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Statistical Function

Calculation of taxonomic distances: This function calculates the averaged taxonomic distances among species or individuals in the community from a classification t... Read more

Input files

This function cannot work without files in your workspace!

Parameters

varstep

check_taxa2dist

Indices of Taxonomic Diversity and Distinctness: This function computes the indices of taxonomic diversity and taxonomic distinctness. Taxonomic diversity can be t... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Select Column in Factor File:

Parameters

match.force

Taxondive parameter:

Computation of dissimilarity indices: This function computes dissimilarity indices that are useful for community ecologists. Gower, Bray-Curtis, Jaccard and Kulczy... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

Parameters

Method:

Binary

diag

upper

na.rm

Hierarchical cluster analysis on a set of dissimilarities and methods for analyzing it.: This function performs a hierarchical cluster analysis using a set of diss... Read more

Input files

This function cannot work without files in your workspace!

Select Column in Factor File:

Parameters

Method

Biological Index Calculation Tool: This function calculates biological indices (Number of species (S), Number of individuals (N), Benthic Quality Index (BQI), Bent... Read more

Input files

This function cannot work without files in your workspace!

Parameters

Species or Family

Principal Components Analysis: This function performs a principal components analysis on the given numeric data matrix.

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Select Column in Factor File:

Constrained Correspondence Analysis: This function performs Constrained Correspondence Analysis (a.k.a. canonical correspondence analysis) (ter Braak 1986), which ... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Factor File Numerous factors can be used to carry out Canonical Correspondence Analysis.

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Select Column in Factor File (Factor3)

Analysis of Similarities: This function provides a way to test statistically whether there is a significant difference between two or more groups of sampling units... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Select Column in Factor File:

Parameters

Permutations:

Method:

Analysis of Variance: This function is used to determine whether there are any significant differences between the means of two or more independent (unrelated) gro... Read more

Input files

This function cannot work without files in your workspace!

Parameters

Factor File Fit an analysis of variance model by a call to lm for each stratum according to the following formulas:

One way Anova- aov.ex1<-aov(Factor1~Factor2, data)

Two way Anova- aov.ex2<-aov(Factor1~Factor2*Factor3, data)

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Select Column in Factor File
(Factor3 - optional for two way Anova)

Permutational Multivariate Analysis of Variance Using Distance Matrices: This function (adonis) is used for analysis and partitioning of sums of squares using semi... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Single parameter - adon<-adonis(abundance_data~Factor1, ENV_data, permutations, distance)

Multiple parameter - adon<-adonis(abundance_data~Factor1*Factor2, ENV_data, permutations, distance)

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Permutations

Method:

Mantel Tests for Dissimilarity Matrices: This function mantel finds the Mantel statistic as a matrix correlation between two dissimilarity matrices. The significan... Read more

Input files

This function cannot work without files in your workspace!

Parameters

Permutations

Method:

Nonmetric Multidimensional Scaling: This funtion performs Nonmetric Multidimensional Scaling (NMDS) and tries to find a stable solution using several random starts... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Select Column in Factor File:

Parameters

Method:

trymax

autotransform

noshare

wascores

expand

trace

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

* info about transformation methods

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Factor File Numerous factors can be used to carry out Canonical Correspondence Analysis.

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Select Column in Factor File (Factor3)

Number of top ranked species

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

* info about transformation methods

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Number of top ranked species

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

* info about transformation methods

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Select Column in Indices File:

Number of top ranked species

2nd stage MDS: This function is computing inter-matrix correlations (‘similarities of similarity matrices’), using a correlation coefficient, to illustrate int... Read more

Input files

Select community data file(s) from loaded files

Select Transformation Method:

Check to transpose matrix

Parameters

Method:

Cor. Coeff.

trymax

autotransform

noshare

wascores

expand

trace

Alternative interactive visualization of the Nonmetric Multidimensional Scaling: This function (SUMMARIZEplot) performs a Nonmetric Multidimensional Scaling of the... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

