Help for package DAMOCLES

Type:

Package

Title:

Dynamic Assembly Model of Colonization, Local Extinction and Speciation

Version:

2.3

Date:

2020-08-12

Depends:

R (≥ 3.0)

Imports:

caper, ape, deSolve, matrixStats, expm, picante, Matrix, DDD (≥ 3.4), stats, methods, Hmisc

Suggests:

testthat (≥ 2.1.0)

Author:

Rampal S. Etienne & Alex L. Pigot

Maintainer:

Rampal S. Etienne <r.s.etienne@rug.nl>

License:

GPL-2

Description:

Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.

Encoding:

UTF-8

RoxygenNote:

7.1.1

NeedsCompilation:

Packaged:

2020-08-12 11:58:52 UTC; rampa

Repository:

CRAN

Date/Publication:

2020-08-12 14:22:11 UTC

Maximization of the loglikelihood under the DAMOCLES model

Description

This function computes the maximum likelihood estimates of the parameters of the DAMOCLES model for a given phylogeny and presence-absence data. It also outputs the corresponding loglikelihood that can be used in model comparisons.

Usage

DAMOCLES_ML(
  phy,
  pa,
  initparsopt,
  idparsopt = 1:length(initparsopt),
  parsfix = NULL,
  idparsfix = NULL,
  idparsequal = NULL,
  pars2 = c(0.001, 1e-04, 1e-05, 1000),
  optimmethod = "subplex",
  pchoice = 0,
  edgeTList = NULL,
  methode = "analytical",
  model = 0,
  verbose = FALSE
)

Arguments

phy

phylogeny in phylo format

pa

presence-absence table.
The first column contains the labels of the species (corresponding to the tip labels in the phylogeny.
The second column contains the presence (1) or absence (0) of species in the local community.

initparsopt

The initial values of the parameters that must be optimized

idparsopt

The ids of the parameters that must be optimized, e.g. 1:2 for extinction rate, and offset of immigration rate The ids are defined as follows:
id == 1 corresponds to mu (extinction rate)
id == 2 corresponds to gamma_0 (offset of immigration rate)
id == 3 corresponds to gamma_1 (parameter controlling decline in immigration rate with time)

parsfix

The values of the parameters that should not be optimized. See idparsfix.

idparsfix

The ids of the parameters that should not be optimized, e.g. c(1,3) if mu and gamma_1 should not be optimized, but only gamma_0. In that case idparsopt must be c(2). The default is to fix all parameters not specified in idparsopt.

idparsequal

The ids of the parameters that should be set equal to the first parameter of the same type.

pars2

Vector of settings:
pars2[1] sets the relative tolerance in the parameters

pars2[2] sets the relative tolerance in the function

pars2[3] sets the absolute tolerance in the parameters

pars2[4] sets the maximum number of iterations

optimmethod

Method used in optimization of the likelihood. Current default is 'subplex'. Alternative is 'simplex' (default of previous version)

pchoice

sets the p-value to optimize:
pchoice == 0 corresponds to the sum of p_0f + p_1f
pchoice == 1 corresponds to p_0f
pchoice == 2 corresponds to p_1f

edgeTList

list of edge lengths that need to be succesively pruned; if not specified, it will computed using compute_edgeTList

methode

method used to solve the ODE. Either 'analytical' for the analytical solution, 'Matrix' for matrix exponentiation using package Matrix or 'expm' using package 'expm' or any of the numerical solvers, used in deSolve.

model

model used. Default is 0 (standard null model). Other options are 1 (binary traits) 2 (trinary environmental trait) or 3 (diversity-dependent colonization - beta version)

verbose

Whether intermediate output should be printed. Default is FALSE.

Details

The output is a dataframe containing estimated parameters and maximum loglikelihood.

