Title: | Interface to 'Phylocom' |
---|---|
Description: | Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more. |
Authors: | Jeroen Ooms [aut],
Scott Chamberlain [aut] |
Maintainer: | Luna Luisa Sanchez Reyes <[email protected]> |
License: | BSD_2_clause + file LICENSE |
Version: | 0.3.4 |
Built: | 2024-08-29 22:56:39 UTC |
Source: | https://github.com/ropensci/phylocomr |
phylocomr
gives you access to Phylocom, specifically the
Phylocom C library (https://github.com/phylocom/phylocom/),
licensed under BSD 2-clause
(http://www.opensource.org/licenses/bsd-license.php)
This package isn't doing system calls to a separately installed Phylocom instance - but actually includes Phylocom itself in the package.
Phylocom is usually used either on the command line or through the R package picante, which has duplicated some of the Phylocom functionality.
In terms of performance, some functionality will be faster here than
in picante
, but the maintainers of picante
have re-written some
Phylocom functionality in C/C++, so performance should be similar in
those cases.
As a convenience you can pass ages, sample and trait data.frame's, and
phylogenies as strings, to phylocomr
functions. However, phylocomr
has to write these data.frame's/strings to disk (your computer's
file system) to be able to run the Phylocom code on them. Internally,
phylocomr
is writing to a temporary file to run Phylocom code, and
then the file is removed.
In addition, you can pass in files instead of data.frame's/strings. These are not themselves used. Instead, we read and write those files to temporary files. We do this for two reasons. First, Phylocom expects the files its using to be in the same directory, so if we control the file paths that becomes easier. Second, Phylocom is case sensitive, so we simply standardize all taxon names by lower casing all of them. We do this case manipulation on the temporary files so that your original data files are not modified.
ecovolve()
/ph_ecovolve()
- interface to ecovolve
executable,
and a higher level interface
phylomatic()
/ph_phylomatic()
- interface to phylomatic
executable, and a higher level interface
phylocom()
- interface to phylocom
executable
ph_aot()
- higher level interface to aot
ph_bladj()
- higher level interface to bladj
ph_comdist()
/ph_comdistnt()
- higher level interface to comdist
ph_comstruct()
- higher level interface to comstruct
ph_comtrait()
- higher level interface to comtrait
ph_pd()
- higher level interface to Faith's phylogenetic diversity
Scott Chamberlain
Jeroen Ooms
Executables
ecovolve(args = "--help", intern = FALSE) phylocom(args = "help", intern = FALSE) phylomatic(args = "--help", intern = FALSE)
ecovolve(args = "--help", intern = FALSE) phylocom(args = "help", intern = FALSE) phylomatic(args = "--help", intern = FALSE)
args |
a character vector of arguments to command. |
intern |
capture output as character vector. Default: |
ecovolve() phylocom() phylomatic()
ecovolve() phylocom() phylomatic()
AOT conducts univariate and bivariate tests of phylogenetic signal and trait correlations, respectively, and node-level analyses of trait means and diversification.
ph_aot( traits, phylo, randomizations = 999, trait_contrasts = 1, ebl_unstconst = FALSE )
ph_aot( traits, phylo, randomizations = 999, trait_contrasts = 1, ebl_unstconst = FALSE )
traits |
(data.frame/character) trait data.frame or path to traits file. required. See Details. |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
randomizations |
(numeric) number of randomizations. Default: 999 |
trait_contrasts |
(numeric) Specify which trait should be used as 'x' variable for contrasts. Default: 1 |
ebl_unstconst |
(logical) Use equal branch lengths and unstandardized
contrasts. Default: |
See phylocomr-inputs for expected input formats
a list of data.frames
In the traits
table, if you're passing in a file, the names in the
first column must be all lowercase; if not, we'll lowercase them for you.
