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