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5 dni temu · Comprehend which libraries are required for analysis of the taxonomy of metagenomes. Create and manage a Phyloseq object.
4 dni temu · Quick index search. Sample-distance and similarity matrices. Relationship/covariance. --make-rel ['cov'] ['meanimpute'] [ {square | square0 | triangle}] [ {zs | bin | bin4}] --make-rel is the primary interface to PLINK's genetic relationship matrix and covariance matrix calculator.
11 cze 2024 · This package follows the general approach to phylogenetic methods as used by the package phylolm (this package is used for model fitting “under the hood”). This means in particular that you line up your phylogenetic tree and data by assigning the tip labels as the row names of your data.frame.
20 cze 2024 · Details. Implementation of the phylogenetic diversity measures is based on the PhyloMeasures package which is much faster than corresponding functions from picante package. MNTD index sometimes is also reffered as MNND (mean nearest neighbour distance).
22 cze 2024 · Description. This function performs phylogenetic PCA following Revell (2009). Usage. phyl.pca(tree, Y, method="BM", mode="cov", ...) ## S3 method for class 'phyl.pca' biplot(x, ...) scores(object, ...) ## S3 method for class 'phyl.pca' scores(object, ...) as.princomp(x, ...) as.prcomp(x, ...) Arguments. Details.
23 cze 2024 · Computes a neighborNet from a distance matrix Description. Computes a neighborNet, i.e. an object of class networx from a distance matrix. Usage neighborNet(x, ord = NULL) Arguments
4 dni temu · Quick index search. Linkage disequilibrium. All of the following calculations only consider founders. If your dataset has a shortage of them, PLINK 1.9 --make-founders may come in handy.
