![]() Object returned by organize.syncsa, the comm argument is used as an alternative way Organize.syncsa using, in this case only the argument comm. In this way the arguments comm, traits, phylodist, envir,Īs well as the arguments put.together and strata, can be specified them as normalĪrguments or by passing them with the object returned by the function Which the communities respond or ecosystem effects of the communities The ecological gradient of interest, which may be one or more factors to May be a mixture of binary and quantitative traits (continual and ordinal),īut not nominal ones (these should be expanded into binary traits) and (4) Phylogenetic pairwise dissimilarities of these species ( DF) (3) a set ofįunctional traits describing the species ( B), which Presences or abundances of species in a set of communities ( W) (2) the It requires data organized into the following matrices: (1) the Use of function organize.syncsa is not requered for run the functions, but ![]() Of the package, placing the matrices of community, traits, phylogenetic distance,Įnvironmental varibles and strata vector in the same order. The function organize.syncsa organizes the data for the functions The ame or matrix must be the same for all dataframe/matrices. Package SYNCSA requires that the species and community sequence in Other parameters for the respective functions. Notification of missing observations should to be shown (Default Logical argument (TRUE or FALSE) to specify if Tip: use parallel::detectCores() (Default parallel = NULL). Number of permutations in assessing significance. ![]() Strata named vector to specify restricting permutations within species Logical argument (TRUE or FALSE) to specify if pairwiseĭistances should be deleted in cases of missing observations (Default na.rm Same weight that one trait outside any group, in the way each group is consideredĪs unique trait (Default put.together = NULL). Method to be used for ordinal variables, see gowdis. Logical argument (TRUE or FALSE) to specify if ordinal variables are = TRUE the matrix with enviromental variables is subjected to centralizationĪnd standardization within each variable. If theĮnviromental variables are measured on different scales, the scale.envir Logical argument (TRUE or FALSE) to specify if theĮnvironmental variables are measured on different scales. Traits is not subjected to standardization, and Euclidean distance isĬalculated to determine the degree of belonging to the species. Standardization within each trait, and Gower Index is used to calculate theĭegree of belonging to the species, and if scale = FALSE the matrix of The same scale and the matrix T is not subjected to standardization.įurthermore, if scale = TRUE the matrix of traits is subjected to When scale = FALSE traits are measured on When scale = TRUE traitsĪre measured on different scales the the matrix T is subjected to Measured on different scales (Default Scale = TRUE). Logical argument (TRUE or FALSE) to specify if the traits are "binomial" or "chao" (Default dist = "euclidean"). "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , Vegdist: "manhattan", "euclidean", "canberra", "bray", "kulczynski", "spearman" or "kendall" (Default method = "pearson").ĭissimilarity index used for Mantel correlation, as accepted by Mantel correlation method, as accepted by cor: "pearson", Method to obtain the correlation, "mantel" or "procrustes" The same order as the one in the environmental data (Default checkdata = TRUE). Trait and in the phylodist matrices and if sampling units in the community data follows Sequence in the community data follows the same order as the one in the Logical argument (TRUE or FALSE) to check if species Must be a complete matrix, not a half diagonal matrix (Default phylodist = NULL).Įnvironmental variables for each community, with variables asĬolumns and sampling units as rows (Default envir = NULL). ![]() Matrix containing phylogenetic distance between species. See details.ĭata frame or matrix data of species described by traits, with traits asĬolumns and species as rows (Default traits = NULL). Traits, phylodist, envir and put.together must be null. When you use the class metacommunity.data the arguments This matrix can contain either presence/absence or abundance data.Īlternatively comm can be an object of class metacommunity.data, an alternative )Ĭommunity data, with species as columns and sampling units as Syncsa ( comm, traits = NULL, phylodist = NULL, envir = NULL, checkdata = TRUE, ro.method = "mantel", method = "pearson", dist = "euclidean", scale = TRUE, scale.envir = TRUE, ranks = TRUE, ord, put.together = NULL, na.rm = FALSE, strata = NULL, permutations = 999, parallel = NULL, notification = TRUE ) # S3 method for class 'syncsa' print ( x.
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