Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices
AU - Pallmann, Philip
AU - Schaarschmidt, Frank
AU - Hothorn, Ludwig A.
AU - Fischer, Christiane
AU - Nacke, Heiko
AU - Priesnitz, Kai U.
AU - Schork, Nicholas J.
PY - 2012/11
Y1 - 2012/11
N2 - Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these ‘raw’ indices can be corrected by transforming them into ‘true’ diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of ‘true’ diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package ‘simboot’.
AB - Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these ‘raw’ indices can be corrected by transforming them into ‘true’ diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of ‘true’ diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package ‘simboot’.
KW - bootstrap
KW - metagenomics
KW - multiple contrasts
KW - Shannon entropy
KW - Simpson index
KW - Westfall-Young
U2 - 10.1111/1755-0998.12004
DO - 10.1111/1755-0998.12004
M3 - Journal article
VL - 12
SP - 1068
EP - 1078
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
SN - 1755-0998
IS - 6
ER -