💖 Fits an Environmental Vector or Factor onto an Ordination adonis Permutational Multivariate Analysis of Variance Using

scores Get Species or Site Scores from an Ordination

adonis Permutational Multivariate Analysis of Variance Using

Clarke and Ainsworth’s BIOENV and BVSTEP and BIOBIO etc

Species Accumulation Curves specaccum vegan

r How are envfit results created Stack Overflow

radfitresult Alternative Rank Abundance Fitting Results

R Variance partitioning for a latent variable model

CCorA Canonical Correlation Analysis R Package Documentation

varpart Partition the Variation of Community Matrix by 2 3

vegetarian package RDocumentation

decostand function RDocumentation

radfit function RDocumentation

Vegan an introduction to ordination R Package Documentation


11 oct. 2024 · The function partitions sums of squares of a multivariate data set, and they are directly analogous to MANOVA (multivariate analysis of variance). McArdle and Anderson (2024) and Anderson (2024) refer to the method as “permutational MANOVA” (formerly “nonparametric MANOVA”). Further, as the inputs are linear predictors, and a response matrix of an arbitrary number of columns, they are. Produces a plot or biplot of the results of a call to rda. It is common for the "species" scores in a PCA to be drawn as biplot arrows that point in the direction of increasing values for that variable. The biplot.rda function provides a wrapper to plot.cca to allow the easy production of such a plot. Function radfit fits all models either to a single site or to all rows of a data frame or a matrix. When fitted to a single site, the function returns an object of class "radfit" with items. y (observed values), family, and models. which is a list of fitted "radline" models. When applied for a data frame or matrix, radfit function returns an. Function CCorA returns a list containing the following elements: Pillai's trace statistic = sum of the canonical eigenvalues. Canonical eigenvalues. They are the squares of the canonical correlations. Canonical correlations. Bimultivariate redundancy coefficients (R-squares) of RDAs of Y|X and X|Y. RDA.Rsquares adjusted for n and the number of. The veganpackage contains all common ordination methods: Principal compo-nent analysis (function rda, or prcompin the base R), correspondence analysis 1 (cca), detrended correspondence analysis (decorana) and a wrapper for non- metric multidimensional sca. 23 août 2009 · The core of the vegetarian library is the d function, which calculates the basic alpha, beta, and gamma diversity 'numbers equivalents' from community data. H uses d to calculate the standard diversity indices. vegetarian (version 1.2) Jost Diversity Measures for Community Data Description This package computes diversity for community data sets using the methods outlined by Jost (2006, 2007). library (vegetarian) help (vegetarian) Run Any scripts or data that you put into this service are public. vegetarian documentation built on May 1, 2019, 8:01 p.m. Note that we can't provide technical support on individual packages. You should contact the package authors for that. Tweet to @rdrrHQ GitHub issue tracker ian@mutexlabs.com. 11 oct. 2024 · Community Ecology Package: Ordination, Diversity and Dissimilarities Description. The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Description Function specaccum finds species accumulation curves or the number of species for a certain number of sampled sites or individuals. Usage specaccum (comm, method = "exact", permutations = 100, conditioned =TRUE, gamma = "jack1", w = NULL, subset, ). This function provides an alternative method of obtaining species accumulation results as provided by specaccum and accumresult. Balanced sampling is achieved by randomly selecting the same number of sites from each stratum. The number of sites selected from each stratum is determined by reps. Description. Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples. Usage. specaccum.psr(samp, tree, permutations = 100, method = "random", ) Arguments. samp. Community data matrix. tree. A phylo tree object or a phylogenetic covariance matrix. 24 mai 2019 · Description Function specaccum finds species accumulation curves or the number of species for a certain number of sampled sites or individuals. Usage 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 specaccum (comm, method = "exact", permutations = 100, conditioned = TRUE, gamma = "jack1", w = NULL, subset, ). Function specaccum finds species accumulation curves or the number of species for a certain number of sampled sites or individuals. Usage specaccum ( comm , method = "exact" , permutations = 100 , conditioned = TRUE , gamma = "jack1" , w = NULL , subset ,. Function envfit finds vectors or factor averages of environmental variables. Function plot.envfit adds these in an ordination diagram. If X is a data.frame , envfit uses factorfit for factor variables and vectorfit for other variables. If X is a matrix or a vector, envfit uses only vectorfit. Description. The function fits environmental vectors or factors to a Co-CA ordination. The projections of points onto vectors have maximum correlation with corresponding environmental variables, and the factors show the