Package: hamlet 0.9.8

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 [aut, cre]

hamlet_0.9.8.tar.gz
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hamlet_0.9.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hamlet/json (API)

# Install 'hamlet' in R:

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

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:

4.19 score 2 packages 26 scripts 382 downloads 18 exports 0 dependencies

Last updated from:7e571f481a. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	179
source / vignettes	OK	198
linux-release-x86_64	OK	166
macos-release-arm64	OK	121
macos-oldrel-arm64	OK	103
windows-devel	OK	85
windows-release	OK	89
windows-oldrel	OK	78
wasm-release	OK	144

Exports:extendsymrange hmap hmap.annotate hmap.key match.allocate match.bb match.dummy match.ga match.mat2vec match.vec2mat mem.getcomp mem.plotran mem.plotresid mem.powersimu mix.binary mix.fun mixplot smartjitter

Dependencies:

Introduction to hamlet

Rendered fromintroduction.Rnwusingutils::Sweave

Last update: 2025-12-08
Started: 2018-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Hierarchical Optimal Matching and Machine Learning Toolbox	hamlet-package hamlet
Extend range of variable limits while retaining a point of symmetricity	extendsymrange
Plot-region based heatmap	hmap
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 arms	match.allocate
Branch and Bound algorithm implementation for performing multigroup non-bipartite matching	match.bb
Create dummy individuals or sinks to a data matrix or a distance/dissimilarity matrix	match.dummy
Non-bipartite matching using the Genetic Algorithm (GA)	match.ga
Transform a binary matching matrix to a matching vector	match.mat2vec
Transform a matching vector to a binary matching matrix	match.vec2mat
Extract per-observation components for fixed and random effects of a mixed-effects model	mem.getcomp
Plot random effects histograms for a fitted mixed-effects model	mem.plotran
Plot residuals of a mixed-effects model along with trend lines	mem.plotresid
Power simulations for the fixed effects of a mixed-effects model through structured bootstrapping of the data and re-fitting of the model	mem.powersimu
Binary coding of categorical variables	mix.binary
Apply function to numerical columns of a mixed data.frame while ignoring non-numeric fields	mix.fun
Scatterplot for mixed type data	mixplot
Long-format longitudinal data for the ORX study	orxlong
Wide-format baseline data for the ORX study	orxwide
Smart jittering function for deterministic shifting of overlapping values	smartjitter
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