Daily trends | Individual-level output

Installing via the plasmogenepi R-universe | Installing Manually | Installing Rcpp | Installing and loading PlasmoSim

Defining the migration matrix and simulating with migration | Genetic distance vs. geographic distance

Overview | Installation | Quick start | Understanding results | Downstream analyses | Posterior allele frequencies | Individual COI with uncertainty | Running Your Own Analysis | Parameter Tuning | Convergence diagnostics | Visualizing results | Multiplicity of Infection (MOI) Distribution | Strain Frequency Analysis | Strain Pattern Heatmap | Host-Strain Allocation Heatmap | Summary Statistics | Next steps | References

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Read and reformat data, estimate COI and population allele frequencies | Estimate relatedness | Visualize the results | Further analysis of related samples

Basic workflow | 1) Plot data | 2) Compute recurrence state posterior probabilities | 3) Plot per-recurrence probabilities | Exploration of relationship graphs

1. Consult sample size tables | 2. Consult power curves | 3. Refine sample sizes | 4. Account for dropout | 5. Iterate and improve | 6. Detecting rare variants (bonus section) | 7. Controling the margin of error (bonus section)

1. The Bayesian hierarchical model

5. A Bayesian approach

Mostly used | You may also try | Example | Reporting Bugs | Citing DEploid

Running MOIRE on Namibia data

Purpose | A Primer on Malaria Genetics | A Primer on the Coalescent | Model Formulation | Understanding the Simulator | Getting the ARG | bv_tree Class | Tree Conversions | Conclusion

Extending the Model for Space | Forwards-in-time Description | A Note on the Migration Matrix | Island Case | Conclusion

Installing and Loading polySimIBD | Dependencies

Overview | Installation | Demonstration | Base Model | Saving different model summaries | Interventions | Space | Seasonality and Specific Locations | IBD Simulations | Summary

Simulation and MCMC | Estimating COI | Estimating effective COI | What is effective COI? | Estimating Relatedness | Estimating allele frequencies | Estimating expected heterozygosity

Installing via the plasmogenepi R-universe | Installing Rcpp | Installing and loading DRpower

Principal Component Analysis (PCA) | Principal Coordinates Analysis (PCoA) from genetic distances

Estimating relatedness between samples | Comparing different distance metrics

Installing Rcpp | Installing and loading MIPanalyzer

Reading in data and understanding the mipanalyzer_biallelic format | Filtering data based on coverage | Filtering based on other criteria

8. Estimating power via simulation | 8.1. Sample size calculation | 8.2. How to choose final sample sizes

1. Available data on pfhrp2/3 deletions | 2. Estimating the ICC

1. Estimate prevalence | 2. Compare prevalence against a threshold | 3. Estimate the ICC

What are pfhrp2/3 deletions? | What are we doing about it? | What does the 2020 Master Protocol recommend? | How does the DRpower method fit in? | Defining our terms

2. Why is this a tricky problem? | 2.1 Dealing with overdispersion

1. Is our Bayesian method biased?

6. The 2020 WHO Master Protocol | 6.1. The logic behind the sample size calculation | 6.2. Working through the updated protocol numbers | 6.3. Issues with the approach | References

3. What is the design effect? | 3.1 The effective sample size | 3.2 Relating $D_{eff}$ to the ICC

7. Power and sample size under the z-test

4. What's the problem?

Introduction | Default parameters | Setting our PLMAF | Overall performance | Simulation parameters | Coverage | Loci | Alpha | Overdispersion | Relatedness | Epsilon | Estimation parameters | COI | Sequencing error | Bins | Bin size

Introduction | Default parameters | Setting our PLMAF | Overall performance | Simulation parameters | Coverage | Loci | Alpha | Overdispersion | Relatedness | Epsilon | Estimation parameters | COI | Sequencing error | Bins | Bin size

Data structure | Estimate the COI | Data visualization

Introduction | Format required by most functions in Hierfstat | Importing data files | Importing FSTAT data files | Importing from adegenet: genind objects | Allelic dosages | Importing from adegenet: genlight objects | importing VCF files | Data generated by external genetic data simulators | Importing from Quantinemo | Importing from ms

Introduction | Loading data | Descriptive statistics | Population statistics | Hierarchical analyses | Testing | Genetic distances | Population Principal coordinate analysis | Population specific $F_{ST}$s | Individual statistics | Individual PCA | kinships, GRM and individual inbreeding coefficients | Simulating genetic data | Exporting to other programs | Miscellaneous | Sex-biased dispersal

Example simulation

Overview | 1. Description of aims of package | 2. Testing Rcpp package

Introduction | Glossary | Marker summaries | Simulated data | Footnote: Mendelian sampling | Footnote: switch rate parameter | References

Overview | Demonstration | Base Model | Summary

From Github | Dependencies

bi-allelic data | Simulation details | Power to detect population structure | Error = 0 | Error = 0.05 | Error = 0.10

Q. Example question | Tabbed test | page 1 | page 2

What is MCMC mixing? | Adaptive MCMC | Improving mixing through Metropolis coupling | References

Background on Bayesian model comparison | Running a thermodynamic MCMC | Checking thermodynamic MCMC behaviour | Plotting results | Comparing different parameter sets

Simulate some data | Create a project and read in data | Define parameters and run basic MCMC | Checking MCMC behaviour | Plot results | Structure plots | Posterior COI plots | Posterior allele frequency plots

More realistic priors on COI | More realistic priors on allele frequencies | Missing data and errors

Loading and running multi-allelic data | Plotting results | Structure plots | Posterior COI plots | Posterior allele frequency plots | More realistic priors on allele frequencies

Installing Rcpp | Installing and loading MALECOT

Running MALECOT in parallel

Problem definition | Thermodynamic integration | Generalised thermodynamic integration | References

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