Value

mu

gives the maximum likelihood estimate of mu

gamma_0

gives the maximum likelihood estimate of gamma_0

gamma_1

gives the maximum likelihood estimate of gamma_1

loglik

gives the maximum loglikelihood

df

gives the number of estimated parameters, i.e. degrees of feedom

conv

gives a message on convergence of optimization; conv = 0 means convergence

Author(s)

Rampal S. Etienne

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

Phylogenetic community structure hypothesis test

Description

This function computes the maximum likelihood estimates of colonisation and local extinction rate for a given phylogeny and presence-absence data under the DAMOCLES model. These rate estimates are used to simulate null communities under the DAMOCLES model. Standardized effect size of mean nearest taxon distance (mntd), mean phylogentic distance (mpd) and loglikelihood are calculated For comparison, standardised effect sizes are also calculated relative to a "Random-Draw" null model i.e. presence absence randomised across tips

Usage

DAMOCLES_bootstrap(
  phy = ape::rcoal(10),
  pa = matrix(c(phy$tip.label, sample(c(0, 1), ape::Ntip(phy), replace = T)), nrow =
    ape::Ntip(phy), ncol = 2),
  initparsopt = c(0.1, 0.1),
  idparsopt = 1:length(initparsopt),
  parsfix = NULL,
  idparsfix = NULL,
  pars2 = c(0.001, 1e-04, 1e-05, 1000),
  pchoice = 0,
  runs = 999,
  estimate_pars = FALSE,
  conf.int = 0.95
)

Arguments

phy

phylogeny in phylo format

pa

initparsopt

The initial values of the parameters that must be optimized

idparsopt

parsfix

The values of the parameters that should not be optimized. See idparsfix.

idparsfix

The ids of the parameters that should not be optimized, e.g. c(1) if mu should not be optimized, but only gamma_0. In that case idparsopt must be c(2). The default is to fix the parameters not specified in idparsopt.

pars2

pchoice

sets which p-value to optimize and with which root state to simulate (default pchoice = 0)
pchoice == 0 correspond to optimizing sum of p_0f + p_1f, and simulating with an equal number of root states being 0 or 1
pchoice == 1 correspond to optimizing p_0f, and simulating with root state being 0
pchoice == 2 correspond to optimizing p_1f, and simulating with root state being 1

runs

the number null communities to generate.

estimate_pars

Whether to estimate parameters on the simulated datasets (default = FALSE).

conf.int

The width of the conifdence intervals calculated on bootstrapped parameter estimates

Details

The output is a list of two dataframes. The first dataframe, summary_table, contains the summary results. The second dataframe, null_community_data, contains decsriptive statistics for each null community.

Value

summary_table

mu gives the maximum likelihood estimate of mu and confidence intervals in brackets if estimate_pars = TRUE gamma_0 gives the maximum likelihood estimate of gamma_0 and confidence intervals in brackets if bootstrap=TRUE loglik gives the maximum loglikelihood df gives the number of estimated parameters, i.e. degrees of feedom conv gives a message on convergence of optimization; conv = 0 means convergence n.obs gives the number of species locally present in the observed community mntd.obs gives the MNTD of the observed community mpd.obs gives the MPD of the observed community runs gives the number of null communities simulated mntd.mean.RD mean of MNTD from null communities generated by a "Random Draw" model mntd.sd.RD standard deviation of MNTD from null communities generated by a "Random Draw" model mntd.obs.z.RD standardized effect size of MNTD compared to null communities generated by a "Random Draw" model (= -1*(mntd.obs - mntd.mean.RD)/ mntd.sd.RD) mntd.obs.rank.RD rank of observed MNTD compared to null communities generated by a "Random Draw" model mntd.obs.q.RD quantile of observed MNTD vs. null communities (= mntd.obs.rank.RD /runs + 1) mpd.mean.RD mean of MPD from null communities generated by a "Random Draw" model mpd.sd.RD standard deviation of MPD from null communities generated by a "Random Draw" model mpd.obs.z.RD standardized effect size of MPD compared to null communities generated by a "Random Draw" model (= -1*(mpd.obs - mpd.mean.RD)/ mpd.sd.RD) mpd.obs.rank.RD rank of observed MPD compared to null communities generated by a "Random Draw" model mpd.obs.q.RD quantile of observed MPD vs. null communities (= mpd.obs.rank.RD /runs + 1) n.mean.DAMOCLES mean number of species locally present in the null communities generated by DAMOCLES mntd.mean.DAMOCLES mean of MNTD from null communities generated by DAMOCLES mntd.sd.DAMOCLES standard deviation of MNTD from null communities generated by DAMOCLES mntd.obs.z.DAMOCLES standardized effect size of MNTD compared to null communities generated by DAMOCLES (= -1*(mntd.obs - mntd.mean.DAMOCLES)/ mntd.sd.DAMOCLES) mntd.obs.rank.DAMOCLES rank of observed MNTD compared to null communities generated by DAMOCLES mntd.obs.q.DAMOCLES quantile of observed MNTD vs. null communities (= mntd.obs.rank.DAMOCLES /runs + 1) mpd.mean.DAMOCLES mean of MPD from null communities generated by DAMOCLES mpd.sd.DAMOCLES standard deviation of MPD from null communities generated by DAMOCLES mpd.obs.z.DAMOCLES standardized effect size of MPD compared to null communities generated by DAMOCLES (= -1*(mpd.obs - mpd.mean.DAMOCLES)/ mpd.sd.DAMOCLES) mpd.obs.rank.DAMOCLES rank of observed MPD compared to null communities generated by DAMOCLES mpd.obs.q.DAMOCLES quantile of observed MPD vs. null communities (= mpd.obs.rank.DAMOCLES /runs + 1) loglik.mean.DAMOCLES mean of loglikelihoods from null communities generated by DAMOCLES loglik.sd.DAMOCLES standard deviation of loglikelihoods from null communities generated by DAMOCLES loglik.obs.z.DAMOCLES standardized effect size of loglikelihood compared to null communities generated by DAMOCLES (= -1*(loglik.obs - loglik.mean.DAMOCLES)/ loglik.sd.DAMOCLES) loglik.obs.rank.DAMOCLES rank of observed loglikelihood compared to null communities generated by DAMOCLES loglik.obs.q.DAMOCLES quantile of observed loglikelihoods vs. null communities (= loglik.obs.rank.DAMOCLES /runs + 1)