If you pass in a data.frame, we'll
lowercase them for your. All phylo tip/node labels are also lowercased
to avoid any casing problems
## Not run: traits_file <- system.file("examples/traits_aot", package = "phylocomr") phylo_file <- system.file("examples/phylo_aot", package = "phylocomr") # from data.frame traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr") traits <- read.table(text = readLines(traitsdf_file), header = TRUE, stringsAsFactors = FALSE) phylo_str <- readLines(phylo_file) (res <- ph_aot(traits, phylo = phylo_str)) # from files traits_str <- paste0(readLines(traits_file), collapse = "\n") traits_file2 <- tempfile() cat(traits_str, file = traits_file2, sep = '\n') phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (res <- ph_aot(traits_file2, phylo_file2)) ## End(Not run)
## Not run: traits_file <- system.file("examples/traits_aot", package = "phylocomr") phylo_file <- system.file("examples/phylo_aot", package = "phylocomr") # from data.frame traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr") traits <- read.table(text = readLines(traitsdf_file), header = TRUE, stringsAsFactors = FALSE) phylo_str <- readLines(phylo_file) (res <- ph_aot(traits, phylo = phylo_str)) # from files traits_str <- paste0(readLines(traits_file), collapse = "\n") traits_file2 <- tempfile() cat(traits_str, file = traits_file2, sep = '\n') phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (res <- ph_aot(traits_file2, phylo_file2)) ## End(Not run)
Bladj take a phylogeny and fixes the root node at a specified age, and fixes other nodes you might have age estimates for. It then sets all other branch lengths by placing the nodes evenly between dated nodes, and between dated nodes and terminals (beginning with the longest 'chains').
ph_bladj(ages, phylo)
ph_bladj(ages, phylo)
ages |
(data.frame/character) ages data.frame, or path to an ages file. required. column names do not matter, and are discarded anyway. the first column must be the node names, and the second column the node ages. See Details. |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
See phylocomr-inputs for expected input formats
newick string with attributes for where ages and phylo files used are stored
A few issues to be aware of:
the ages table must have a row for the root node with an age estimate. bladj will not work without that. We attempt to check this but can only check it if you pass in a phylo object; there's no easy way to parse a newick string without requiring ape
bladj is case sensitive. internally we lowercase all tip and node labels and taxon names in your ages file to avoid any case sensitivity problems
## Not run: ages_file <- system.file("examples/ages", package = "phylocomr") phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr") # from data.frame ages_df <- data.frame( a = c('malpighiales','eudicots','ericales_to_asterales','plantaginaceae', 'malvids', 'poales'), b = c(81, 20, 56, 76, 47, 71) ) phylo_str <- readLines(phylo_file) (res <- ph_bladj(ages = ages_df, phylo = phylo_str)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = res)) } # from files ages_file2 <- file.path(tempdir(), "ages") write.table(ages_df, file = ages_file2, row.names = FALSE, col.names = FALSE, quote = FALSE) phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (res <- ph_bladj(ages_file2, phylo_file2)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = res)) } # using a ape phylo phylogeny object x <- read.tree(text = phylo_str) if (requireNamespace("ape")) { library(ape) plot(x) } (res <- ph_bladj(ages_file2, x)) if (requireNamespace("ape")) { library(ape) tree <- read.tree(text = res) plot(tree) } ## End(Not run)
## Not run: ages_file <- system.file("examples/ages", package = "phylocomr") phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr") # from data.frame ages_df <- data.frame( a = c('malpighiales','eudicots','ericales_to_asterales','plantaginaceae', 'malvids', 'poales'), b = c(81, 20, 56, 76, 47, 71) ) phylo_str <- readLines(phylo_file) (res <- ph_bladj(ages = ages_df, phylo = phylo_str)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = res)) } # from files ages_file2 <- file.path(tempdir(), "ages") write.table(ages_df, file = ages_file2, row.names = FALSE, col.names = FALSE, quote = FALSE) phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (res <- ph_bladj(ages_file2, phylo_file2)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = res)) } # using a ape phylo phylogeny object x <- read.tree(text = phylo_str) if (requireNamespace("ape")) { library(ape) plot(x) } (res <- ph_bladj(ages_file2, x)) if (requireNamespace("ape")) { library(ape) tree <- read.tree(text = res) plot(tree) } ## End(Not run)
Outputs the phylogenetic distance between samples, based on phylogenetic distances of taxa in one sample to the taxa in the other
ph_comdist( sample, phylo, rand_test = FALSE, null_model = 0, randomizations = 999, abundance = TRUE ) ph_comdistnt( sample, phylo, rand_test = FALSE, null_model = 0, randomizations = 999, abundance = TRUE )
ph_comdist( sample, phylo, rand_test = FALSE, null_model = 0, randomizations = 999, abundance = TRUE ) ph_comdistnt( sample, phylo, rand_test = FALSE, null_model = 0, randomizations = 999, abundance = TRUE )
sample |
(data.frame/character) sample data.frame or path to a sample file |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
rand_test |
(logical) do you want to use null models?
