phylocomr gives you access to the Phylocom C
library, licensed under BSD
2-clause
ecovolve/ph_ecovolve- interface toecovolveexecutable, and a higher level interfacephylomatic/ph_phylomatic- interface tophylomaticexecutable, and a higher level interfacephylocom- interface tophylocomexecutableph_aot- higher level interface toaotph_bladj- higher level interface tobladjph_comdist/ph_comdistnt- higher level interface to comdistph_comstruct- higher level interface to comstructph_comtrait- higher level interface to comtraitph_pd- higher level interface to Faith’s phylogenetic diversity
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.
Stable version:
install.packages("phylocomr")
Development version:
remotes::install_github("ropensci/phylocomr")
library("phylocomr")
library("ape")
ph_ecovolve(speciation = 0.05, extinction = 0.005, time_units = 50)
taxa_file <- system.file("examples/taxa", package = "phylocomr")
phylo_file <- system.file("examples/phylo", package = "phylocomr")
(taxa_str <- readLines(taxa_file))
#> [1] "campanulaceae/lobelia/lobelia_conferta"
#> [2] "cyperaceae/mapania/mapania_africana"
#> [3] "amaryllidaceae/narcissus/narcissus_cuatrecasasii"
(phylo_str <- readLines(phylo_file))
#> [1] "(((((eliea_articulata,homalanthus_populneus)malpighiales,rosa_willmottiae),((macrocentrum_neblinae,qualea_clavata),hibiscus_pohlii)malvids),(((lobelia_conferta,((millotia_depauperata,(layia_chrysanthemoides,layia_pentachaeta)layia),senecio_flanaganii)asteraceae)asterales,schwenkia_americana),tapinanthus_buntingii)),(narcissus_cuatrecasasii,mapania_africana))poales_to_asterales;"
ph_phylomatic(taxa = taxa_str, phylo = phylo_str)
#> [1] "(lobelia_conferta:5.000000,(mapania_africana:1.000000,narcissus_cuatrecasasii:1.000000):1.000000)poales_to_asterales:1.000000;\n"
#> attr(,"taxa_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/taxa_577357322292"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_57731c7bcbf7"
use various different references trees
library(brranching)
library(ape)
r2 <- ape::read.tree(text=brranching::phylomatic_trees[['R20120829']])
smith2011 <- ape::read.tree(text=brranching::phylomatic_trees[['smith2011']])
zanne2014 <- ape::read.tree(text=brranching::phylomatic_trees[['zanne2014']])
# R20120829 tree
taxa_str <- c(
"asteraceae/bidens/bidens_alba",
"asteraceae/cirsium/cirsium_arvense",
"fabaceae/lupinus/lupinus_albus"
)
ph_phylomatic(taxa = taxa_str, phylo = r2)
#> [1] "(((bidens_alba:13.000000,cirsium_arvense:13.000000):19.000000,lupinus_albus:27.000000):12.000000)euphyllophyte:1.000000;\n"
#> attr(,"taxa_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/taxa_577350fa1f1c"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_5773551090cc"
# zanne2014 tree
taxa_str <- c(
"zamiaceae/dioon/dioon_edule",
"zamiaceae/encephalartos/encephalartos_dyerianus",
"piperaceae/piper/piper_arboricola"
)
ph_phylomatic(taxa = taxa_str, phylo = zanne2014)
#> [1] "(((dioon_edule:121.744843,encephalartos_dyerianus:121.744850)zamiaceae:230.489838,piper_arboricola:352.234711)spermatophyta:88.058670):0.000000;\n"
#> attr(,"taxa_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/taxa_577332926cb5"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_57732b1ef903"
# zanne2014 subtree
zanne2014_subtr <- ape::extract.clade(zanne2014, node='Loganiaceae')
zanne_subtree_file <- tempfile(fileext = ".txt")
ape::write.tree(zanne2014_subtr, file = zanne_subtree_file)
taxa_str <- c(
"loganiaceae/neuburgia/neuburgia_corynocarpum",
"loganiaceae/geniostoma/geniostoma_borbonicum",
"loganiaceae/strychnos/strychnos_darienensis"
)
ph_phylomatic(taxa = taxa_str, phylo = zanne2014_subtr)
#> [1] "((neuburgia_corynocarpum:32.807743,(geniostoma_borbonicum:32.036335,strychnos_darienensis:32.036335):0.771406):1.635496)loganiaceae:0.000000;\n"
#> attr(,"taxa_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/taxa_57737ac12496"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_57731e4932d0"
ph_phylomatic(taxa = taxa_str, phylo = zanne_subtree_file)
#> [1] "((neuburgia_corynocarpum:32.807743,(geniostoma_borbonicum:32.036335,strychnos_darienensis:32.036335):0.771406):1.635496)loganiaceae:0.000000;\n"