null_community_data

run gives the simulation run root.state.print gives the state of the ancestral species in the local community assumed in the simulation, i.e. present (1) or absent (0) n gives the number of species locally present in the observed community n.RD gives the number of species locally present in the null community generated by a "Random Draw" model mntd.RD gives the MNTD of the null community generated by a "Random Draw" model mpd.RD gives the MPD of the null community generated by a "Random Draw" model n.DAMOCLES gives the number of species locally present in the null community generated by DAMOCLES mntd.DAMOCLES gives the MNTD of the null community generated by DAMOCLES mpd.DAMOCLES gives the MPD of the null community generated by DAMOCLES loglik.DAMOCLES gives the maximum loglikelihood for the null community generated by DAMOCLES mu.DAMOCLES gives the maximum likelihood estimate of mu for the null community generated by DAMOCLES gamma_0.DAMOCLES gives the maximum likelihood estimate of gamma_0 for the null community generated by DAMOCLES

Author(s)

Rampal S. Etienne

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

Likelihood for DAMOCLES model

Description

Computes likelihood for the presence-absence data of species in a local community for a given phylogeny of species in the region.

Usage

DAMOCLES_loglik(
  phy,
  pa,
  pars,
  pchoice = 0,
  edgeTList = NULL,
  methode = "analytical",
  model = 0,
  Mlist = NULL,
  verbose = FALSE
)

Arguments

phy

phylogeny in phylo format

pa

presence-absence table with the first column the species labels and the second column the presence (1) or absence (0) of the species

pars

Vector of model parameters:
pars[1] corresponds to mu (extinction rate in local community)
pars[2] corresponds to gamma_0 in formula gamma(t) = gamma_0/(1 + gamma_1 * t) where gamma(t) is immigration rate into local community)
pars[3] corresponds to gamma_1 in formula gamma(t) = gamma_0/(1 + gamma_1 * t) where gamma(t) is immigration rate into local community)

pchoice

sets the p-value to optimize:
pchoice == 0 corresponds to the sum of p_0f + p_1f
pchoice == 1 corresponds to p_0f
pchoice == 2 corresponds to p_1f

edgeTList

list of edge lengths that need to be succesively pruned; if not specified, it will computed using compute_edgeTList

methode

model

model used. Default is 0 (standard null model). Other options are 1 (binary traits) 2 (trinary environmental trait) or 3 (diversity-dependent colonization - beta version)

Mlist

list of M matrices that can be specified when methode = 'analytical'. If set at NULL (default) and methode = 'analytical', Mlist will be computed.

verbose

Whether intermediate output should be printed. Default is FALSE.