Default: |
null_model |
(integer) which null model to use. See Details. |
randomizations |
(numeric) number of randomizations. Default: 999 |
abundance |
(logical) If |
See phylocomr-inputs for expected input formats
data.frame or a list of data.frame's if use null models
0 - Phylogeny shuffle: This null model shuffles species labels across the entire phylogeny. This randomizes phylogenetic relationships among species.
1 - Species in each sample become random draws from sample pool: This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species actually occurring in at least one sample. Thus, species in the phylogeny that are not actually observed to occur in a sample will not be included in the null communities
2 - Species in each sample become random draws from phylogeny pool: This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species in the phylogeny pool. All species in the phylogeny will have equal probability of being included in the null communities. By changing the phylogeny, different species pools can be simulated. For example, the phylogeny could include the species present in some larger region.
3 - Independent swap: The independent swap algorithm (Gotelli and Entsminger, 2003); also known as ‘SIM9’ (Gotelli, 2000) creates swapped versions of the sample/species matrix.
In the sample
table, if you're passing in a file, the names in the
third column must be all lowercase; if not, we'll lowercase them for you.
If you pass in a data.frame, we'll lowercase them for your. All phylo
tip/node labels are also lowercased to avoid any casing problems
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_comdist(sample = sampledf, phylo = phylo_str) ph_comdistnt(sample = sampledf, phylo = phylo_str) ph_comdist(sample = sampledf, phylo = phylo_str, rand_test = TRUE) ph_comdistnt(sample = sampledf, phylo = phylo_str, rand_test = TRUE) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() cat(phylo_str, file = pfile2, sep = '\n') ph_comdist(sample = sfile2, phylo = pfile2) ph_comdistnt(sample = sfile2, phylo = pfile2) ph_comdist(sample = sfile2, phylo = pfile2, rand_test = TRUE) ph_comdistnt(sample = sfile2, phylo = pfile2, rand_test = TRUE)
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_comdist(sample = sampledf, phylo = phylo_str) ph_comdistnt(sample = sampledf, phylo = phylo_str) ph_comdist(sample = sampledf, phylo = phylo_str, rand_test = TRUE) ph_comdistnt(sample = sampledf, phylo = phylo_str, rand_test = TRUE) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() cat(phylo_str, file = pfile2, sep = '\n') ph_comdist(sample = sfile2, phylo = pfile2) ph_comdistnt(sample = sfile2, phylo = pfile2) ph_comdist(sample = sfile2, phylo = pfile2, rand_test = TRUE) ph_comdistnt(sample = sfile2, phylo = pfile2, rand_test = TRUE)
Calculates mean phylogenetic distance (MPD) and mean nearest phylogenetic taxon distance (MNTD; aka MNND) for each sample, and compares them to MPD/MNTD values for randomly generated samples (null communities) or phylogenies.
ph_comstruct( sample, phylo, null_model = 0, randomizations = 999, swaps = 1000, abundance = TRUE )
ph_comstruct( sample, phylo, null_model = 0, randomizations = 999, swaps = 1000, abundance = TRUE )
sample |
(data.frame/character) sample data.frame or path to a sample file |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
null_model |
(integer) which null model to use. See Details. |
randomizations |
(numeric) number of randomizations. Default: 999 |
swaps |
(numeric) number of swaps. Default: 1000 |
abundance |
(logical) If |
See phylocomr-inputs for expected input formats
data.frame
0 - Phylogeny shuffle: This null model shuffles species labels across the entire phylogeny. This randomizes phylogenetic relationships among species.
1 - Species in each sample become random draws from sample pool: This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species actually occurring in at least one sample. Thus, species in the phylogeny that are not actually observed to occur in a sample will not be included in the null communities
2 - Species in each sample become random draws from phylogeny pool: This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species in the phylogeny pool. All species in the phylogeny will have equal probability of being included in the null communities. By changing the phylogeny, different species pools can be simulated. For example, the phylogeny could include the species present in some larger region.
