R Cmdr Plugins

MARS 6910 – Spring 2015

David Hyrenbach

Starting Rcmdr Plugins A number of available plugins provide direct access to R packages through the Rcmdr interface. Plugins installed in same way as other R packages (for installation information see www.UsingRcmdr.com) and can be loaded via the R-console or by using the Rcmdr menu: `Tools, Load Rcmdr plugin(s)'.

(Hint: make sure packages installed in R)

Jan 2015: 29 plugins support specific analyses, graphics, and and teaching. Full information about plugins available by following the links provided in the table...

RcmdrPlugin.coin Rcmdr Coin Plug-In RcmdrPlugin.depthTools R commander Depth Tools Plug-In RcmdrPlugin.doBy Rcmdr doBy Plug-In RcmdrPlugin.doex Rcmdr plugin for Stat 4309 course RcmdrPlugin.EACSPIR Plugin de R-Commander para EACSPIR RcmdrPlugin.EBM Rcmdr Evidence Based Medicine Plug-In RcmdrPlugin.epack Rcmdr plugin for time series RcmdrPlugin.EZR R Commander Plug-in for (Easy R) Package RcmdrPlugin.HH Rcmdr support for the HH package RcmdrPlugin.IPSUR An IPSUR Plugin for the R Commander RcmdrPlugin.KMggplot2 Kaplan-Meier Plots Using the ggplot2 Package RcmdrPlugin.mosaic Adds menu to produce mosaic pand assoc plots RcmdrPlugin.MPAStats R Commander Plug-in for MPA Statistics RcmdrPlugin.orloca orloca Rcmdr Plug-in RcmdrPlugin.plotByGroup Rcmdr plots by group using lattice RcmdrPlugin.qcc Rcmdr qcc Plug-In RcmdrPlugin.qual Rcmdr plugin for quality control course RcmdrPlugin.SCDA Rcmdr plugin for single-case experiments RcmdrPlugin.seeg Rcmdr Plugin for seeg RcmdrPlugin.SLC SLC Rcmdr Plug-in RcmdrPlugin.SM Rcmdr Sport Management Plug-In RcmdrPlugin.StatisticalURV Statistical URV Rcmdr Plug-In RcmdrPlugin.steepness Steepness Rcmdr Plug-in RcmdrPlugin.survival R Commander Plug-in for the survival Package RcmdrPlugin.TeachingDemos Rcmdr Teaching Demos Plug-In

(http://www.rcommander.com/) Rcmdr Plugins

RcmdrPlugin.survival R Commander Plugin survival Package

Reference Manual as a PDF file

Checking out Rcmdr Plugins

Hint: Type “help(RcmdrPlugin.survival)” in R console It opens web browser and takes you to meta-data

RcmdrPlugin.survival R Commander Plugin survival Package

Plug-in integrated with the R Commander menu interface:

Data -> Survival data, Statistics -> Survival analysis Statistics -> Fit Models, Models -> Hypothesis tests Models -> Numerical diagnostics Models -> Graphs

Checking out Rcmdr Plugins

RcmdrPlugin.survival Includes two Datasets

Hint: Menu: Data -> Data in packages List and read datasets in packages

Checking out R Cmdr Plugin Datsets

Checking out Rcmdr Plugin Datasets

Meta-data on Dataset

List of Variables (62):

Viewing the Dataset:

Checking out Rcmdr Plugin Datasets

Checking out Rcmdr Plugin Tools

Rachel Tolliver

RcmdrPlugin.EcoVirtual

Designed for teaching

ecological models

using simulations

Returns graphs of

different ecological

phenomena

RcmdrPlugin.EcoVirtual

PROS: - Many different simulations to choose from and manipulate - Help button on each simulation that provides link to meta- data and “how to”

CONS: - Does not work with outside data directly, can only make models based on already known parameters

RcmdrPlugin.EcoVirtual

New menu option

Example: Simple model of logistical growth

RcmdrPlugin.EcoVirtual

Two Species Competition Model Ex: When will invasion species abundance exceed native species abundance?

When will native species reach extinction?

EZR Rcmdr Plugin Meagan Putts

• To install: load R and type >install.packages("RcmdrPlugin.EZR", dependencies=TRUE)

*you will have to restart Rcmdr (and possibly R) to load the plugin

• Enables the application of statistical functions that are frequently used in clinical studies

• Point-and-click access to functions: – Discrete and continuous variable parametric analyses – Nonparametric tests for continuous variables – Survival analyses – Diagnostic test analyses – Match-pair analyses – Meta-analysis and meta-regression test – Sample size and power calculation

Tools

– File, Edit, Tools and Help –

Same as original Rcmdr

– Active data set –

Modify data set, save & export

– Statistical analyses –

For all your statistical needs

– Graphs and Tables –

Choose and modify your output

– Original menu –

Tabs from original Rcmdr

Dataset

• MASS, Car, datasets, multcomp, sandwich, survival, TH.data

• Use help to understand variables and data collection

Relapse non-relapse

ANOVA

Cox Survival

Export data to Excel

Helpful guides for using EZR

• http://minato.sip21c.org/grad/infop-text2012.pdf

• http://www.nature.com/bmt/journal/v48/n3/pdf/bmt2012244a.pdf

• http://www.jichi.ac.jp/saitama-sct/SaitamaHP.files/statmedEN.html