Determination of diagnostic species with statistical fidelity
measures

J 2002

Determination of diagnostic species with statistical fidelity measures

CHYTRÝ, Milan, Lubomír TICHÝ, Jason HOLT and Zoltán BOTTA-DUKÁT

Basic information

Original name

Determination of diagnostic species with statistical fidelity measures

Authors

CHYTRÝ, Milan (203 Czech Republic, guarantor), Lubomír TICHÝ (203 Czech Republic), Jason HOLT (840 United States of America) and Zoltán BOTTA-DUKÁT (348 Hungary)

Edition

Journal of Vegetation Science, Uppsala, Opulus Press, 2002, 110-9233

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Sweden

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

RIV identification code

RIV/00216224:14310/02:00005547

Organization unit

Faculty of Science

UT WoS

000175252300009

Keywords in English

Character species; Differential species; Frequency; Indicator species; Non-parametric statistics; Phytosociological database; Plant community; Vegetation classification

Abstract

V originále

Statistical measures of fidelity, i.e. the concentration of species occurrences in vegetation units, are reviewed and compared. The focus is on measures suitable for categorical data which are based on observed species frequencies within a vegetation unit compared with the frequencies expected under random distribution. Particular attention is paid to Bruelheides u value. It is shown that its original form, based on binomial distribution, is an asymmetric measure of fidelity of a species to a vegetation unit which tends to assign comparatively high fidelity values to rare species. Here, a hypergeometric form of u is introduced which is a symmetric measure of the joint fidelity of species to a vegetation unit and vice versa. It is also shown that another form of the binomial u value may be defined which measures the asymmetric fidelity of a vegetation unit to a species. These u values are compared with phi coefficient, chi-square, G statistic and Fishers exact test. Contrary to the other measures, phi coefficient is independent of the number of relevés in the data set, and like the hypergeometric form of u and the chi-square it is little affected by the relative size of the vegetation unit. It is therefore particularly useful when comparing species fidelity values among differently sized data sets and vegetation units. However, unlike the other measures it does not measure any statistical significance and may produce unreliable results for small vegetation units and small data sets. The above measures, all based on the comparison of observed/expected frequencies, are compared with the categorical form of the Dufrene-Legendre Indicator Value Index, an index strongly underweighting the fidelity of rare species. These fidelity measures are applied to a data set of 15 989 relevés of Czech herbaceous vegetation. In a small subset of this data set which simulates a phytosociological table, we demonstrate that traditional table analysis fails to determine diagnostic species of general validity in different habitats and large areas. On the other hand, we show that fidelity calculations used in conjunction with large data sets can replace expert knowledge in the determination of generally valid diagnostic species. Averaging positive fidelity values for all species within a vegetation unit is a useful approach to measure quality of delimination of the vegetation unit. We propose a new way of ordering species in synoptic species-by-relevé tables, using fidelity calculations.

Links

GA206/99/1523, research and development project

Name: Parametrizace fytocenologického systému pomocí velkých souborů dat

Investor: Czech Science Foundation, Parameterization of the phytosociological classification using large datasets

MSM 143100010, plan (intention)

Name: Časoprostorová dynamika biodiverzity v ekosystémech střední Evropy.

Investor: Ministry of Education, Youth and Sports of the CR, Spatiotemporal biodiversity dynamics in ecosystems of Central Europe

Citovat

CHYTRÝ, Milan, Lubomír TICHÝ, Jason HOLT and Zoltán BOTTA-DUKÁT. Determination of diagnostic species with statistical fidelity measures. Journal of Vegetation Science. Uppsala: Opulus Press, 2002, vol. 13, No 1, p. 79-90. ISSN 110-9233.

@article{399431,
   author = {Chytrý, Milan and Tichý, Lubomír and Holt, Jason and BottaandDukát, Zoltán},
   article_location = {Uppsala},
   article_number = {1},
   keywords = {Character species; Differential species; Frequency; Indicator species; Non-parametric statistics; Phytosociological database; Plant community; Vegetation classification},
   language = {eng},
   issn = {110-9233},
   journal = {Journal of Vegetation Science},
   title = {Determination of diagnostic species with statistical fidelity measures},
   url = {http://www.sci.muni.cz/botany/chytry/JVS2002.pdf},
   volume = {13},
   year = {2002}
}

TY  - JOUR
ID  - 399431
AU  - Chytrý, Milan - Tichý, Lubomír - Holt, Jason - Botta-Dukát, Zoltán
PY  - 2002
TI  - Determination of diagnostic species with statistical fidelity measures
JF  - Journal of Vegetation Science
VL  - 13
IS  - 1
SP  - 79
EP  - 79
PB  - Opulus Press
SN  - 1109233
KW  - Character species
KW  - Differential species
KW  - Frequency
KW  - Indicator species
KW  - Non-parametric statistics
KW  - Phytosociological database
KW  - Plant community
KW  - Vegetation classification
UR  - http://www.sci.muni.cz/botany/chytry/JVS2002.pdf
N2  - Statistical measures of fidelity, i.e. the concentration of species occurrences in vegetation units, are reviewed and compared. The focus is on measures suitable for categorical data which are based on observed species frequencies within a vegetation unit compared with the frequencies expected under random distribution. Particular attention is paid to Bruelheides u value. It is shown that its original form, based on binomial distribution, is an asymmetric measure of fidelity of a species to a vegetation unit which tends to assign comparatively high fidelity values to rare species. Here, a hypergeometric form of u is introduced which is a symmetric measure of the joint fidelity of species to a vegetation unit and vice versa. It is also shown that another form of the binomial u value may be defined which measures the asymmetric fidelity of a vegetation unit to a species. These u values are compared with phi coefficient, chi-square, G statistic and Fishers exact test. Contrary to the other measures, phi coefficient is independent of the number of relevés in the data set, and like the hypergeometric form of u and the chi-square it is little affected by the relative size of the vegetation unit. It is therefore particularly useful when comparing species fidelity values among differently sized data sets and vegetation units. However, unlike the other measures it does not measure any statistical significance and may produce unreliable results for small vegetation units and small data sets. The above measures, all based on the comparison of observed/expected frequencies, are compared with the categorical form of the Dufrene-Legendre Indicator Value Index, an index strongly underweighting the fidelity of rare species. These fidelity measures are applied to a data set of 15 989 relevés of Czech herbaceous vegetation. In a small subset of this data set which simulates a phytosociological table, we demonstrate that traditional table analysis fails to determine diagnostic species of general validity in different habitats and large areas. On the other hand, we show that fidelity calculations used in conjunction with large data sets can replace expert knowledge in the determination of generally valid diagnostic species. Averaging positive fidelity values for all species within a vegetation unit is a useful approach to measure quality of delimination of the vegetation unit. We propose a new way of ordering species in synoptic species-by-relevé tables, using fidelity calculations.
ER  -

CHYTRÝ, Milan, Lubomír TICHÝ, Jason HOLT and Zoltán BOTTA-DUKÁT. Determination of diagnostic species with statistical fidelity measures. \textit{Journal of Vegetation Science}. Uppsala: Opulus Press, 2002, vol.~13, No~1, p.~79-90. ISSN~110-9233.

Detailed Information on Publication Record