Nothing
R/data.R
In TreeSearch: Phylogenetic Analysis with Discrete Character Data
#' Thirty datasets with inapplicable data
#'
#' These are the datasets used to evaluate the behaviour of the inapplicable
#' algorithm in \insertCite{Brazeau2018;textual}{TreeTools}.
#' The name of each item corresponds to the datasets listed below.
#' Datasets are sorted into two subsets, each sorted alphabetically;
#' the first subset comprise simpler datasets with faster processing times.
#' `inapplicable.datasets` provide the data in the matrix format generated by
#' [`read.nexus.data()`]; `inapplicable.phyData` are in \code{phyDat} format.
#' `inapplicable.trees` lists for each dataset a sample of up to 50 trees
#' obtained by tree search under each inapplicable treatment, named accordingly.
#' `inapplicable.citations` is a named character vector specifying the source of
#' each dataset.
#'
#' @source {
#' Subset one (faster processing):
#'
#' \describe{
#' \item{Agnarsson2004}{AGNARSSON, I. 2004. Morphological phylogeny of cobweb spiders and their
#' relatives (Araneae, Araneoidea, Theridiidae). Zoological Journal of the
#' Linnean Society, 141, 447--626.}
#' \item{Capa2011}{CAPA, M., HUTCHINGS, P., AGUADO, M. T. and BOTT, N. J. 2011. Phylogeny of
#' Sabellidae (Annelida) and relationships with other taxa inferred from
#' morphology and multiple genes. Cladistics, 27, 449--469.}
#' \item{DeAssis2011}{ DE ASSIS, J. E. and CHRISTOFFERSEN, M. L. 2011. Phylogenetic relationships
#' within Maldanidae (Capitellida, Annelida), based on morphological characters.
#' Systematics and Biodiversity, 9, 233--245.}
#' \item{OLeary1999}{ O'LEARY, M. A. and GEISLER, J. H. 1999. The position of Cetacea within
#' Mammalia: phylogenetic analysis of morphological data from extinct and
#' extant taxa. Systematic Biology, 48, 455--490.}
#' \item{Rousset2004}{ ROUSSET, V., ROUSE, G. W., SIDDALL, M. E., TILLIER, A. and PLEIJEL, F.
#' 2004. The phylogenetic position of Siboglinidae (Annelida) inferred from
#' 18S rRNA, 28S rRNA and morphological data. Cladistics, 20, 518--533.}
#' \item{Sano2011}{ SANO, M. and AKIMOTO, S.-I. 2011. Morphological phylogeny of
#' gall-forming aphids of the tribe Eriosomatini (Aphididae: Eriosomatinae).
#' Systematic Entomology, 36, 607--627.}
#' \item{Sansom2010}{ SANSOM, R. S., FREEDMAN, K., GABBOTT, S. E., ALDRIDGE, R. J. and
#' PURNELL, M. A. 2010. Taphonomy and affinity of an enigmatic Silurian vertebrate,
#' \emph{Jamoytius kerwoodi} White. Palaeontology, 53, 1393--1409.}
#' \item{Schulze2007}{ SCHULZE, A., CUTLER, E. B. and GIRIBET, G. 2007. Phylogeny of sipunculan
#' worms: A combined analysis of four gene regions and morphology. Molecular Phylogenetics and Evolution, 42, 171--92.}
#' \item{Shultz2007}{ SHULTZ, J. W. 2007. A phylogenetic analysis of the arachnid orders based
#' on morphological characters. Zoological Journal of the Linnean Society, 150, 221--265.}
#' \item{Wetterer2000}{ WETTERER, A. L., ROCKKMAN, M. V. and SIMMONS, N. B. 2000. Phylogeny of
#' phyllostomid bats (Mammalia: Chiroptera): data from diverse morphological
#' systems, sex chromosomes, and restriction sites. Bulletin of the American Museum of Natural History, 248, 1--200.}
#' \item{Wills2012}{ WILLS, M. A., GERBER, S., RUTA, M. and HUGHES, M. 2012. The disparity of
#' priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data.