3 - Independent swap: The independent swap algorithm (Gotelli and Entsminger, 2003); also known as ‘SIM9’ (Gotelli, 2000) creates swapped versions of the sample/species matrix.
In the sample
table, if you're passing in a file, the names in the
third column must be all lowercase; if not, we'll lowercase them for you.
If you pass in a data.frame, we'll lowercase them for your. All phylo
tip/node labels are also lowercased to avoid any casing problems
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) (res <- ph_comstruct(sample = sampledf, phylo = phylo_str)) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() cat(phylo_str, file = pfile2, sep = '\n') (res <- ph_comstruct(sample = sfile2, phylo = pfile2)) # different null models ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 0) ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 1) ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 2) # ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 3)
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) (res <- ph_comstruct(sample = sampledf, phylo = phylo_str)) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() cat(phylo_str, file = pfile2, sep = '\n') (res <- ph_comstruct(sample = sfile2, phylo = pfile2)) # different null models ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 0) ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 1) ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 2) # ph_comstruct(sample = sfile2, phylo = pfile2, null_model = 3)
Calculate measures of trait dispersion within each community, and compare observed patterns to those expected under a null model.
ph_comtrait( sample, traits, binary = NULL, metric = "variance", null_model = 0, randomizations = 999, abundance = TRUE )
ph_comtrait( sample, traits, binary = NULL, metric = "variance", null_model = 0, randomizations = 999, abundance = TRUE )
sample |
(data.frame/character) sample data.frame or path to a sample file |
traits |
(data.frame/character) traits data.frame or path to a traits file |
binary |
(logical) a logical vector indicating what columns are to be treated as binary characters - all others are treated as continuous |
metric |
(integer) metric to calculate. One of variance, mpd, mntd, or range (converted to phylocom integer format internally) |
null_model |
(integer) which null model to use. See Details. |
randomizations |
(numeric) number of randomizations. Default: 999 |
abundance |
(logical) If |
See phylocomr-inputs for expected input formats
If you give a data.frame to traits
parameter it expects data.frame like
species - the taxon labels matching the sample data to sample
parameter
col1,col2,col3,etc. - any number of trait columns - column names do not matter
When giving a data.frame to traits
make sure to pass in a binary
vector for what traits are to be treated as binary.
data.frame of the form:
trait - Trait name
sample - Sample name
ntaxa - Number of taxa in sample
mean - Mean value of trait in sample
metric - Observed metric in sample
meanrndmetric - Mean value of metric in null models
sdrndmetric - Standard deviation of metric in null models
sesmetric - Standardized effect size of metric
ranklow - Number of randomizations with metric lower than observed
rankhigh - Number of randomizations with metric higher than observed
runs - Number of randomizations
0 - This null model shuffles trait values across species.
1 - Species in each sample become random draws from sample pool. This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species actually occurring in at least one sample
2 - Species in each sample become random draws from traits data. This null model maintains the species richness of each sample, but the identities of the species occurring in each sample are randomized. For each sample, species are drawn without replacement from the list of all species with trait values. This function is redundant since by definition the sample and trait species must match, but is included for consistency with the comstruct function.
