simboot
Installation
For installation, please download the newest R-version for your operation system. Then use the package manager to install the simboot package or run the following command inside R:
install.packages("simboot")
library(simboot)
Description
Package simboot provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre–specified multiple comparison types are available to choose. Further user–defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p–values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups while simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered as appropriate and useful indices for measuring diversity.
Usage
A tutorial for usage with metagenomic data will be created on the tutorial page.
Talk
Foils about the methods and about the usage of simboot for metagenomic trials.
Corresponding publications
The simultaneous confidence intervals for Shannon's and Simpson's indices are described and compared in the SCfDI paper:
Scherer, R., Schaarschmidt, F., Prescher, S. and Priesnitz, K. U. (2013), Simultaneous confidence intervals for comparing biodiversity indices estimated from overdispersed count data. Biom. J., 55: 246–263. doi: 10.1002/bimj.201200157
The comparison of two or more groups of observations, while simultaneously testing a user-defined selection of a number of 'true' diversity measures is published in the Hill paper:
Pallmann, P., Schaarschmidt, F., Hothorn, L. A., Fischer, C., Nacke, H., Priesnitz, K. U. and Schork, N. J. (2012), Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices. Molecular Ecology Resources, 12: 1068–1078. doi: 10.1111/1755-0998.12004
Questions and issues
To post feature requests or ask for help, try the simboot Issue Tracker.
Development version
To install the development version of the simboot package, it is easiest to use the devtools package:
install.packages("devtools") # if needed..
library(devtools)
install_github("simboot", "shearer")
library(simboot)