#' Journal of Evolutionary Biology, 25, 2056--2076.}
#' }
#'
#' Subset two (longer processing times):
#'
#' \describe{
#' \item{Aguado2009}{ AGUADO, M. T. and SAN MARTIN, G. 2009. Phylogeny of Syllidae (Polychaeta)
#' based on morphological data. Zoologica Scripta, 38, 379--402.}
#' \item{Aria2015}{ ARIA, C., CARON, J. B. and GAINES, R. 2015. A large new leanchoiliid from
#' the Burgess Shale and the influence of inapplicable states on stem arthropod
#' phylogeny. Palaeontology, 58, 629--660.}
#' \item{Asher2005}{ASHER, R. J. and HOFREITER, M. 2006. Tenrec phylogeny and the noninvasive
#' extraction of nuclear DNA. Systematic biology, 55, 181--94.}
#' \item{Baker2009}{ BAKER, W. J., SAVOLAINEN, V., ASMUSSEN-LANGE, C. B., CHASE, M. W.,
#' DRANSFIELD, J., FOREST, F., HARLEY, M. M., UHL, N. W. and WILKINSON, M. 2009.
#' Complete generic-level phylogenetic analyses of palms (Arecaceae) with
#' comparisons of supertree and supermatrix approaches.
#' Systematic Biology, 58, 240--256.}
#' \item{Bouchenak2010}{ BOUCHENAK-KHELLADI, Y., VERBOOM, G. A., SAVOLAINEN, V. and HODKINSON, T. R.
#' 2010. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal
#' evolutionary history in geographical space and geological time. Botanical
#' Journal of the Linnean Society, 162, 543--557.}
#' \item{Conrad2008}{ CONRAD, J. L. 2008. Phylogeny And Systematics Of Squamata (Reptilia) Based
#' On Morphology. Bulletin of the American Museum of Natural History, 310, 1--182.}
#' \item{Dikow2009}{ DIKOW, T. 2009. A phylogenetic hypothesis for Asilidae based on a total
#' evidence analysis of morphological and DNA sequence data (Insecta: Diptera:
#' Brachycera: Asiloidea). Organisms Diversity and Evolution, 9, 165--188.}
#' \item{Eklund2004}{ EKLUND, H., DOYLE, J. A. and HERENDEEN, P. S. 2004. Morphological
#' phylogenetic analysis of living and fossil Chloranthaceae. International
#' Journal of Plant Sciences, 165, 107--151.}
#' \item{Geisler2001}{ GEISLER, J. H. 2001. New morphological evidence for the phylogeny of
#' Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates, 3344, 53.}
#' \item{Giles2015}{ GILES, S., FRIEDMAN, M. and BRAZEAU, M. D. 2015. Osteichthyan-like cranial
#' conditions in an Early Devonian stem gnathostome. Nature, 520, 82--85.}
#' \item{Griswold1999}{ GRISWOLD, C. E., CODDINGTON, J. A., PLATNICK, N. I. and FORSTER, R. R. 1999.
#' Towards a phylogeny of entelegyne spiders (Araneae, Araneomorphae, Entelegynae).
#' Journal of Arachnology, 27, 53--63.}
#' \item{Liljeblad2008}{ LILJEBLAD, J., RONQUIST, F., NIEVES-ALDREY, J. L., FONTAL-CAZALLA, F.,
#' ROS-FARRE, P., GAITROS, D. and PUJADE-VILLAR, J. 2008. A fully web-illustrated
#' morphological phylogenetic study of relationships among oak gall wasps and
#' their closest relatives (Hymenoptera: Cynipidae).}
#' \item{Loconte1991}{ LOCONTE, H. and STEVENSON, D. W. 1991. Cladistics of the Magnoliidae.
