matrix.p: Matrix P

In SYNCSA: Analysis of Functional and Phylogenetic Patterns in Metacommunities

Description

Function to obtain a matrix containing phylogeny-weighted species composition. For more details, see syncsa.

Usage

matrix.p(comm, phylodist, notification = TRUE)

Arguments

comm	Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.
phylodist	Matrix containing phylogenetic distance between species. Must be a complete matrix (not a diagonal resemblance matrix).
notification	Logical argument (TRUE or FALSE) to specify if notifications for missing observations are to be shown (Default notification = TRUE).

Value

matrix.w	Standardized community matrix, where rows are communities and columns species. Row totals (communities) = 1.
matrix.q	Standardized matrix containing the degree of belonging of species in relation to each other. Row totals (species) = 1.
matrix.P	Phylogeny-weighted species composition matrix. Row totals (communities) = 1.

Note

IMPORTANT: Species sequence in the community data matrix MUST be the same as the one in the phylogenetic distance matrix. See organize.syncsa.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

References

Pillar, V.D.; Duarte, L.d.S. (2010). A framework for metacommunity analysis of phylogenetic structure. Ecology Letters, 13, 587-596.

See Also

syncsa, organize.syncsa, belonging, matrix.t, matrix.x

Examples

data(ADRS)
matrix.p(ADRS$community, ADRS$phylo)

Example output

$matrix.w
             Sp_1      Sp_2      Sp_3      Sp_4      Sp_5       Sp_6
Site_1  0.3333333 0.6666667 0.0000000 0.0000000 0.0000000 0.00000000
Site_2  0.0000000 0.0000000 0.0000000 0.0000000 0.3333333 0.66666667
Site_3  0.0000000 0.1428571 0.0000000 0.0000000 0.8571429 0.00000000
Site_4  0.4583333 0.1666667 0.0000000 0.0000000 0.3333333 0.04166667
Site_5  0.2750000 0.1250000 0.4250000 0.1750000 0.0000000 0.00000000
Site_6  0.3913043 0.2608696 0.0000000 0.0000000 0.2608696 0.08695652
Site_7  0.2307692 0.1794872 0.3333333 0.2564103 0.0000000 0.00000000
Site_8  0.3181818 0.3636364 0.0000000 0.0000000 0.1818182 0.13636364
Site_9  0.1794872 0.2307692 0.2564103 0.3333333 0.0000000 0.00000000
Site_10 0.2380952 0.4761905 0.0000000 0.0000000 0.0952381 0.19047619

$matrix.q
          Sp_1      Sp_2      Sp_3      Sp_4      Sp_5      Sp_6
Sp_1 0.3603012 0.3292163 0.3104825 0.0000000 0.0000000 0.0000000
Sp_2 0.3292163 0.3603012 0.3104825 0.0000000 0.0000000 0.0000000
Sp_3 0.3164101 0.3164101 0.3671798 0.0000000 0.0000000 0.0000000
Sp_4 0.0000000 0.0000000 0.0000000 0.4950730 0.3167818 0.1881452
Sp_5 0.0000000 0.0000000 0.0000000 0.3167818 0.4950730 0.1881452
Sp_6 0.0000000 0.0000000 0.0000000 0.2159205 0.2159205 0.5681591

$matrix.P
             Sp_1       Sp_2       Sp_3       Sp_4       Sp_5       Sp_6
Site_1  0.3395779 0.34993954 0.31048254 0.00000000 0.00000000 0.00000000
Site_2  0.0000000 0.00000000 0.00000000 0.24954091 0.30897131 0.44148778
Site_3  0.0470309 0.05147159 0.04435465 0.27152726 0.42434830 0.16126730
Site_4  0.2200074 0.21094100 0.19405159 0.11459062 0.17402102 0.08638836
Site_5  0.2747091 0.27004641 0.28024444 0.08663778 0.05543682 0.03292541
Site_6  0.2268699 0.22281538 0.20248861 0.10141442 0.14792517 0.09848649
Site_7  0.2477066 0.24611246 0.24977073 0.12694180 0.08122610 0.04824235
Site_8  0.2343563 0.23576924 0.21169264 0.08704039 0.11945697 0.11168445
Site_9  0.2217732 0.22336732 0.22152612 0.16502434 0.10559393 0.06271506
Site_10 0.2425557 0.24995682 0.22177324 0.07129740 0.08827752 0.12613937

SYNCSA documentation built on Jan. 11, 2020, 9:26 a.m.