* info about transformation methods

Check to transpose matrix

Parameters

Number of top ranked species

Method:

trymax_viz

Rank – Abundance or Dominance / Diversity Models: This function constructs rank – abundance or dominance / diversity or Whittaker plots and fit brokenstick, pr... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

Parameters

Select Column from community data matrix:

BIO-ENV: This function finds the best subset of environmental variables, so that the Euclidean distances of scaled environmental variables have the maximum (rank) ... Read more

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Method

index:

upto

trace

Similarity Percentages: This function attempts to assess the average percent contribution of individual variables to the dissimilarity between sampling units in a ... Read more

Input files

This function cannot work without files in your workspace!

Check to transpose matrix

This function cannot work without files in your workspace!

Select Column in Factor File:

Parameters

Permutations:

Trace

Input files

This function cannot work without files in your workspace!

Select Transformation Method:

Check to transpose matrix

Parameters

Factor File lm is used to fit linear models. It can be used to carry out regression according to the following formulas:

Single linear regression - fit<-lm(Factor1~Factor2, data)

Multiple linear regression- fit2<-lm(Factor1~Factor2+Factor3, data)

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Select Column in Factor File
(Factor3 - optional for multiple linear regression)

Parallelized function for calculation of taxonomic distances: This function is the parallelized implementation of the taxa2dist function. It should be used for med... Read more

Input files

This function cannot work without files in your workspace!

Parameters

varstep

check

Number of Processors

PostgreSQL function for calculation of taxonomic distances: This function is the PostgreSQL implementation of the taxa2dist function. It should be used for dataset... Read more

Input files

This function cannot work without files in your workspace!

Parameters

varstep

check

Number of Processors

Parallelized function for Analysis of Similarities: This function is the parallelized implementation of the anosim function.

Input files

This function cannot work without files in your workspace!

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Number of Processors

Select Column in Factor File:

Permutations:

Method:

Parallelized function for Mantel Tests for Dissimilarity Matrices: This function is the parallelized implementation of the mantel function.

Input files

This function cannot work without files in your workspace!

Parameters

Number of Processors

Permutations

Method:

Parallelized function for calculation of taxonomic distances and Indices of Taxonomic Diversity and Distinctness: This function is the parallelized implementation ... Read more

Input files

This function cannot work without files in your workspace!

Parameters

Number of Processors

varstep

Parallelized function for Permutational Multivariate Analysis of Variance Using Distance Matrices: This function is the parallelized implementation of the adonis f... Read more

Input files

This function cannot work without files in your workspace!

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Single parameter - adon<-adonis(abundance_data~Factor1, ENV_data, permutations, distance)

Multiple parameter - adon<-adonis(abundance_data~Factor1*Factor2, ENV_data, permutations, distance)

Select Column in Factor File (Factor1)

Select Column in Factor File (Factor2)

Permutations

Method:

Number of Processors

Input files

This function cannot work without files in your workspace!

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Number of Processors

Method

Index:

upto

trace

Input files

This function cannot work without files in your workspace!

Check to transpose matrix

This function cannot work without files in your workspace!

Parameters

Number of Processors

Select Column in Factor File:

Permutations:

trace

Input files

Select data in standard csv format from loaded files

Parameters

Abunfance File Reshape data to create an abundance file according the following equation: geotransformed<-cast(geo, Header1~Header2, Function_to_run, value=\"Header3\")

Header 1

Header 2

Header 3

Function to run

Factor File create a factor file by selecting from three availbale headers.

Factor Header 1

Factor Header 2

Factor Header 3

If you use RvLab in a publication, please cite: "Varsos C, Patkos T, Oulas A, Pavloudi C, Gougousis A, Ijaz U, Filiopoulou I, Pattakos N, Vanden Berghe E, Fernández-Guerra A, Faulwetter S, Chatzinikolaou E, Pafilis E, Bekiari C, Doerr M, Arvanitidis C (2016) Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab). Biodiversity Data Journal 4: e8357." https://doi.org/10.3897/BDJ.4.e8357