#' Cladistics, 7, 267--296.}
#' \item{Longrich2010}{ LONGRICH, N. R., SANKEY, J. and TANKE, D. 2010. \emph{Texacephale langstoni},
#' a new genus of pachycephalosaurid (Dinosauria: Ornithischia) from the upper
#' Campanian Aguja Formation, southern Texas, USA. Cretaceous Research, 31, 274--284.}
#' \item{OMeara2014}{ O'MEARA, R. N. and THOMPSON, R. S. 2014. Were There Miocene Meridiolestidans?
#' Assessing the phylogenetic placement of \emph{Necrolestes patagonensis} and the
#' presence of a 40 million year Meridiolestidan ghost lineage. Journal
#' of Mammalian Evolution, 21, 271--284.}
#' \item{Rougier2012}{ ROUGIER, G. W., WIBLE, J. R., BECK, R. M. D. and APESTEGUIA, S. 2012.
#' The Miocene mammal \emph{Necrolestes} demonstrates the survival of a
#' Mesozoic nontherian lineage into the late Cenozoic of South America.
#' Proceedings of the National Academy of Sciences, 109, 20053--8.}
#' \item{Sharkey2011}{ SHARKEY, M. J., CARPENTER, J. M., VILHELMSEN, L., HERATY, J., LILJEBLAD, J.,
#' DOWLING, A. P. G., SCHULMEISTER, S., MURRAY, D., DEANS, A. R., RONQUIST, F.,
#' KROGMANN, L. and WHEELER, W. C. 2012. Phylogenetic relationships among
#' superfamilies of Hymenoptera. Cladistics, 28, 80--112.}
#' \item{Sundue2010}{ SUNDUE, M. A., ISLAM, M. B. and RANKER, T. A. 2010. Systematics of
#' Grammitid Ferns (Polypodiaceae): Using Morphology and Plastid Sequence Data
#' to Resolve the Circumscriptions of Melpomene and the Polyphyletic Genera
#' \emph{Lellingeria} and \emph{Terpsichore}. Systematic Botany, 35, 701--715.}
#' \item{Vinther2008}{ VINTHER, J., VAN ROY, P. and BRIGGS, D. E. G. 2008. Machaeridians are
#' Palaeozoic armoured annelids. Nature, 451, 185--188.}
#' \item{Wilson2003}{ WILSON, G. D. F. and EDGECOMBE, G. D. 2003. The Triassic isopod
#' \emph{Protamphisopus wianamattensis} (Chilton) and comparison by extant
#' taxa (Crustacea, Phreatoicidea). Journal of Paleontology, 77, 454--470.}
#' \item{Wortley2006}{ WORTLEY, A. H. and SCOTLAND, R. W. 2006. The effect of combining molecular
#' and morphological data in published phylogenetic analyses.
#' Systematic Biology, 55, 677--685.}
#' \item{Zanol2014}{ ZANOL, J., HALANYCH, K. M. and FAUCHALD, K. 2014. Reconciling taxonomy and
#' phylogeny in the bristleworm family Eunicidae (Polychaete, Annelida).
#' Zoologica Scripta, 43, 79--100.}
#' \item{Zhu2013}{ ZHU, M., YU, X., AHLBERG, P. E., CHOO, B., LU, J., QIAO, T., QU, Q., ZHAO, W.,
#' JIA, L., BLOM, H. and ZHU, Y. 2013. A Silurian placoderm with osteichthyan-like
#' marginal jaw bones. Nature, 502, 188--193.}
#' }
#' }
#'
#'
#' @references
#' \insertAllCited{}
#' @examples
#' data("inapplicable.datasets", package = "TreeSearch")
#' names(inapplicable.datasets)
#' @keywords datasets
"inapplicable.datasets"
#' @rdname inapplicable.datasets
"inapplicable.phyData"
#' @rdname inapplicable.datasets
"inapplicable.trees"
#' @rdname inapplicable.datasets
"inapplicable.citations"
#' 100 simulated data matrices
#'
#' Contains the 100 simulated matrices generated by
#' \insertCite{Congreve2016}{TreeSearch} using a heterogeneous Markov-k model,
#' generated from the \link{referenceTree} topology, with
#' all branches sharing an equal length.
