April 2022 list of packages of interest
- Introduction
- flexclust: Flexible Cluster Algorithms
- rrtable: Reproducible Research with a Table of R Codes
- beanplot: Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
- valuemap: Making Choropleth Map
- tessellation: Delaunay and Voronoï Tessellations
- mockr: Mocking in R
- waves: Vis-NIR Spectral Analysis Wrapper
- ffmanova: Fifty-Fifty MANOVA
- lmtest: Testing Linear Regression Models
- raymolecule: Parse and Render Molecular Structures in 3D
- reporter: Creates Statistical Reports
TOC
- rrtable: Reproducible Research with a Table of R Codes
- beanplot: Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
- valuemap: Making Choropleth Map
- tessellation: Delaunay and Voronoï Tessellations
- mockr: Mocking in R
- waves: Vis-NIR Spectral Analysis Wrapper
- ffmanova: Fifty-Fifty MANOVA
- lmtest: Testing Linear Regression Models
- raymolecule: Parse and Render Molecular Structures in 3D
- reporter: Creates Statistical Reports
Introduction
Each month I will describe the package that I've discovered or rediscovered and the ones that I've used the most of my time. I will start with the package used in my work and the the one that I would like to try/did not had time to use for work and also fun
Each card is organised as this
Name of the package: short description
mytags: #example tag
links
[cran package link]
[cran vignette link]
[github link]
description from the author/vignette
mynotes
flexclust: Flexible Cluster Algorithms
mytags: #classificatrion #clusters #multivariate
links
[cran package link] https://cran.r-project.org/package=flexclust
description from the author/vignette
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.
mynotes
rrtable: Reproducible Research with a Table of R Codes
mytags: #tables #reproducible research
links
[cran package link] https://cran.r-project.org/package=rrtable
[vignette link] https://cran.r-project.org/web/packages/rrtable/vignettes/rrtable.html
description from the author/vignette
Makes documents containing plots and tables from a table of R codes. Can make "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents with or without R code. In the package, modularized 'shiny' app codes are provided. These modules are intended for reuse across applications.
mynotes
beanplot: Visualization via Beanplots (Like Boxplot/Stripchart/Violin Plot)
mytags: #plot #distributions #boxplot
links
[cran package link] https://cran.r-project.org/package=beanplot
[vignette link] https://cran.r-project.org/web/packages/beanplot/vignettes/beanplot.pdf
description from the author/vignette
Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.
mynotes need to test it and compare with violins
valuemap: Making Choropleth Map
mytags: #plot #valuemap
links
[cran package link] https://CRAN.R-project.org/package=valuemap
description from the author/vignette
You can easily visualize your 'sf' polygons or data.frame with h3 address. While 'leaflet' package is too raw for data analysis, this package can save data analysts' efforts & time with pre-set visualize options.
mynotes
tessellation: Delaunay and Voronoï Tessellations
mytags: #tesselation #voronoi #delaunay
links
[cran package link] https://cran.r-project.org/package=tessellation
description from the author/vignette
Delaunay and Voronoï tessellations, with emphasis on the two-dimensional and the three-dimensional cases (the package provides functions to plot the tessellations for these cases). Delaunay tessellations are computed in C with the help of the 'Qhull' library http://www.qhull.org/. mynotes
mockr: Mocking in R
mytags: #testing
links
[cran package link] https://cran.r-project.org/package=mockr
[vignette link] https://cran.r-project.org/web/packages/mockr/vignettes/mockr.html
description from the author/vignette
Delaunay and Voronoï tessellations, with emphasis on the two-dimensional and the three-dimensional cases (the package provides functions to plot the tessellations for these cases). Delaunay tessellations are computed in C with the help of the 'Qhull' library http://www.qhull.org/. mynotes
waves: Vis-NIR Spectral Analysis Wrapper
mytags: #spectroscopy #preprocessing #filtering #model training
links
[cran package link] https://cran.r-project.org/package=waves
[vignette link] https://cran.r-project.org/web/packages/waves/vignettes/waves.html
description from the author/vignette
Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal doi:10.1002/ppj2.20012. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) doi:10.3835/plantgenome2016.12.0130. Example data is from Ikeogu et al. (2017) doi:10.1371/journal.pone.0188918. mynotes
ffmanova: Fifty-Fifty MANOVA
mytags: #manova àmancova
links
[cran package link] https://cran.r-project.org/package=ffmanova
[vignette link] https://cran.r-project.org/web/packages/ffmanova/ffmanova.pdf
[github link] https://github.com/olangsrud/ffmanova
description from the author/vignette
General linear modeling with multiple responses (MANCOVA). An overall p-value for each model term is calculated by the 50-50 MANOVA method by Langsrud (2002) doi:10.1111/1467-9884.00320, which handles collinear responses. Rotation testing, described by Langsrud (2005) doi:10.1007/s11222-005-4789-5, is used to compute adjusted single response p-values according to familywise error rates and false discovery rates (FDR). The approach to FDR is described in the appendix of Moen et al. (2005) doi:10.1128/AEM.71.4.2086-2094.2005. Unbalanced designs are handled by Type II sums of squares as argued in Langsrud (2003) doi:10.1023/A:1023260610025. Furthermore, the Type II philosophy is extended to continuous design variables as described in Langsrud et al. (2007) doi:10.1080/02664760701594246. This means that the method is invariant to scale changes and that common pitfalls are avoided. mynotes
lmtest: Testing Linear Regression Models
mytags: #linear regression #testing
links
[cran package link] https://cran.r-project.org/package=lmtest
[vignette link] https://cran.r-project.org/web/packages/lmtest/vignettes/lmtest-intro.pdf
description from the author/vignette
A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.
mynotes
raymolecule: Parse and Render Molecular Structures in 3D
mytags: #chemistry #rendering
links
[cran package link] https://cran.r-project.org/package=raymolecule
description from the author/vignette
Downloads and parses 'SDF' (Structural Description Format) and 'PDB' (Protein Database) files for 3D rendering..
mynotes
reporter: Creates Statistical Reports
mytags: #statistics #report
links
[cran package link] https://CRAN.R-project.org/package=reporter
[vignette link] https://cran.r-project.org/web/packages/reporter/vignettes/reporter-faq.html
description from the author/vignette
Contains functions to create regulatory-style statistical reports. Originally designed to create tables, listings, and figures for the pharmaceutical, biotechnology, and medical device industries, these reports are generalized enough that they could be used in any industry. Generates text, rich-text, PDF, HTML, and Microsoft Word file formats. The package specializes in printing wide and long tables with automatic page wrapping and splitting. Reports can be produced with a minimum of function calls, and without relying on other table packages. The package supports titles, footnotes, page header, page footers, spanning headers, page by variables, and automatic page numbering.
mynotes