averages of factor levels. Examples. Run this code. # NOT RUN { data (varespec, varechem) ord. 31 mars 2024 · I have a question regarding how to recreate the results from the envfit () function in the vegan package. Here is an example of envfit () being used with an ordination and an environmental vector. data (varespec) data (varechem) ord. Function envfit finds vectors or factor averages of environmental variables. Function plot.envfit adds these in an ordination diagram. If X is a data.frame, envfit uses factorfit for factor variables and vectorfit for other variables. If X is a matrix or a vector, envfit uses only vectorfit. Description The function partitions the variation in community data or community dissimilarities with respect to two, three, or four explanatory tables, using adjusted R 2 in redundancy analysis ordination (RDA) or distance-based redundancy analysis. If response is a single vector, partitioning is by partial regression. Description. This function performs variation partitioning (Borcard et al. 1992) among two factors (e.g. Ribas et al. 2006) or three factors (e.g. Real et al. 2024) for either linear regression models (LM) or generalized linear models (GLM). Vector containing the proportion of variance (in the linear predictor) for each response, which is explained by the covariate matrix. varpart.lv. Vector containing the proportion of variance (in the linear predictor) for each response, which is explained by the latent variables. varpart.row. 2 mai 2019 · Introduction to ordination in vegan Partition of Variation add1.cca: Add or Drop Single Terms to a Constrained Ordination Model adipart: Additive Diversity Partitioning and Hierarchical Null Model adonis: Permutational Multivariate Analysis of Variance Using Analysis of Similarities. varPart: Variation partitioning. Description. This function performs variation partitioning (Borcard et al. 1992) among two factors (e.g. Ribas et al. 2006) or three factors (e.g. Real et al. 2024) for either multiple linear regression models (LM) or generalized linear models (GLM). Usage. Function ordiplot3d displays three-dimensional ordination graphics using scatterplot3d. Function ordirgl displays three-dimensional dynamic ordination graphs which can be rotated and zoomed into using rgl package. Both work with all ordination results form vegan and all ordination results known by scores function. Description. Function ordiplot3d displays three-dimensional ordination graphics using scatterplot3d. Function works with all ordination results form vegan and all ordination results known by scores function. It returns invisibly an object of class ordiplot which can be used by identify.ordiplot to label selected sites or species, or constraints in cca and rda. The function can handle output from several alternative ordination methods. For cca, rda and decorana it uses their plot method with option type = "points". 24 mai 2019 · Function ordiplot3d displays three-dimensional ordination graphics using scatterplot3d. Function ordirgl displays three-dimensional dynamic ordination graphs which can be rotated and zoomed into using rgl package. Both work with all ordination results form vegan and all ordination results known by scores function. 14 août 2024 · The ordiplot3d() function uses scatterplot3d() from the scatterplot3d package and that function gives you what you need. First we have to capture the output from ordiplot3d() because that contains the function we need to plot the labels: out. The scatterplot3d package draws static 3D graphics, and vegan3d provides an interface for ordination and clustering objects. You must consult the scatterplot3d documentation for configuring your plots. Function ordiplot3d is similar to ordirgl or ordiplot and draws a static 3D plot in the standard graphical device. Description. Function finds the best subset of environmental variables, so that the Euclidean distances of scaled environmental variables have the maximum (rank) correlation with community dissimilarities. 2 mai 2019 · vegan documentation built on May 2, 2019, 5:51 p.m. Function finds the best subset of environmental variables, so that the Euclidean distances of scaled environmental variables have the maximum (rank) correlation with community dissimilarities. 24 mai 2019 · Details The function calculates a community dissimilarity matrix using vegdist. Then it selects all possible subsets of environmental variables, scale s the variables, and calculates Euclidean distances for this subset using dist. env.profile returns a list with the following components: size the number of chains that can be stored in the hash table, nchains the number of non-empty chains in the table (as reported by HASHPRI ), and counts an integer vector giving the length of each chain (zero for empty chains). 30 juin 2024 · The R package “vegan” contains a version of Clarke and Ainsworth's (1993) BIOENV analysis allowing for the comparison of distance/similarity matrices between two sets of data having either samples or variables in common. Value. Returns the standardized data frame, and adds an attribute. "decostand" giving the name of applied standardization. "method" and attribute "parameters" with appropriate transformation parameters. 