Original node

Documentations

The original documentation page address, kept for continuity with the old site.

User guide, dependencies, and fixes

This page collects the user guide and hints for the most common inconveniences that can occur while installing the package and its dependencies.

Both the guide and these notes were still under development when the original page was published, and a vignette was planned. The guide below remains the practical starting point, while the paper is the main reference for the package.

The project paper

The main reference for VMSbase has been published in PLoS One. Read the paper for the methods and the design of the package.

Read the paper on PLoS One

User guide

The standard R user guide for the package is available as a PDF. It covers the main interface and the steps behind a typical analysis.

VMSbase user guide

Open or download the guide, then follow the installation notes on the download page.

Open the user guide

Dependencies

VMSbase is built on R and a set of add on packages. The complete list on the original page comprises:

Package	Scope
AMORE	A MORE flexible neural network package
CairoDevice	Cairo based cross platform antialiased graphics device driver
chron	Chronological objects which can handle dates and times
cluster	Cluster Analysis Extended Rousseeuw et al
e1071	Misc functions of the Department of Statistics, TU Wien
Ecodist	Dissimilarity based functions for ecological analysis
Fields	Tools for spatial data
foreign	Read data stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, and other formats
ggmap	A package for spatial visualization with Google Maps and OpenStreetMap
Gwidgets	gWidgets API for building toolkit independent, interactive GUIs
GWidgetsRGtk	Toolkit implementation of gWidgets for RGtk2
intervals	Weighted Logrank tests and NPMLE for interval censored data
mapdata	Extra map databases
maps	Draw geographical maps
maptools	Tools for reading and handling spatial objects
marmap	Import, plot, and analyze bathymetric and topographic data
outliers	Tests for outliers
PBSmapping	Mapping fisheries data and spatial analysis tools
plotrix	Various plotting functions
sp	Classes and methods for spatial data
sqldf	Perform SQL selects on R data frames

The add on packages are available from the VMSbase CRAN page and the wider R Project.

Troubleshoots

VMSbase has several dependencies. Although the package is self installing, users can experience occasional setbacks. Most of these are easy to fix. The notes below summarize the common cases from the original page.

Issue 1: Curl library missing on Ubuntu

After running the installation for devtools, some systems report that the Curl library cannot be found, followed by errors for httr and devtools.

Use APT to install the curl development library and the XML development library, then retry the installation in R. This restores the libraries that the R packages need to build.

Issue 2: GTK library missing

The GTK library is usually installed by the operating system and is necessary for the package and all of its features. Some users need to install it manually.

On Windows, install and load the gwidgets package, then run gwindow() in the R console. A dialog will offer to download and install the GTK libraries.

On Ubuntu, use APT to install the GTK development libraries, then restart R.

Issue 3: netcdf library missing

This problem can occur while installing the marmap package, when the ncdf dependency is not available.

Open Ubuntu Software Center or Synaptic Package Manager, search for libnetcdf, netcdf, and the netcdf binary package, mark them and their dependencies for installation, apply the changes, restart R, and install the ncdf and marmap packages.

Issue 4: Windows 64 bit installation

Some users with Windows 64 bit have difficulty installing VMSbase even when the package version is appropriate for that system.

Install a 32 bit version of R and retry the installation.

Need more help? Write to the support address on the support and contacts page, or read the installation steps.