3 - Independent swap: Same as for ph_comdist and ph_comstruct
In the sample
and trait
tables, if you're passing in a file, the names
in the third and first columns, respectively, must be all lowercase; if not,
we'll lowercase them for you. If you pass in a data.frame, we'll lowercase
them for your. All phylo tip/node labels are also lowercased to avoid
any casing problems
## Not run: sfile <- system.file("examples/sample_comstruct", package = "phylocomr") tfile <- system.file("examples/traits_aot", package = "phylocomr") # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') traits_str <- paste0(readLines(tfile), collapse = "\n") tfile2 <- tempfile() cat(traits_str, file = tfile2, sep = '\n') ph_comtrait(sample = sfile2, traits = tfile2) # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr") traitsdf <- read.table(text = readLines(traitsdf_file), header = TRUE, stringsAsFactors = FALSE) ph_comtrait(sample = sampledf, traits = traitsdf, binary = c(FALSE, FALSE, FALSE, TRUE)) ## End(Not run)
## Not run: sfile <- system.file("examples/sample_comstruct", package = "phylocomr") tfile <- system.file("examples/traits_aot", package = "phylocomr") # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') traits_str <- paste0(readLines(tfile), collapse = "\n") tfile2 <- tempfile() cat(traits_str, file = tfile2, sep = '\n') ph_comtrait(sample = sfile2, traits = tfile2) # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr") traitsdf <- read.table(text = readLines(traitsdf_file), header = TRUE, stringsAsFactors = FALSE) ph_comtrait(sample = sampledf, traits = traitsdf, binary = c(FALSE, FALSE, FALSE, TRUE)) ## End(Not run)
Ecovolve generates a phylogeny via a random birth and death process, generates a traits file with five randomly evolving, in-dependent traits, and a sample file with a single sample unit (‘alive’) containing all extant members of the phylogeny.
ph_ecovolve( speciation = 0.05, extinction = 0.01, time_units = 100, out_mode = 3, prob_env = "3211000000", extant_lineages = FALSE, only_extant = FALSE, taper_change = NULL, competition = FALSE )
ph_ecovolve( speciation = 0.05, extinction = 0.01, time_units = 100, out_mode = 3, prob_env = "3211000000", extant_lineages = FALSE, only_extant = FALSE, taper_change = NULL, competition = FALSE )
speciation |
(numeric) Probability of speciation per unit time. Default: 0.05 |
extinction |
(numeric) Probability of extinction per unit time. Default: 0.01 |
time_units |
(integer) Time units to simulate over. Default: 100 |
out_mode |
(integer) Output mode (2 = LTT; 3 = newick). Default: 3 |
prob_env |
(character) Probability envelope for character change. must be a string of 10 integers. Default: 3211000000 |
extant_lineages |
(logical) Stop simulation after this number of
extant lineages. Default: |
only_extant |
(logical) Output phylogeny pruned only for extant taxa.
Default: |
taper_change |
(numeric/integer) Taper character change by
|
competition |
(logical) Simulate competition, with trait proximity
increasing extinction. Default: |
a list with three elements:
phylogeny - a phylogeny as a newick string. In the case of
out_mode = 2
gives a Lineage Through Time data.frame instead of a
newick phylogeny
sample - a data.frame with three columns, "sample" (all "alive"),
"abundance" (all 1's), "name" (the species code). In the case of
out_mode = 2
gives an empty data.frame
traits - a data.frame with first column with spcies code ("name"),
then 5 randomly evolved and independent traits. In the case of
out_mode = 2
gives an empty data.frame
Two files, "ecovolve.sample" and "ecovolve.traits" are written to the current working directory when this function runs - we read these files in, then delete the files via unlink
Function occasionally fails with error "call to 'ecovolve' failed with status 8. only 1 taxon; > 1 required" - this just means that only 1 taxon was created in the random process, so the function can't proceed
## Not run: # ph_ecovolve(speciation = 0.05) # ph_ecovolve(speciation = 0.1) # ph_ecovolve(extinction = 0.005) # ph_ecovolve(time_units = 50) # ph_ecovolve(out_mode = 2) # ph_ecovolve(extant_lineages = TRUE) # ph_ecovolve(extant_lineages = FALSE) # ph_ecovolve(only_extant = FALSE) # ph_ecovolve(only_extant = TRUE, speciation = 0.1) # ph_ecovolve(taper_change = 2) # ph_ecovolve(taper_change = 10) # ph_ecovolve(taper_change = 500) if (requireNamespace("ape")) { # library(ape) # x <- ph_ecovolve(speciation = 0.05) # plot(read.tree(text = x$phylogeny)) } ## End(Not run)
## Not run: # ph_ecovolve(speciation = 0.05) # ph_ecovolve(speciation = 0.1) # ph_ecovolve(extinction = 0.005) # ph_ecovolve(time_units = 50) # ph_ecovolve(out_mode = 2) # ph_ecovolve(extant_lineages = TRUE) # ph_ecovolve(extant_lineages = FALSE) # ph_ecovolve(only_extant = FALSE) # ph_ecovolve(only_extant = TRUE, speciation = 0.1) # ph_ecovolve(taper_change = 2) # ph_ecovolve(taper_change = 10) # ph_ecovolve(taper_change = 500) if (requireNamespace("ape")) { # library(ape) # x <- ph_ecovolve(speciation = 0.05) # plot(read.tree(text = x$phylogeny)) } ## End(Not run)
Calculates Faith’s (1992) index of phylogenetic diversity (PD) for each sample in the phylo.
