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Convert rectangular pairwise matrices to triangular matrices

Source: R/rectangular_to_triangular.R
rectangular_to_triangular.Rd

rectangular_to_triangular converts rectangular pairwise matrices as those output by many PhenotypeSpace functions into triangular pairwise matrices.

Usage

rectangular_to_triangular(X, distance = TRUE, symmetric = TRUE)

Arguments

X

Data frame containing three columns. The first two columns must contain group labels which will appear as rows (1 column) and column names (2 column) in the output triangular matrix. The third column (and fourth column if symmetric = FALSE) must have the numeric values to be included in the output triangular matrix.

distance

Logical argument to control if the input data contains pairwise distances (dissimilarities) or similarities. If TRUE then diagonal values are filled with 0, otherwise they are filled with 1. Note that diagonal values can be set with diag.

symmetric

Logical argument to define if values are duplicated on both off-diagonal triangles (a symmetric triangular matrix, symmetric = TRUE, default) or each triangle is filled with values from different columns (a non-symmetric triangular matrix, symmetric = FALSE). In the latter the upper triangle is filled with the first column and the lower triangle with the second column. In this case, a fourth column with numeric values should be supplied.

Value

A pairwise triangular matrix in which labels from the first group column in 'X' are shown in the columns and labels from the second group are shown in the rows. If symmetric = FALSE the same information is shown below and above the diagonal.

Details

The function converts rectangular pairwise matrices as those output by many PhenotypeSpace functions into triangular pairwise matrices. It takes a data frame in which each observation (row) contains the pairwise value and related labels of the 'groups' being compared. The first two columns must contain group labels which will appear as rows (1 column) and column names (2 column) in the output triangular matrix. The third column (and fourth column if symmetric = FALSE) must have the numeric values to be included in the output triangular matrix.

References

Araya-Salas, M, & K. Odom. 2022, PhenotypeSpace: an R package to quantify and compare phenotypic trait spaces R package version 0.1.0.

See also

distance_to_rectangular, binary_triangular_matrix

Author

Marcelo Araya-Salas marcelo.araya@ucr.ac.cr)

Examples

{
# load data
data("example_space")

# get proportion of space that overlaps 
prop_overlaps <- space_similarity(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "proportional.overlap")

# get symmetric triangular matrix
rectangular_to_triangular(prop_overlaps)

# get minimum convex polygon overlap for each group (non-symmetric)
mcp_overlaps <- space_similarity(
 formula = group ~ dimension_1 + dimension_2,
 data = example_space,
 method = "mcp.overlap")

# get a non-symmetric triangular matrix
rectangular_to_triangular(mcp_overlaps, symmetric = FALSE)
}
#>            G1        G2        G3        G4        G5
#> G1 0.00000000 0.0000000 0.6043801 0.0000000 0.0000000
#> G2 0.00000000 0.0000000 1.0000000 0.0000000 0.0000000
#> G3 0.05339738 0.1419746 0.0000000 0.0000000 0.0000000
#> G4 0.00000000 0.0000000 0.0000000 0.0000000 0.4057546
#> G5 0.00000000 0.0000000 0.0000000 0.2076138 0.0000000