#'
#' @format A list with 100 entries, each comprising a `phyDat` object of 55
#' characters for 22 taxa
#'
#' @references
#' \insertAllCited{}
#'
#' @examples
#' data("referenceTree")
#' data("congreveLamsdellMatrices")
#' TreeLength(referenceTree, congreveLamsdellMatrices[[17]], "profile")
#'
#' @source \doi{10.5061/dryad.7dq0j}
#'
#' @keywords datasets
"congreveLamsdellMatrices"
#' Tree topology for matrix simulation
#'
#' The tree topology used to generate the matrices in
#' \code{\link{congreveLamsdellMatrices}}
#'
#' @format A single phylogenetic tree saved as an object of class \code{phylo}
#'
#' @references
#' \insertRef{Congreve2016}{TreeSearch}
#' \insertRef{Congreve2016dd}{TreeSearch}
#'
#' @examples
#' data(referenceTree)
#' plot(referenceTree)
#'
#' @source Congreve & Lamsdell (2016); \doi{10.1111/pala.12236}
#'
#' @keywords datasets
"referenceTree"
#' Empirically counted profiles for small trees
#'
#' The base 2 logarithm of the number of trees containing _s_ steps, calculated
#' by scoring a character on each _n_-leaf tree.
#'
#' @format A list with the structure
#' `profiles[[number of leaves]][[number of tokens]][[tokens in smallest split]]`
#' The list entry returns a named numeric vector; each entry lists
#' log2(proportion of _n_-leaf trees with _s_ or fewer steps for this character).
#'
#' @examples
#' data(profiles)
#'
#' # Load profile for a character of the structure 0 0 0 1 1 1 1 1
#' profile3.5 <- profiles[[8]][[2]][[3]]
#'
#' # Number of trees with _s_ or fewer steps on that character
#' TreeTools::NUnrooted(8) * 2 ^ profile3.5
#' @family profile parsimony functions
"profiles"
Try the TreeSearch package in your browser
Any scripts or data that you put into this service are public.
TreeSearch documentation built on Aug. 26, 2023, 9:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Thirty datasets with inapplicable data
#'
#' These are the datasets used to evaluate the behaviour of the inapplicable
#' algorithm in \insertCite{Brazeau2018;textual}{TreeTools}.
#' The name of each item corresponds to the datasets listed below.
#' Datasets are sorted into two subsets, each sorted alphabetically;
#' the first subset comprise simpler datasets with faster processing times.
#' `inapplicable.datasets` provide the data in the matrix format generated by
#' [`read.nexus.data()`]; `inapplicable.phyData` are in \code{phyDat} format.
#' `inapplicable.trees` lists for each dataset a sample of up to 50 trees
#' obtained by tree search under each inapplicable treatment, named accordingly.
#' `inapplicable.citations` is a named character vector specifying the source of
#' each dataset.
#'
#' @source {
#' Subset one (faster processing):
#'
#' \describe{
#' \item{Agnarsson2004}{AGNARSSON, I. 2004. Morphological phylogeny of cobweb spiders and their
#' relatives (Araneae, Araneoidea, Theridiidae). Zoological Journal of the
#' Linnean Society, 141, 447--626.}
#' \item{Capa2011}{CAPA, M., HUTCHINGS, P., AGUADO, M. T. and BOTT, N. J. 2011. Phylogeny of
#' Sabellidae (Annelida) and relationships with other taxa inferred from
#' morphology and multiple genes. Cladistics, 27, 449--469.}
#' \item{DeAssis2011}{ DE ASSIS, J. E. and CHRISTOFFERSEN, M. L. 2011. Phylogenetic relationships
#' within Maldanidae (Capitellida, Annelida), based on morphological characters.
#' Systematics and Biodiversity, 9, 233--245.}
#' \item{OLeary1999}{ O'LEARY, M. A. and GEISLER, J. H. 1999. The position of Cetacea within
#' Mammalia: phylogenetic analysis of morphological data from extinct and
#' extant taxa. Systematic Biology, 48, 455--490.}
#' \item{Rousset2004}{ ROUSSET, V., ROUSE, G. W., SIDDALL, M. E., TILLIER, A. and PLEIJEL, F.