#> attr(,"taxa_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/taxa_577357a70538"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_57731647cc7d"
traits_file <- system.file("examples/traits_aot", package = "phylocomr")
phylo_file <- system.file("examples/phylo_aot", package = "phylocomr")
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)
ph_aot(traits = traits, phylo = phylo_str)
#> $trait_conservatism
#> # A tibble: 124 × 28
#> trait trait.n…¹ node name age ntaxa n.nodes tip.mn tmn.r…² tmn.r…³ tip.sd
#> <int> <chr> <int> <chr> <dbl> <int> <int> <dbl> <int> <int> <dbl>
#> 1 1 traitA 0 a 5 32 2 1.75 1000 1000 0.440
#> 2 1 traitA 1 b 4 16 2 1.75 647 660 0.447
#> 3 1 traitA 2 c 3 8 2 1.75 700 688 0.463
#> 4 1 traitA 3 d 2 4 2 1.5 264 959 0.577
#> 5 1 traitA 4 e 1 2 2 1 65 1000 0
#> 6 1 traitA 7 f 1 2 2 2 1000 544 0
#> 7 1 traitA 10 g 2 4 2 2 1000 294 0
#> 8 1 traitA 11 h 1 2 2 2 1000 549 0
#> 9 1 traitA 14 i 1 2 2 2 1000 542 0
#> 10 1 traitA 17 j 3 8 2 1.75 648 716 0.463
#> # … with 114 more rows, 17 more variables: tsd.ranklow <int>, tsd.rankhi <int>,
#> # node.mn <dbl>, nmn.ranklow <int>, nmn.rankhi <int>, nod.sd <dbl>,
#> # nsd.ranklow <int>, nsd.rankhi <int>, sstipsroot <dbl>, sstips <dbl>,
#> # percvaramongnodes <dbl>, percvaratnode <dbl>, contributionindex <dbl>,
#> # sstipvnoderoot <dbl>, sstipvnode <dbl>, ssamongnodes <dbl>,
#> # sswithinnodes <dbl>, and abbreviated variable names ¹trait.name,
#> # ²tmn.ranklow, ³tmn.rankhi
#>
#> $independent_contrasts
#> # A tibble: 31 × 17
#> node name age n.nodes contrast1 contrast2 contr…¹ contr…² contr…³ lowval1
#> <int> <chr> <dbl> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0 a 5 2 0 0 0 0.254 1.97 1.75
#> 2 1 b 4 2 0 1.03 0 0.516 1.94 1.75
#> 3 2 c 3 2 0.267 0.535 0 0 1.87 1.5
#> 4 3 d 2 2 0.577 0 1.15 0 1.73 1
#> 5 4 e 1 2 0 0 0.707 0 1.41 1
#> 6 7 f 1 2 0 0 0.707 0 1.41 2
#> 7 10 g 2 2 0 0 1.15 0 1.73 2
#> 8 11 h 1 2 0 0 0.707 0 1.41 2
#> 9 14 i 1 2 0 0 0.707 0 1.41 2
#> 10 17 j 3 2 0.267 0.535 0 0 1.87 1.5
#> # … with 21 more rows, 7 more variables: hival1 <dbl>, lowval2 <dbl>,
#> # hival2 <dbl>, lowval3 <dbl>, hival3 <dbl>, lowval4 <dbl>, hival4 <dbl>, and
#> # abbreviated variable names ¹contrast3, ²contrast4, ³contrastsd
#>
#> $phylogenetic_signal
#> # A tibble: 4 × 5
#> trait ntaxa varcontr varcn.ranklow varcn.rankhi
#> <chr> <int> <dbl> <int> <int>
#> 1 traitA 32 0.054 1 1000
#> 2 traitB 32 0.109 1 1000
#> 3 traitC 32 0.622 51 950
#> 4 traitD 32 0.011 1 1000
#>
#> $ind_contrast_corr
#> # A tibble: 3 × 6
#> xtrait ytrait ntaxa picr npos ncont
#> <chr> <chr> <int> <dbl> <dbl> <int>
#> 1 traitA traitB 32 0.248 18.5 31
#> 2 traitA traitC 32 0.485 27.5 31
#> 3 traitA traitD 32 0 16.5 31
ages_file <- system.file("examples/ages", package = "phylocomr")
phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr")
ages_df <- data.frame(
a = c('malpighiales','salicaceae','fabaceae','rosales','oleaceae',
'gentianales','apocynaceae','rubiaceae'),
b = c(81,20,56,76,47,71,18,56)
)
phylo_str <- readLines(phylo_file)
(res <- ph_bladj(ages = ages_df, phylo = phylo_str))
#> [1] "((((((lomatium_concinnum:20.250000,campanula_vandesii:20.250000):20.250000,(((veronica_candidissima:10.125000,penstemon_paniculatus:10.125000)plantaginaceae:10.125000,justicia_oblonga:20.250000):10.125000,marsdenia_gilgiana:30.375000):10.125000):10.125000,epacris_alba-compacta:50.625000)ericales_to_asterales:10.125000,((daphne_anhuiensis:20.250000,syzygium_cumini:20.250000)malvids:20.250000,ditaxis_clariana:40.500000):20.250000):10.125000,thalictrum_setulosum:70.875000)eudicots:10.125000,((dendrocalamus_giganteus:27.000000,guzmania_densiflora:27.000000)poales:27.000000,warczewiczella_digitata:54.000000):27.000000)malpighiales:1.000000;\n"
#> attr(,"ages_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/ages"
#> attr(,"phylo_file")
#> [1] "/var/folders/ss/2tpkp325521_kfgn59g44vd80000gn/T//RtmpeMkOMc/phylo_577376efe8a"
plot(ape::read.tree(text = res))
- Please report any issues or bugs.
- License: MIT
- Get citation information for
phylocomrin R doingcitation(package = 'phylocomr') - Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
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