Package: admix 2.3.1

Xavier Milhaud

admix: Package Admix for Admixture (aka Contamination) Models

Implements techniques to estimate the unknown quantities related to two-component admixture models, where the two components can belong to any distribution (note that in the case of multinomial mixtures, the two components must belong to the same family). Estimation methods depend on the assumptions made on the unknown component density; see Bordes and Vandekerkhove (2010) <doi:10.3103/S1066530710010023>, Patra and Sen (2016) <doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both the mixture weight and the unknown component density in a wide variety of frameworks. On top of that, hypothesis tests can be performed in one and two-sample contexts to test the unknown component density (see Milhaud, Pommeret, Salhi and Vandekerkhove (2022) <doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi, Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of unknown mixture components is also feasible in a K-sample setting (see Milhaud, Pommeret, Salhi, Vandekerkhove (2024) <https://jmlr.org/papers/v25/23-0914.html>).

Authors:Xavier Milhaud [aut, cre], Pierre Vandekerkhove [ctb], Denys Pommeret [ctb], Yahia Salhi [ctb]

admix_2.3.1.tar.gz
admix_2.3.1.tar.gz(r-4.5-noble)admix_2.3.1.tar.gz(r-4.4-noble)
admix_2.3.1.tgz(r-4.4-emscripten)admix_2.3.1.tgz(r-4.3-emscripten)
admix.pdf |admix.html
admix/json (API)

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

Peer review:

Bug tracker:https://github.com/xaviermilhaud/admix-rpackage/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • allGalaxies - Measurements of heliocentric velocities in four galaxies
  • milkyWay - Heliocentric velocity for the Milky Way
  • mortality_sample - Deaths statistics in 11 european countries
  • stmf_small - Short-term Mortality Fluctuations (STMF) data

3.78 score 8 scripts 353 downloads 2 mentions 17 exports 39 dependencies

Last updated 6 days agofrom:47956ed104. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-linux-x86_64OKOct 25 2024

Exports:admix_clusteradmix_estimadmix_modeladmix_testBVdk_varCov_estimatorsdecontaminated_cdfdecontaminated_densityestim_BVdkestim_IBMestim_PSgaussianity_testgetmixingWeightgetmixtDataIBM_k_samples_testIBM_tabul_stochasticIntegorthobasis_testtwoComp_mixt

Dependencies:clicolorspacecubatureEnvStatsfansifarverfdrtoolggplot2gluegtableIsoisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmenortestorthopolynompillarpkgconfigpolynompracmaR6rbibutilsRColorBrewerRcppRdpackrlangscalestibbleutf8vctrsviridisLitewithr

Clustering of unknown subpopulations in admixture models

Rendered fromadmixture-clustering.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2024-10-24
Started: 2021-06-14

Estimation of unknown elements in admixture models

Rendered fromadmixture-weight-estimation.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2024-10-24
Started: 2021-06-14

Hypothesis test in admixture models

Rendered fromtest-hypothesis.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2024-10-24
Started: 2021-06-14

Readme and manuals

Help Manual

Help pageTopics
Clustering of K populations following admixture modelsadmix_cluster
Estimate the unknown parameters of the admixture model(s)admix_estim
Create an object of class 'admix_model'admix_model
Equality test for the unknown components of admixture modelsadmix_test
Measurements of heliocentric velocities in four galaxiesallGalaxies
Variance of estimators in an admixture model with symmetric unknown density.BVdk_varCov_estimators
Estimates the decontaminated CDF of the unknown component in an admixturedecontaminated_cdf
Estimates the decontaminated density of the unknown component in an admixturedecontaminated_density
Estimation of the admixture parameters by Bordes & Vandekerkhove (2010)estim_BVdk
Estimates weights of unknown components from 2 admixtures using IBMestim_IBM
Estimates in an admixture using Patra and Sen approachestim_PS
Gaussianity test in an admixture modelgaussianity_test
Extractor for object of class 'admix_estim'getmixingWeight
Extractor for object of class 'twoComp_mixt'getmixtData
Equality test of K unknown component distributionsIBM_k_samples_test
Simulated distribution of the contrast using IBMIBM_tabul_stochasticInteg
Heliocentric velocity for the Milky WaymilkyWay
Deaths statistics in 11 european countriesmortality_sample
Equality test of two unknown component distributions using polynomial expansionsorthobasis_test
Plot method for class 'decontaminated_density'plot.decontaminated_density
Plots several mixture densities on the same graphplot.twoComp_mixt
Print method for object of class 'admix_cluster'print.admix_cluster
Print the estimated parameters from K admixture modelsprint.admix_estim
Print method for objects of class 'admix_model'print.admix_model
Print method for objects 'admix_test'print.admix_test
Print method for object of class 'decontaminated_density'print.decontaminated_density
Print method for objects 'estim_BVdk'print.estim_BVdk
Print method for objects of class 'estim_IBM'print.estim_IBM
Print method for objects of class 'estim_PS'print.estim_PS
Print method for objects 'gaussianity_test'print.gaussianity_test
Print method for objects 'IBM_test'print.IBM_test
Print method for objects of class 'orthobasis_test'print.orthobasis_test
Print method for objects 'twoComp_mixt'print.twoComp_mixt
Short-term Mortality Fluctuations (STMF) datastmf_small
Summary method for object of class 'admix_cluster'summary.admix_cluster
Results of estimated parameters from K admixture modelssummary.admix_estim
Summary method for 'admix_test' objectssummary.admix_test
Summary method for objects 'estim_BVdk'summary.estim_BVdk
Summary method for objects 'estim_IBM'summary.estim_IBM
Summary method for objects 'estim_PS'summary.estim_PS
Summary method for objects 'gaussianity_test'summary.gaussianity_test
Summary method for objects 'IBM_test'summary.IBM_test
Summary method for objects of class 'orthobasis_test'summary.orthobasis_test
Simulation of a two-component mixture modeltwoComp_mixt