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hamlet (version 0.9.6)

Hierarchical Optimal Matching and Machine Learning Toolbox

Description

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.

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Version

Install

install.packages('hamlet')

Monthly Downloads

213

Version

0.9.6

License

GPL (>= 2)

Maintainer

Teemu Daniel Laajala

Last Published

May 26th, 2018

Functions in hamlet (0.9.6)

mix.binary

Binary coding of categorical variables
match.vec2mat

Transform a matching vector to a binary matching matrix
smartjitter

Smart jittering function for deterministic shifting of overlapping values
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.
match.bb

Branch and Bound algorithm implementation for performing multigroup non-bipartite matching
mem.plotran

Plot random effects histograms for a fitted mixed-effects model
hmap

Plot-region based heatmap
extendsymrange

Extend range of variable limits while retaining a point of symmetricity
mem.plotresid

Plot residuals of a mixed-effects model along with trend lines
match.dummy

Create dummy individuals or sinks to a data matrix or a distance/dissimilarity matrix
hmap.annotate

Add a row and column annotations to a plot-region based heatmap built with 'hmap'
mem.powersimu

Power simulations for the fixed effects of a mixed-effects model through structured bootstrapping of the data and re-fitting of the model
match.ga

Non-bipartite matching using the Genetic Algorithm (GA)
hmap.key

Add a color key to a plot-region based heatmap built with 'hmap'
match.allocate

Allocation of matched units to intervention arms
hamlet-package

Hierarchical Optimal Matching and Machine Learning Toolbox
orxlong

Long-format longitudinal data for the ORX study
mix.fun

Apply function to numerical columns of a mixed data.frame while ignoring non-numeric fields
orxwide

Wide-format baseline data for the ORX study
mixplot

Scatterplot for mixed type data
mem.getcomp

Extract per-observation components for fixed and random effects of a mixed-effects model
match.mat2vec

Transform a binary matching matrix to a matching vector