#' 2004. The phylogenetic position of Siboglinidae (Annelida) inferred from
#' 18S rRNA, 28S rRNA and morphological data. Cladistics, 20, 518--533.}
#' \item{Sano2011}{ SANO, M. and AKIMOTO, S.-I. 2011. Morphological phylogeny of
#' gall-forming aphids of the tribe Eriosomatini (Aphididae: Eriosomatinae).
#' Systematic Entomology, 36, 607--627.}
#' \item{Sansom2010}{ SANSOM, R. S., FREEDMAN, K., GABBOTT, S. E., ALDRIDGE, R. J. and
#' PURNELL, M. A. 2010. Taphonomy and affinity of an enigmatic Silurian vertebrate,
#' \emph{Jamoytius kerwoodi} White. Palaeontology, 53, 1393--1409.}
#' \item{Schulze2007}{ SCHULZE, A., CUTLER, E. B. and GIRIBET, G. 2007. Phylogeny of sipunculan
#' worms: A combined analysis of four gene regions and morphology. Molecular Phylogenetics and Evolution, 42, 171--92.}
#' \item{Shultz2007}{ SHULTZ, J. W. 2007. A phylogenetic analysis of the arachnid orders based
#' on morphological characters. Zoological Journal of the Linnean Society, 150, 221--265.}
#' \item{Wetterer2000}{ WETTERER, A. L., ROCKKMAN, M. V. and SIMMONS, N. B. 2000. Phylogeny of
#' phyllostomid bats (Mammalia: Chiroptera): data from diverse morphological
#' systems, sex chromosomes, and restriction sites. Bulletin of the American Museum of Natural History, 248, 1--200.}
#' \item{Wills2012}{ WILLS, M. A., GERBER, S., RUTA, M. and HUGHES, M. 2012. The disparity of
#' priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data.
#' Journal of Evolutionary Biology, 25, 2056--2076.}
#' }
#'
#' Subset two (longer processing times):
#'
#' \describe{
#' \item{Aguado2009}{ AGUADO, M. T. and SAN MARTIN, G. 2009. Phylogeny of Syllidae (Polychaeta)
#' based on morphological data. Zoologica Scripta, 38, 379--402.}
#' \item{Aria2015}{ ARIA, C., CARON, J. B. and GAINES, R. 2015. A large new leanchoiliid from
#' the Burgess Shale and the influence of inapplicable states on stem arthropod
#' phylogeny. Palaeontology, 58, 629--660.}
#' \item{Asher2005}{ASHER, R. J. and HOFREITER, M. 2006. Tenrec phylogeny and the noninvasive
#' extraction of nuclear DNA. Systematic biology, 55, 181--94.}
#' \item{Baker2009}{ BAKER, W. J., SAVOLAINEN, V., ASMUSSEN-LANGE, C. B., CHASE, M. W.,
#' DRANSFIELD, J., FOREST, F., HARLEY, M. M., UHL, N. W. and WILKINSON, M. 2009.
#' Complete generic-level phylogenetic analyses of palms (Arecaceae) with
#' comparisons of supertree and supermatrix approaches.
#' Systematic Biology, 58, 240--256.}
#' \item{Bouchenak2010}{ BOUCHENAK-KHELLADI, Y., VERBOOM, G. A., SAVOLAINEN, V. and HODKINSON, T. R.
