README.md
In phylocomr: Interface to 'Phylocom'

phylocomr

phylocomr gives you access to the Phylocom C library, licensed under BSD 2-clause

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

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 phylocomr in R doing citation(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.