Value

The loglikelihood

Author(s)

Rampal S. Etienne

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

Examples


  #TEST IT WORKS
  library(ape)
  phy = ape::rcoal(100)
  pars = c(0.5,0.1,0.1)
  pa = rbinom(100,c(0,1),0.5)
  pa = matrix(c(phy$tip.label,pa),nrow = length(phy$tip.label),ncol = 2)

  # - without a root edge
  loglik = DAMOCLES_loglik(phy,pa,pars)
  loglik

  # - with a root edge
  phy$root.edge = 2
  loglik = DAMOCLES_loglik(phy,pa,pars)
  loglik

Simulating DAMOCLES

Description

Simulates DAMOCLES

Usage

DAMOCLES_sim(
  phy,
  gamma_0,
  gamma_td,
  mu,
  sigma,
  psiBranch,
  psiTrait,
  z,
  phi,
  traitOpt,
  br0,
  br_td,
  nTdim,
  root.state,
  root.trait.state,
  plotit = FALSE,
  keepExtinct = FALSE
)

Arguments

phy

phylogeny in phylo format

gamma_0

initial per lineage rate of immigration (gamma)

gamma_td

time dependency in gamma

mu

per lineage rate of local extinction

sigma

probability of local (i.e. in-situ) speciation

psiBranch

phylogenetic distance at which gamma is half gamma_0

psiTrait

trait distance at which gamma is half gamma_0

z

shape of increase in gamma with increasing trait or phylogenetic distance

phi

rate of decline in gamma with distance from trait optima

traitOpt

trait value at which gamma = gamma_0

br0

Brownian rate parameter

br_td

rate of temporal decline in Brownian rate parameter

nTdim

number of independent trait dimensions

root.state

geographic state of ancestor i.e. present (1) or absent(0)

root.trait.state

trait value of ancestor

plotit

whether to plot the phylogeny and timing of immigration/local extinction events

keepExtinct

whether to retain data for extinct lineages

Value

A list of two tables. The first table contains the following columns: The first column contains the vector of tip labels in the phylogeny The last column contains the presence (1) or absence (0) of the species The second table has dimensions d x N where d is the number of trait dimensions and N is the number of species. It contains the trait values.

Author(s)

Alex L. Pigot

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

Examples


#create random phylogeny
library(ape)
phy = ape::rcoal(10)
		
#run DAMOCLES		
out = DAMOCLES_sim(
  phy,
  gamma_0 = 1.5,
  gamma_td =0,
  mu = 0,
  sigma = 0,
  psiBranch = 0,
  psiTrait = 0,
  z = 10,
  phi = 0,
  traitOpt = 1,
  br0 = 0.1,
  br_td = -0.1,
  nTdim = 2,
  root.state = 1,
  root.trait.state = 0,
  plotit = FALSE,
  keepExtinct = FALSE
  )

#the output consists of a list		
patable = out[[1]] # the first element is the presence absence table
traits = out[[2]] # this is a matrix of traits values

#show presence/absence on the tree
patable$col = rep("black",dim(patable)[1])
patable$col[which(patable$state == 1)] = "red"
plot(phy,tip.col = patable$col)

Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu

Description

A list with two elements.
. phy is a dated molecular phylogeny for 94 species of New World Primates extracted from the maximum likelihood tree (AUTOsoft dated) of Springer et al. (2012). 1 time unit = 100 million years.
pa is the presence-absence matrix of NW Primates in Manu from Solari et al. (2006). The first column indicate the species tip labels and the second column indicates presence (1) and absence (0).

Format

A list with two elements. The first element (phy) is the primate phylogeny in nexus format. The second element (pa) is the presence-absence matrix with 94 rows and 2 columns.

Source

Solari, S., Pacheco, V., Luna, L., Velazco, P.M. & Patterson, B.D. 2006 Mammals of the manu biosphere reserve. Fieldiana Zoology 110, 13-22.
Springer, M.S., Meredith, R.W., Gatesy, J., Emerling, C.A., Park, J., Rabosky, D.L., Stadler, T., Steiner, C., Ryder, O.A., Janecka, J.E., et al. 2012 Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. Plos One 7. (doi:ARTN e49521 DOI 10.1371/journal.pone.0049521).

Maximization of the loglikelihood under the DAMOCLES model

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Phylogenetic community structure hypothesis test

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Likelihood for DAMOCLES model

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

Simulating DAMOCLES

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu

Description

Format

Source

See Also