Package: hamlet 0.9.7

hamlet: Hierarchical Optimal Matching and Machine Learning Toolbox

Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.

Authors:Teemu Daniel Laajala <[email protected]>

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hamlet.pdf |hamlet.html✨
hamlet/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/syksy/hamlet/issues

Datasets:
  • orxlong - Long-format longitudinal data for the ORX study
  • orxwide - Wide-format baseline data for the ORX study
  • vcaplong - Long-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.
  • vcapwide - Wide-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.

On CRAN:

4.18 score 2 packages 25 scripts 274 downloads 18 exports 0 dependencies

Last updated 1 years agofrom:3cd5191ef6. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 15 2024
R-4.5-winNOTEOct 15 2024
R-4.5-linuxNOTEOct 15 2024
R-4.4-winNOTEOct 15 2024
R-4.4-macNOTEOct 15 2024
R-4.3-winNOTEOct 15 2024
R-4.3-macNOTEOct 15 2024

Exports:extendsymrangehmaphmap.annotatehmap.keymatch.allocatematch.bbmatch.dummymatch.gamatch.mat2vecmatch.vec2matmem.getcompmem.plotranmem.plotresidmem.powersimumix.binarymix.funmixplotsmartjitter

Dependencies:

Introduction to hamlet

Rendered fromintroduction.Rnwusingutils::Sweaveon Oct 15 2024.

Last update: 2018-07-17
Started: 2018-07-17

Readme and manuals

Help Manual

Help pageTopics
Hierarchical Optimal Matching and Machine Learning Toolboxhamlet-package hamlet
Extend range of variable limits while retaining a point of symmetricityextendsymrange
Plot-region based heatmaphmap
Add a row and column annotations to a plot-region based heatmap built with 'hmap'hmap.annotate
Add a color key to a plot-region based heatmap built with 'hmap'hmap.key
Allocation of matched units to intervention armsmatch.allocate
Branch and Bound algorithm implementation for performing multigroup non-bipartite matchingmatch.bb
Create dummy individuals or sinks to a data matrix or a distance/dissimilarity matrixmatch.dummy
Non-bipartite matching using the Genetic Algorithm (GA)match.ga
Transform a binary matching matrix to a matching vectormatch.mat2vec
Transform a matching vector to a binary matching matrixmatch.vec2mat
Extract per-observation components for fixed and random effects of a mixed-effects modelmem.getcomp
Plot random effects histograms for a fitted mixed-effects modelmem.plotran
Plot residuals of a mixed-effects model along with trend linesmem.plotresid
Power simulations for the fixed effects of a mixed-effects model through structured bootstrapping of the data and re-fitting of the modelmem.powersimu
Binary coding of categorical variablesmix.binary
Apply function to numerical columns of a mixed data.frame while ignoring non-numeric fieldsmix.fun
Scatterplot for mixed type datamixplot
Long-format longitudinal data for the ORX studyorxlong
Wide-format baseline data for the ORX studyorxwide
Smart jittering function for deterministic shifting of overlapping valuessmartjitter
Long-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.vcaplong
Wide-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.vcapwide