal.R		seir.w.seasonal.R
seir_cumInc.R		seir_cumInc.R
study.R		study.R

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