Package: MALECOT 0.1.1

Bob Verity

MALECOT: Joint estimation of COI and population structure for malaria genetic data

Carries out joint estimation of complexity of infection (COI) and population structure on malaria genetic data. Assumes a simple model in which individuals have genotypes sampled from one or more subpopulations, and the number of genotypes in an individual is equal to the COI, which is also unknown. All unknown parameters are inferred using MCMC.

Authors:Bob Verity [aut, cre]

MALECOT_0.1.1.tar.gz
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MALECOT_0.1.1.tgz(r-4.6-x86_64)MALECOT_0.1.1.tgz(r-4.6-arm64)MALECOT_0.1.1.tgz(r-4.5-x86_64)MALECOT_0.1.1.tgz(r-4.5-arm64)
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MALECOT_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MALECOT/json (API)

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

Bug tracker:https://github.com/bobverity/malecot/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

4.56 score 6 stars 10 scripts 35 exports 21 dependencies

Last updated from:713d220d14. Checks:11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE162
linux-devel-x86_64NOTE176
source / vignettesOK426
linux-release-arm64NOTE185
linux-release-x86_64NOTE175
macos-release-arm64NOTE161
macos-release-x86_64NOTE248
macos-oldrel-arm64NOTE135
macos-oldrel-x86_64NOTE232
windows-develNOTE169
windows-releaseNOTE165
windows-oldrelNOTE182
wasm-releaseOK139

Exports:active_setbind_data_biallelicbind_data_multialleliccheck_MALECOT_loadeddelete_setget_ESSget_group_orderis.malecot_projectmalecot_filemalecot_projectmore_coloursnew_setplot_acfplot_COIplot_COI_meanplot_couplingplot_densityplot_eplot_GTI_pathplot_logevidence_Kplot_logevidence_modelplot_loglikeplot_loglike_dignosticplot_pplot_posterior_Kplot_posterior_modelplot_prior_COIplot_prior_pplot_structureplot_traceprint_fullrecalculate_evidencerun_mcmcsim_datasim_data_safe

Dependencies:clicodacpp11farverggplot2gluegridExtragtableisobandlabelinglatticelifecycleR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

Power analysis - within model
bi-allelic data | Simulation details | Power to detect population structure | Error = 0 | Error = 0.05 | Error = 0.10
Rendered frompower-analysis-within-model.Rmdusingknitr::rmarkdown

Last update: 2019-02-26
Started: 2018-09-24

Frequently Asked Questions
Q. Example question | Tabbed test | page 1 | page 2
Rendered fromfaq.Rmdusingknitr::rmarkdown

Last update: 2018-11-16
Started: 2018-08-23

Ensuring good mixing
What is MCMC mixing? | Adaptive MCMC | Improving mixing through Metropolis coupling | References
Rendered fromensuring-good-mixing.Rmdusingknitr::rmarkdown

Last update: 2018-10-01
Started: 2018-09-25

Tutorial 4: Comparing models (estimating K)
Background on Bayesian model comparison | Running a thermodynamic MCMC | Checking thermodynamic MCMC behaviour | Plotting results | Comparing different parameter sets
Rendered fromcomparing-models.Rmdusingknitr::rmarkdown

Last update: 2018-09-29
Started: 2018-09-17

Bi-allelic data
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
Rendered fromtutorial-biallelic.Rmdusingknitr::rmarkdown

Last update: 2018-09-28
Started: 2018-09-14

More realistic models
More realistic priors on COI | More realistic priors on allele frequencies | Missing data and errors
Rendered fromcomplex-priors.Rmdusingknitr::rmarkdown

Last update: 2018-09-28
Started: 2018-09-16

Multi-allelic data
Loading and running multi-allelic data | Plotting results | Structure plots | Posterior COI plots | Posterior allele frequency plots | More realistic priors on allele frequencies
Rendered frommultiallelic-data.Rmdusingknitr::rmarkdown

Last update: 2018-09-28
Started: 2018-08-23

Installing MALECOT
Installing Rcpp | Installing and loading MALECOT
Rendered frominstallation.Rmdusingknitr::rmarkdown

Last update: 2018-09-26
Started: 2018-08-22

Tutorial 5: running in parallel
Running MALECOT in parallel
Rendered fromrunning-in-parallel.Rmdusingknitr::rmarkdown

Last update: 2018-09-25
Started: 2018-09-25

GTI mathematical details
Problem definition | Thermodynamic integration | Generalised thermodynamic integration | References
Rendered fromgti-mathematical-details.Rmdusingknitr::rmarkdown

Last update: 2018-09-25
Started: 2018-09-24

Power analysis - between models
Rendered frompower-analysis-between-models.Rmdusingknitr::rmarkdown

Last update: 2018-09-25
Started: 2018-09-25

Known Issues
Example issue title
Rendered fromknown-issues.Rmdusingknitr::rmarkdown

Last update: 2018-09-21
Started: 2018-08-23

Readme and manuals

Help Manual

Help pageTopics
Change the active set of a MALECOT projectactive_set
Bind bi-allelic data to projectbind_data_biallelic
Bind multi-allelic format data to projectbind_data_multiallelic
Check that MALECOT package has loaded successfullycheck_MALECOT_loaded
Delete parameter setdelete_set
Get ESSget_ESS
Match grouping against q-matrixget_group_order
Determine if object is of class malecot_projectis.malecot_project
MALECOT packageMALECOT-package MALECOT
Import filemalecot_file
Define empty malecot_project objectmalecot_project
Expand series of colours by interpolationmore_colours
Create new MALECOT parameter setnew_set
Produce MCMC autocorrelation plotplot_acf
Plot COI 95% credible intervalsplot_COI
Plot COI_mean 95% credible intervalsplot_COI_mean
Plot Metropolis-coupling acceptance ratesplot_coupling
Produce MCMC density plotplot_density
Plot error rate 95% credible intervalsplot_e
Plot GTI path of current active setplot_GTI_path
Plot log-evidence estimates over Kplot_logevidence_K
Plot log-evidence estimates over parameter setsplot_logevidence_model
Plot loglikelihood 95% credible intervalsplot_loglike
Produce diagnostic plots of log-likelihoodplot_loglike_dignostic
Plot allele frequency 95% credible intervalsplot_p
Plot posterior Kplot_posterior_K
Plot posterior modelplot_posterior_model
Plot prior on COIplot_prior_COI
Plot prior on allele frequenciesplot_prior_p
Posterior allocation plotplot_structure
Produce MCMC trace plotplot_trace
Ordinary print function for class malecot_projectprint_full
Custom print function for class malecot_projectprint.malecot_project
Recalculate evidence and posterior estimatesrecalculate_evidence
Run main MCMCrun_mcmc
Simulate genetic datasim_data
Simulate genetic data subject to constraintssim_data_safe
Print summary for class malecot_projectsummary.malecot_project