Cayetano Gutiérrez-Cánovas, David Sánchez-Fernández, Josefa Velasco, Andrés Millán, and Núria Bonada. 2015. Similarity in difference: changes in community functional features along natural and anthropogenic stress gradients. Ecology 96:2458–2466. http://dx.doi.org/10.1890/14-1447.1


Supplement

Fuzzy coded affinities of each taxon to the number of generations per year, body form, and degree of sclerotisation, R functions for estimating functional measures using fuzzy coded trait data and R script for studying the effect of stressors on functional measures.
Ecological Archives E096-216-S1.

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Authors
File list (downloads)
Description


Author(s)

Cayetano Gutiérrez-Cánovas
Departamento de Ecología e Hidrología, Universidad de Murcia
Campus de Excelencia Internacional Regional "Campus Mare Nostrum"
30100 Murcia
E-mail: cayeguti@um.es

David Sánchez-Fernández
Institut de Biologia Evolutiva (CSIC-UPF)
Passeig Marítim de la Barceloneta 37-49
08003 Barcelona
E-mail: davidsan@um.es

Josefa Velasco
Departamento de Ecología e Hidrología, Universidad de Murcia
Campus de Excelencia Internacional Regional "Campus Mare Nostrum"
30100 Murcia
E-mail: jvelasco@um.es

Andrés Millán
Departamento de Ecología e Hidrología, Universidad de Murcia
Campus de Excelencia Internacional Regional "Campus Mare Nostrum"
30100 Murcia
E-mail: acmillan@um.es

Núria Bonada
Grup de Recerca Freshwater Ecology and Management (FEM)
Department d’Ecologia, Facultat de Biologia, Universitat de Barcelona
Diagonal 643, 08028 Barcelona
E-mail: bonada@ub.edu


File list

All_files.zip (MD5: 12a8ece890d711d13148e464ed4565fe)

Fuzzy_code_traits.txt (MD5: d6a6faa36a1d0441d2af793551123646)

Fuzzy_Functions.R (MD5: 97ebdc4e37a8f42bc069f12fc440ab3d)

Script.R (MD5: 9cbe775d3056d0415b54891f7ccdc56c)

Description

All_files.zip Compressed file containing Fuzzy_code_traits.txt, Fuzzy_functions.R and Script.R

Fuzzy_code_traits.txt is a tab-separated file containing fuzzy code trait information for body form and degree of sclerotization of stream insect genera. Fuzzy values for each genera and trait category go from 0 (no affinity) to 3 (maximum affinity). Column definitions are:

1. Taxon: the 212 genus names

2-6 The trait categories for body form and degree of sclerotization. Column label meaning:

Body_Form_Flattened: Affinity for flattened body form

Body_Form_Cylindrical: Affinity for cylindrical body form

Body_Form_Elongated: Affinity for elongated body form

Sclerotization_Slightly: Affinity for slightly sclerotization degree

Sclerotization_Partially: Affinity for partially sclerotization degree

Sclerotization_Fully: Affinity for fully sclerotization degree

Fuzzy_functions.R is a file containing R functions for estimating taxon and community-level functional measures from fuzzy code trait data

Input variables:

ATTENTION: check that trait, taxonomic and stressor matrices have the row and column names ordered in the same way

traits: matrix of traits. Must be fuzzy coded or percentages of affinity for each trait category (taxa × trait categories)

taxa: taxonomic matrix of count or presence / absence data (sites × taxa)

col.blocks: vector containing the number of categories of each trait. Names are the trait names.

funcNiche() and funcNiche.pca() are the two functions that estimate the taxon and community functional properties. This file contains further information about the intermediate functions used to estimate each metric.

Input variables to run funcNiche() and funcNiche.pca()

rdt: number of randomizations to generate the taxon niche space

m: number of axes

Output functional variables:

fpc: functional space (functional principal components)

tfric.data: area and axis centroid of each taxon in the functional space

overlap.mat: triangular matrix of niche overlap between taxon pairs

tFRic: mean taxon functional richness for each community

FSim: mean functional similarity between taxon pairs

FDis: functional dispersion of each community

FRic: functional richness of each community

Script.R is a file containing the R code necessary to run the analyses performed in this study. This file is provided just an example of how to estimate and analyse the functional features along environmental gradients. It can be easily adapted to other data if input matrices are appropriate (see Fuzzy_functions.R description). In case of using this file, besides taxonomic and trait data, it should be provided the environmental data. The data set should be in the working directory of R when running this code.

The data sets 'taxa_sal.txt', 'taxa_lu.txt', 'env_sal.txt', 'env_lu.txt', 'traits_sal.txt' and 'traits_lu.txt' are not available for release at the moment.