ph_pd(sample, phylo)
ph_pd(sample, phylo)
sample |
(data.frame/character) sample data.frame or path to a sample file. required |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
See phylocomr-inputs for expected input formats
A single data.frame, with the colums:
sample - community name/label
ntaxa - number of taxa
pd - Faith's phylogenetic diversity
treebl - tree BL
proptreebl - proportion tree BL
In the sample
table, if you're passing in a file, the names
in the third column must be all lowercase; if not,
we'll lowercase them for you. If you pass in a data.frame, we'll lowercase
them for your. All phylo tip/node labels are also lowercased to avoid
any casing problems
Other phylogenetic-diversity:
ph_rao()
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_pd(sample = sampledf, phylo = phylo_str) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() phylo_str <- readLines(pfile) cat(phylo_str, file = pfile2, sep = '\n') ph_pd(sample = sfile2, phylo = pfile2)
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # from data.frame sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_pd(sample = sampledf, phylo = phylo_str) # from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() phylo_str <- readLines(pfile) cat(phylo_str, file = pfile2, sep = '\n') ph_pd(sample = sfile2, phylo = pfile2)
Phylomatic is a tool for extracting a phylogeny from a master phylogeny using only a user-supplied list of taxa.
ph_phylomatic(taxa, phylo, tabular = FALSE, lowercase = FALSE, nodes = FALSE)
ph_phylomatic(taxa, phylo, tabular = FALSE, lowercase = FALSE, nodes = FALSE)
taxa |
(character) all taxa as a character vector (will be written to a temp file if provided) - OR a path to taxa file. Required. See Details. |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
tabular |
(logical) Output a tabular representation of phylogeny.
Default: |
lowercase |
(logical) Convert all chars in taxa file to lowercase.
Default: |
nodes |
(logical) label all nodes with default names.
Default: |
The taxa
character vector must have each element of the
form family/genus/genus_epithet
. If a file is passed in, each
line should have a family/genus/genus_epithet
string - make sure
only one per line, and a newline (i.e., press ENTER) at the end of
each line
Phylomatic is also available as a web service (https://github.com/camwebb/phylomatic-ws) - but is based on a different code base (https://github.com/camwebb/phylomatic-ws) See Webb and Donoghue (2005) doi:10.1111/j.1471-8286.2004.00829.x for more information on the goals of Phylomatic.
## Not run: taxa_file <- system.file("examples/taxa", package = "phylocomr") phylo_file <- system.file("examples/phylo", package = "phylocomr") # from strings (taxa_str <- readLines(taxa_file)) (phylo_str <- readLines(phylo_file)) (tree <- ph_phylomatic(taxa = taxa_str, phylo = phylo_str)) # from files taxa_file2 <- tempfile() cat(taxa_str, file = taxa_file2, sep = '\n') phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (tree <- ph_phylomatic(taxa = taxa_file2, phylo = phylo_file2)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = tree)) } ## End(Not run)
## Not run: taxa_file <- system.file("examples/taxa", package = "phylocomr") phylo_file <- system.file("examples/phylo", package = "phylocomr") # from strings (taxa_str <- readLines(taxa_file)) (phylo_str <- readLines(phylo_file)) (tree <- ph_phylomatic(taxa = taxa_str, phylo = phylo_str)) # from files taxa_file2 <- tempfile() cat(taxa_str, file = taxa_file2, sep = '\n') phylo_file2 <- tempfile() cat(phylo_str, file = phylo_file2, sep = '\n') (tree <- ph_phylomatic(taxa = taxa_file2, phylo = phylo_file2)) if (requireNamespace("ape")) { library(ape) plot(read.tree(text = tree)) } ## End(Not run)
A measure of within- and among-community diversity taking species dissimilarity (phylogenetic dissimilarity) into account
ph_rao(sample, phylo)
ph_rao(sample, phylo)
sample |
(data.frame/character) sample data.frame or path to a sample file |
phylo |
(character/phylo) One of: phylogeny as a newick string (will be
written to a temp file) - OR path to file with a newick
string - OR a an ape |
