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]

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MALECOT.pdf |MALECOT.html✨
MALECOT/json (API)

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

Peer review:

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

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

On CRAN:

4.26 score 3 stars 10 scripts 35 exports 31 dependencies

Last updated 6 years agofrom:713d220d14. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

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:clicodacolorspacefansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

Bi-allelic data

Bob Verity

Rendered fromtutorial-biallelic.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Tutorial 4: Comparing models (estimating K)

Bob Verity

Rendered fromcomparing-models.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Ensuring good mixing

Bob Verity

Rendered fromensuring-good-mixing.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Frequently Asked Questions

Bob Verity

Rendered fromfaq.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

GTI mathematical details

Bob Verity

Rendered fromgti-mathematical-details.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Installing MALECOT

Bob Verity

Rendered frominstallation.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Known Issues

Bob Verity

Rendered fromknown-issues.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

More realistic models

Bob Verity

Rendered fromcomplex-priors.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Multi-allelic data

Bob Verity

Rendered frommultiallelic-data.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Power analysis - between models

Bob Verity

Rendered frompower-analysis-between-models.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Power analysis - within model

Bob Verity

Rendered frompower-analysis-within-model.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Tutorial 5: running in parallel

Bob Verity

Rendered fromrunning-in-parallel.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

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