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.

Author
Teemu Daniel Laajala <teelaa@utu.fi>
Date of publication
2016-10-25 10:30:32
Maintainer
Teemu Daniel Laajala <teelaa@utu.fi>
License
GPL (>= 2)
Version
0.9.5

View on CRAN

Man pages

extendsymrange
Extend range of variable limits while retaining a point of...
hamlet-package
Hierarchical Optimal Matching and Machine Learning Toolbox
hmap
Plot-region based heatmap
hmap.annotate
Add a row and column annotations to a plot-region based...
hmap.key
Add a color key to a plot-region based heatmap built with...
match.allocate
Allocation of matched units to intervention arms
match.bb
Branch and Bound algorithm implementation for performing...
match.dummy
Create dummy individuals or sinks to a data matrix or a...
match.ga
Non-bipartite matching using the Genetic Algorithm (GA)
match.mat2vec
Transform a binary matching matrix to a matching vector
match.vec2mat
Transform a matching vector to a binary matching matrix
mem.getcomp
Extract per-observation components for fixed and random...
mem.plotran
Plot random effects histograms for a fitted mixed-effects...
mem.plotresid
Plot residuals of a mixed-effects model along with trend...
mem.powersimu
Power simulations for the fixed effects of a mixed-effects...
mix.binary
Binary coding of categorical variables
mix.fun
Apply function to numerical columns of a mixed data.frame...
mixplot
Scatterplot for mixed type data
orxlong
Long-format longitudinal data for the ORX study
orxwide
Wide-format baseline data for the ORX study
smartjitter
Smart jittering function for deterministic shifting of...
vcaplong
Long-format data of the Castration-resistant Prostate Cancer...
vcapwide
Wide-format data of the Castration-resistant Prostate Cancer...

Files in this package

hamlet
hamlet/inst
hamlet/inst/CITATION
hamlet/inst/doc
hamlet/inst/doc/introduction.Rnw
hamlet/inst/doc/introduction.R
hamlet/inst/doc/introduction.pdf
hamlet/NAMESPACE
hamlet/data
hamlet/data/orxwide.rda
hamlet/data/vcapwide.rda
hamlet/data/orxlong.rda
hamlet/data/vcaplong.rda
hamlet/R
hamlet/R/mixtools.R
hamlet/R/internal.R
hamlet/R/matchtools.R
hamlet/R/plottools.R
hamlet/R/simurun.R
hamlet/R/memtools.R
hamlet/vignettes
hamlet/vignettes/introduction-016.pdf
hamlet/vignettes/introduction-007.pdf
hamlet/vignettes/workflow.pdf
hamlet/vignettes/introduction-019.pdf
hamlet/vignettes/example.csv
hamlet/vignettes/excelexample.JPG
hamlet/vignettes/introduction-020.pdf
hamlet/vignettes/introduction.Rnw
hamlet/vignettes/introduction-023.pdf
hamlet/vignettes/introduction-017.pdf
hamlet/vignettes/introduction-013.pdf
hamlet/vignettes/introduction-022.pdf
hamlet/vignettes/introduction-014.pdf
hamlet/MD5
hamlet/build
hamlet/build/vignette.rds
hamlet/DESCRIPTION
hamlet/man
hamlet/man/hmap.annotate.Rd
hamlet/man/figures
hamlet/man/figures/hmapex.pdf
hamlet/man/figures/hmapex.png
hamlet/man/mixplot.Rd
hamlet/man/hmap.Rd
hamlet/man/hmap.key.Rd
hamlet/man/vcapwide.Rd
hamlet/man/match.allocate.Rd
hamlet/man/match.dummy.Rd
hamlet/man/mem.plotresid.Rd
hamlet/man/orxwide.Rd
hamlet/man/smartjitter.Rd
hamlet/man/mem.powersimu.Rd
hamlet/man/match.mat2vec.Rd
hamlet/man/orxlong.Rd
hamlet/man/vcaplong.Rd
hamlet/man/hamlet-package.Rd
hamlet/man/match.bb.Rd
hamlet/man/mix.binary.Rd
hamlet/man/match.vec2mat.Rd
hamlet/man/mix.fun.Rd
hamlet/man/match.ga.Rd
hamlet/man/mem.getcomp.Rd
hamlet/man/mem.plotran.Rd
hamlet/man/extendsymrange.Rd