24 févr. 2024 · decostand(x) returns a character vector depending on the number of methods. decostand(x). 2 mai 2019 · The function offers following standardization methods for community data: total: divide by margin total (default MARGIN = 1). max: divide by margin maximum (default MARGIN = 2). freq: divide by margin maximum and multiply by the number of non-zero items, so that the average of non-zero entries is one (Oksanen 1983; default MARGIN = 2). The function provides some popular (and effective) standardization methods for community ecologists. Usage decostand(x, method, MARGIN, range.global, logbase = 2, na.rm=FALSE, ) wisconsin(x). argument test = "permutation" the functions will add test results from anova.cca. Function drop1.cca will call anova.cca with argument by = "margin". Function add1.cca will implement a test for single term additions that is not directly available in anova.cca. Functions are used implicitly in step, ordiR2stepand ordistep. The deviance.ccaand. Description This function wraps several commonly-used ordination methods. The type of ordination depends upon the argument to method. Try ordinate ("help") or ordinate ("list") for the currently supported method options. Usage ordinate (physeq, method = "DCA", distance = "bray", formula = NULL, ) Arguments physeq (Required). Description Function performs a singular value decomposition of ordinary least squares (OLS) or generalized least squares (GLS) residuals, aligned to an alternative matrix, plus projection of data onto vectors obtained. Usage ordinate ( Y, A = NULL, Cov = NULL, transform. = TRUE, scale. = FALSE, tol = NULL, rank. = NULL, newdata = NULL ). 21 oct. 2024 · This is a convenience function to fit an ordination model to a data object, wrap the result as a tbl_ord, and annotate this output with metadata from the model and possibly from the data. Usage ordinate(x, model, ) ## Default S3 method: ordinate(x, model, ) ## S3 method for class 'array' ordinate(x, model, ) ## S3 method for. This is a convenience function to fit an ordination model to a data object, wrap the result as a tbl_ord, and annotate this output with metadata from the model and possibly from the data. Usage ordinate(x, model, ) ## Default S3 method: ordinate(x, model, ) ## S3 method for class 'array' ordinate(x, model, ) ## S3 method for class. Many different classes of ordination are defined by R packages. Ordination classes currently supported/created by the ordinate function are supported here. There is no default, as the expectation is that the ordination will be performed and saved prior to calling this plot function. type. (Optional). 4 nov. 2024 · This function wraps several commonly-used ordination methods. The type of ordination depends upon the argument to method . Try ordinate("help") or ordinate("list") for the currently supported method options. Proper scoring rules for Poisson or negative binomial predictions of count data are described in Czado et al. (2009). The following scores are implemented: logarithmic score ( logs ), ranked probability score ( rps ), Dawid-Sebastiani score ( dss ), squared error score ( ses ). type. "z" calculates normal scores (differences between each value and the mean divided by sd), "t" calculates t-Student scores (transformed by (z*sqrt (n-2))/sqrt (z-1-t^2) formula, "chisq" gives chi-squared scores (squares of differences between values and mean divided by variance. Generic functions for calculating the Continuous Ranked Probability Score and the Logarithmic Score of R objects. scoringRules provides default methods ( crps.numeric , logs.numeric ) to calculate scores of forecasts that are members of families of parametric distributions. Description This function computes factor scores by various methods. The function will acceptan an object of class faMain or, alternatively, user-input factor pattern (i.e., Loadings) and factor correlation ( Phi) matrices. Usage faScores ( X = NULL, faMainObject = NULL, Loadings = NULL, Phi = NULL, Method = "Thurstone" ) Arguments Details. Elasticsearch uses Lucene under the hood, so the scoring is based on Lucene’s Practical Scoring Function which brings together some models like the TF-IDF, Vector Space Model and Boolean Model to score the document. If you want to lean more about how that function is used in Elasticsearch, you can check out this section of elastic.co guide. Description. The varespec data frame has 24 rows and 44 columns. Columns are estimated cover values of 44 species. The variable names are formed from the scientific names, and are self explanatory for anybody familiar with the vegetation type. October 11th, 2024 Functions in vegan (2.6-4) adonis Permutational Multivariate Analysis of Variance Using Distance Matrices adipart Additive Diversity Partitioning and Hierarchical Null Model Testing MDSrotate Rotate First MDS Dimension Parallel to an External Variable BCI Barro Colorado Island Tree Counts CCorA Canonical Correlation Analysis. Examples data (varespec) data (varechem) The varespec data frame has 24 rows and 44 columns. Columns are estimated cover values of 44 species. The variable names are formed from the scientific names, and are self explanatory for anybody familiar with the vegetation type.