See phylocomr-inputs for expected input formats
A list of 6 data.frame's: Diversity components:
overall alpha (within-site)
beta (among-site)
total diversity
Fst statistic of differentiation for diversity and phylogenetic diversity
Within-community diversity:
Plot - Plot name
NSpp - Number of species
NIndiv - Number of individuals
PropIndiv - Proportion of all individuals found in this plot
D - Diversity (= Simpson’s diversity)
Dp - Phylogenetic diversity (= Diversity weighted by interspecific phylogenetic distances)
The remaining 4 tables compare each community pairwise:
among_community_diversity_d - Among-community diversities
among_community_diversity_h - Among-community diversities excluding within-community diversity
among_community_phylogenetic_diversity_dp - Among-community phylogenetic diversities
among_community_phylogenetic_diversity_hp - Among-community phylogenetic diversities excluding within-community diversity
In the sample
table, if you're passing in a file, the names
in the third column must be all lowercase; if not,
we'll lowercase them for you. If you pass in a data.frame, we'll lowercase
them for your. All phylo tip/node labels are also lowercased to avoid
any casing problems
Other phylogenetic-diversity:
ph_pd()
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # sample from data.frame, phylogeny from a string sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_rao(sample = sampledf, phylo = phylo_str) # both from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() phylo_str <- readLines(pfile) cat(phylo_str, file = pfile2, sep = '\n') ph_rao(sample = sfile2, phylo = pfile2)
sfile <- system.file("examples/sample_comstruct", package = "phylocomr") pfile <- system.file("examples/phylo_comstruct", package = "phylocomr") # sample from data.frame, phylogeny from a string sampledf <- read.table(sfile, header = FALSE, stringsAsFactors = FALSE) phylo_str <- readLines(pfile) ph_rao(sample = sampledf, phylo = phylo_str) # both from files sample_str <- paste0(readLines(sfile), collapse = "\n") sfile2 <- tempfile() cat(sample_str, file = sfile2, sep = '\n') pfile2 <- tempfile() phylo_str <- readLines(pfile) cat(phylo_str, file = pfile2, sep = '\n') ph_rao(sample = sfile2, phylo = pfile2)
Expected inputs
A file or data.frame, with 2 columns:
(character) node taxonomic name
(numeric) age estimate for the node
If a file path is used, the table must not have headers
Applies to:
A file or data.frame, with 3 columns, sorted by column 1, one row per taxon:
(character) sample plot/quadrat/trap/etc. name (no spaces, must begin with a letter, not a number or symbol)
(integer) abundance (leave as 1 for presence/absence data)
(character) species code (same as in the phylogeny, must begin with a letter, not a number or symbol)
If a file path is used, the table must not have headers, and must be tab-delimited
Applies to:
A tab-delimited file with the first line as
type<TAB>n<TAB>n<TAB>... [up to the number of traits]
, for example:
type<TAB>3<TAB>3<TAB>3<TAB>0
where n indicates the type of trait in each of the four columns. Types:
0
: binary (only one binary trait may be included, and it must be in
the first column) 1 for unordered multistate (no algorithms currently
implemented)
2
: ordered multistate (currently treated as continuous)
3
: continuous
Optional: The second line can start with the word name (lower case only) and then list the names of the traits in order. These will appear in the full output file
Subsequent lines should have the taxon name, which must be identical to
its appearance in phylo, and the data columns separated by tabs. For
example: sp1<TAB>1<TAB>1<TAB>1<TAB>0
OR -
A data.frame, where the first column called name
has each taxon, followed by
any number of columns with traits. The first column name must be name
, and
the following columns should be named using the name of the trait.
Applies to:
Phylocom expects trees in Newick format. The basic Newick format used by
Phylocom is: ((A,B),C);
. See the Phylocom manual
(https://phylodiversity.net/phylocom/) for more details on what they expect.
Applies to: all functions except ph_phylomatic()
and ph_ecovolve()