inapplicable.datasets: Thirty datasets with inapplicable data
In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data
inapplicable.datasets R Documentation
Thirty datasets with inapplicable data
Description
These are the datasets used to evaluate the behaviour of the inapplicable
algorithm in \insertCiteBrazeau2018;textualTreeTools.
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 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.
Usage
inapplicable.datasets
inapplicable.phyData
inapplicable.trees
inapplicable.citations
Format
An object of class list of length 30.
An object of class list of length 30.
An object of class list of length 31.
An object of class character of length 30.
Source
Subset one (faster processing):
- Agnarsson2004
AGNARSSON, I. 2004. Morphological phylogeny of cobweb spiders and their
relatives (Araneae, Araneoidea, Theridiidae). Zoological Journal of the
Linnean Society, 141, 447–626.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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,
Jamoytius kerwoodi White. Palaeontology, 53, 1393–1409.
- 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.
- 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.
- 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.
- 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):
- Aguado2009
AGUADO, M. T. and SAN MARTIN, G. 2009. Phylogeny of Syllidae (Polychaeta)
based on morphological data. Zoologica Scripta, 38, 379–402.
- 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.
- Asher2005
ASHER, R. J. and HOFREITER, M. 2006. Tenrec phylogeny and the noninvasive
extraction of nuclear DNA. Systematic biology, 55, 181–94.
- 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.
- 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.
- 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.
- 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.
- 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.
- Geisler2001
GEISLER, J. H. 2001. New morphological evidence for the phylogeny of
Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates, 3344, 53.
- Giles2015
GILES, S., FRIEDMAN, M. and BRAZEAU, M. D. 2015. Osteichthyan-like cranial
conditions in an Early Devonian stem gnathostome. Nature, 520, 82–85.
- 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.
- 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).
- Loconte1991
LOCONTE, H. and STEVENSON, D. W. 1991. Cladistics of the Magnoliidae.
Cladistics, 7, 267–296.
- Longrich2010
LONGRICH, N. R., SANKEY, J. and TANKE, D. 2010. Texacephale langstoni,
a new genus of pachycephalosaurid (Dinosauria: Ornithischia) from the upper
Campanian Aguja Formation, southern Texas, USA. Cretaceous Research, 31, 274–284.
- OMeara2014
O'MEARA, R. N. and THOMPSON, R. S. 2014. Were There Miocene Meridiolestidans?
Assessing the phylogenetic placement of Necrolestes patagonensis and the
presence of a 40 million year Meridiolestidan ghost lineage. Journal
of Mammalian Evolution, 21, 271–284.
- Rougier2012
ROUGIER, G. W., WIBLE, J. R., BECK, R. M. D. and APESTEGUIA, S. 2012.
The Miocene mammal 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.
- 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.
- 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
Lellingeria and Terpsichore. Systematic Botany, 35, 701–715.
- Vinther2008
VINTHER, J., VAN ROY, P. and BRIGGS, D. E. G. 2008. Machaeridians are
Palaeozoic armoured annelids. Nature, 451, 185–188.
- Wilson2003
WILSON, G. D. F. and EDGECOMBE, G. D. 2003. The Triassic isopod
Protamphisopus wianamattensis (Chilton) and comparison by extant
taxa (Crustacea, Phreatoicidea). Journal of Paleontology, 77, 454–470.
- 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.
- 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.
- 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)
ms609/TreeSearch documentation built on April 7, 2024, 7:06 p.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.
| inapplicable.datasets | R Documentation |
Thirty datasets with inapplicable data
Description
These are the datasets used to evaluate the behaviour of the inapplicable
algorithm in \insertCiteBrazeau2018;textualTreeTools.
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 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.
Usage
inapplicable.datasets
inapplicable.phyData
inapplicable.trees
inapplicable.citations
Format
An object of class list of length 30.
An object of class list of length 30.
An object of class list of length 31.
An object of class character of length 30.
Source
Subset one (faster processing):
- Agnarsson2004
AGNARSSON, I. 2004. Morphological phylogeny of cobweb spiders and their relatives (Araneae, Araneoidea, Theridiidae). Zoological Journal of the Linnean Society, 141, 447–626.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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, Jamoytius kerwoodi White. Palaeontology, 53, 1393–1409.
- 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.
- 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.
- 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.
- 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):
- Aguado2009
AGUADO, M. T. and SAN MARTIN, G. 2009. Phylogeny of Syllidae (Polychaeta) based on morphological data. Zoologica Scripta, 38, 379–402.
- 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.
- Asher2005
ASHER, R. J. and HOFREITER, M. 2006. Tenrec phylogeny and the noninvasive extraction of nuclear DNA. Systematic biology, 55, 181–94.
- 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.
- 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.
- 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.
- 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.
- 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.
- Geisler2001
GEISLER, J. H. 2001. New morphological evidence for the phylogeny of Artiodactyla, Cetacea, and Mesonychidae. American Museum Novitates, 3344, 53.
- Giles2015
GILES, S., FRIEDMAN, M. and BRAZEAU, M. D. 2015. Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome. Nature, 520, 82–85.
- 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.
- 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).
- Loconte1991
LOCONTE, H. and STEVENSON, D. W. 1991. Cladistics of the Magnoliidae. Cladistics, 7, 267–296.
- Longrich2010
LONGRICH, N. R., SANKEY, J. and TANKE, D. 2010. Texacephale langstoni, a new genus of pachycephalosaurid (Dinosauria: Ornithischia) from the upper Campanian Aguja Formation, southern Texas, USA. Cretaceous Research, 31, 274–284.
- OMeara2014
O'MEARA, R. N. and THOMPSON, R. S. 2014. Were There Miocene Meridiolestidans? Assessing the phylogenetic placement of Necrolestes patagonensis and the presence of a 40 million year Meridiolestidan ghost lineage. Journal of Mammalian Evolution, 21, 271–284.
- Rougier2012
ROUGIER, G. W., WIBLE, J. R., BECK, R. M. D. and APESTEGUIA, S. 2012. The Miocene mammal 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.
- 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.
- 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 Lellingeria and Terpsichore. Systematic Botany, 35, 701–715.
- Vinther2008
VINTHER, J., VAN ROY, P. and BRIGGS, D. E. G. 2008. Machaeridians are Palaeozoic armoured annelids. Nature, 451, 185–188.
- Wilson2003
WILSON, G. D. F. and EDGECOMBE, G. D. 2003. The Triassic isopod Protamphisopus wianamattensis (Chilton) and comparison by extant taxa (Crustacea, Phreatoicidea). Journal of Paleontology, 77, 454–470.
- 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.
- 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.
- 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
\insertAllCitedExamples
data("inapplicable.datasets", package = "TreeSearch")
names(inapplicable.datasets)
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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