#' 2010. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal
#' evolutionary history in geographical space and geological time. Botanical
#' Journal of the Linnean Society, 162, 543--557.}
#' \item{Conrad2008}{ CONRAD, J. L. 2008. Phylogeny And Systematics Of Squamata (Reptilia) Based
#' On Morphology. Bulletin of the American Museum of Natural History, 310, 1--182.}
#' \item{Dikow2009}{ DIKOW, T. 2009. A phylogenetic hypothesis for Asilidae based on a total
#' evidence analysis of morphological and DNA sequence data (Insecta: Diptera:
#' Brachycera: Asiloidea). Organisms Diversity and Evolution, 9, 165--188.}
#' \item{Eklund2004}{ EKLUND, H., DOYLE, J. A. and HERENDEEN, P. S. 2004. Morphological
#' phylogenetic analysis of living and fossil Chloranthaceae. International
#' Journal of Plant Sciences, 165, 107--151.}
#' \item{Geisler2001}{ GEISLER, J. H. 2001. New morphological evidence for the phylogeny of
#' Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates, 3344, 53.}
#' \item{Giles2015}{ GILES, S., FRIEDMAN, M. and BRAZEAU, M. D. 2015. Osteichthyan-like cranial
#' conditions in an Early Devonian stem gnathostome. Nature, 520, 82--85.}
#' \item{Griswold1999}{ GRISWOLD, C. E., CODDINGTON, J. A., PLATNICK, N. I. and FORSTER, R. R. 1999.
#' Towards a phylogeny of entelegyne spiders (Araneae, Araneomorphae, Entelegynae).
#' Journal of Arachnology, 27, 53--63.}
#' \item{Liljeblad2008}{ LILJEBLAD, J., RONQUIST, F., NIEVES-ALDREY, J. L., FONTAL-CAZALLA, F.,
#' ROS-FARRE, P., GAITROS, D. and PUJADE-VILLAR, J. 2008. A fully web-illustrated
#' morphological phylogenetic study of relationships among oak gall wasps and
#' their closest relatives (Hymenoptera: Cynipidae).}
#' \item{Loconte1991}{ LOCONTE, H. and STEVENSON, D. W. 1991. Cladistics of the Magnoliidae.
#' Cladistics, 7, 267--296.}
#' \item{Longrich2010}{ LONGRICH, N. R., SANKEY, J. and TANKE, D. 2010. \emph{Texacephale langstoni},
#' a new genus of pachycephalosaurid (Dinosauria: Ornithischia) from the upper
#' Campanian Aguja Formation, southern Texas, USA. Cretaceous Research, 31, 274--284.}
#' \item{OMeara2014}{ O'MEARA, R. N. and THOMPSON, R. S. 2014. Were There Miocene Meridiolestidans?
#' Assessing the phylogenetic placement of \emph{Necrolestes patagonensis} and the
#' presence of a 40 million year Meridiolestidan ghost lineage. Journal
#' of Mammalian Evolution, 21, 271--284.}
#' \item{Rougier2012}{ ROUGIER, G. W., WIBLE, J. R., BECK, R. M. D. and APESTEGUIA, S. 2012.
#' The Miocene mammal \emph{Necrolestes} demonstrates the survival of a
#' Mesozoic nontherian lineage into the late Cenozoic of South America.
#' Proceedings of the National Academy of Sciences, 109, 20053--8.}
#' \item{Sharkey2011}{ SHARKEY, M. J., CARPENTER, J. M., VILHELMSEN, L., HERATY, J., LILJEBLAD, J.,
#' DOWLING, A. P. G., SCHULMEISTER, S., MURRAY, D., DEANS, A. R., RONQUIST, F.,
#' KROGMANN, L. and WHEELER, W. C. 2012. Phylogenetic relationships among
#' superfamilies of Hymenoptera. Cladistics, 28, 80--112.}
#' \item{Sundue2010}{ SUNDUE, M. A., ISLAM, M. B. and RANKER, T. A. 2010. Systematics of
#' Grammitid Ferns (Polypodiaceae): Using Morphology and Plastid Sequence Data
#' to Resolve the Circumscriptions of Melpomene and the Polyphyletic Genera
#' \emph{Lellingeria} and \emph{Terpsichore}. Systematic Botany, 35, 701--715.}
#' \item{Vinther2008}{ VINTHER, J., VAN ROY, P. and BRIGGS, D. E. G. 2008. Machaeridians are
#' Palaeozoic armoured annelids. Nature, 451, 185--188.}
#' \item{Wilson2003}{ WILSON, G. D. F. and EDGECOMBE, G. D. 2003. The Triassic isopod
#' \emph{Protamphisopus wianamattensis} (Chilton) and comparison by extant
#' taxa (Crustacea, Phreatoicidea). Journal of Paleontology, 77, 454--470.}
#' \item{Wortley2006}{ WORTLEY, A. H. and SCOTLAND, R. W. 2006. The effect of combining molecular
#' and morphological data in published phylogenetic analyses.
#' Systematic Biology, 55, 677--685.}
#' \item{Zanol2014}{ ZANOL, J., HALANYCH, K. M. and FAUCHALD, K. 2014. Reconciling taxonomy and
#' phylogeny in the bristleworm family Eunicidae (Polychaete, Annelida).
#' Zoologica Scripta, 43, 79--100.}
#' \item{Zhu2013}{ ZHU, M., YU, X., AHLBERG, P. E., CHOO, B., LU, J., QIAO, T., QU, Q., ZHAO, W.,
#' JIA, L., BLOM, H. and ZHU, Y. 2013. A Silurian placoderm with osteichthyan-like
#' marginal jaw bones. Nature, 502, 188--193.}
#' }
#' }
#'
#'
#' @references
#' \insertAllCited{}
#' @examples
#' data("inapplicable.datasets", package = "TreeSearch")
#' names(inapplicable.datasets)
#' @keywords datasets
"inapplicable.datasets"
#' @rdname inapplicable.datasets
"inapplicable.phyData"
#' @rdname inapplicable.datasets
"inapplicable.trees"
#' @rdname inapplicable.datasets
"inapplicable.citations"
#' 100 simulated data matrices
#'
#' Contains the 100 simulated matrices generated by
#' \insertCite{Congreve2016}{TreeSearch} using a heterogeneous Markov-k model,
#' generated from the \link{referenceTree} topology, with
#' all branches sharing an equal length.
#'
#' @format A list with 100 entries, each comprising a `phyDat` object of 55
#' characters for 22 taxa
#'
#' @references
#' \insertAllCited{}
#'
#' @examples
#' data("referenceTree")
#' data("congreveLamsdellMatrices")
#' TreeLength(referenceTree, congreveLamsdellMatrices[[17]], "profile")
#'
#' @source \doi{10.5061/dryad.7dq0j}
#'
#' @keywords datasets
"congreveLamsdellMatrices"
#' Tree topology for matrix simulation
#'
#' The tree topology used to generate the matrices in
#' \code{\link{congreveLamsdellMatrices}}
#'
#' @format A single phylogenetic tree saved as an object of class \code{phylo}
#'
#' @references
#' \insertRef{Congreve2016}{TreeSearch}
#' \insertRef{Congreve2016dd}{TreeSearch}
#'
#' @examples
#' data(referenceTree)
#' plot(referenceTree)
#'
#' @source Congreve & Lamsdell (2016); \doi{10.1111/pala.12236}
#'
#' @keywords datasets
"referenceTree"
#' Empirically counted profiles for small trees
#'
#' The base 2 logarithm of the number of trees containing _s_ steps, calculated
#' by scoring a character on each _n_-leaf tree.
#'
#' @format A list with the structure
#' `profiles[[number of leaves]][[number of tokens]][[tokens in smallest split]]`
#' The list entry returns a named numeric vector; each entry lists
#' log2(proportion of _n_-leaf trees with _s_ or fewer steps for this character).
#'
#' @examples
#' data(profiles)
#'
#' # Load profile for a character of the structure 0 0 0 1 1 1 1 1
#' profile3.5 <- profiles[[8]][[2]][[3]]
#'
#' # Number of trees with _s_ or fewer steps on that character
#' TreeTools::NUnrooted(8) * 2 ^ profile3.5
#' @family profile parsimony functions
"profiles"
Try the TreeSearch package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.