TreeSearch-0.4.3.zip
ms609-TreeSearch-8d902c7
.Rbuildignore
304 Bytes
.gitattributes
378 Bytes
.gitignore
249 Bytes
.travis.yml
1.1 kB
CODE_OF_CONDUCT.md
1.4 kB
CONTRIBUTING.md
2.2 kB
DESCRIPTION
1.5 kB
NAMESPACE
3.1 kB
NEWS.md
4.9 kB
R
Bootstrap.R
4.3 kB
Fitch.R
7.6 kB
IWScore.R
4.1 kB
Jackknife.R
4.5 kB
NNI.R
5.9 kB
RandomTreeScore.R
1.4 kB
Ratchet.R
15.1 kB
ReleaseQuestions.R
429 Bytes
SPR.R
13.4 kB
Sectorial.R
15.7 kB
SuccessiveApproximations.R
5.2 kB
TBR.R
20.0 kB
TreeSearch.R
7.9 kB
data.R
2.9 kB
data_manipulation.R
6.6 kB
mpl_morphy_objects.R
6.2 kB
mpl_morphyex.R
17.1 kB
mpl_prepare_data.R
974 Bytes
mpl_visualise.R
6.2 kB
pp_ProfileScore.R
4.2 kB
pp_info_extra_step.r
10.5 kB
tree_rearrangement.R
4.5 kB
zzz.R
1.1 kB
README.md
3.6 kB
TreeSearch.Rproj
410 Bytes
_config.yml
27 Bytes
codemeta.json
8.4 kB
cran-comments.md
585 Bytes
data
congreveLamsdellMatrices.RData
33.7 kB
inapplicable.citations.R
6.3 kB
inapplicable.datasets.rda
70.5 kB
inapplicable.phyData.rda
75.0 kB
referenceTree.RData
338 Bytes
data-raw
Agnarsson2004.nex
17.1 kB
Aguado2009.nex
11.2 kB
Aria2015.nex
3.0 kB
Asher2005.nex
3.8 kB
Capa2011.nex
11.4 kB
Conrad2008.nex
25.7 kB
DeAssis2011.nex
3.3 kB
Dikow2009.nex
23.1 kB
Eklund2004.nex
9.4 kB
Geisler2001.nex
15.2 kB
Giles2015.nex
20.6 kB
Griswold1999.nex
7.2 kB
Liljeblad2008.nex
23.8 kB
Loconte1991.nex
7.6 kB
Longrich2010.nex
2.8 kB
Longrich2010.xlsx
14.9 kB
OLeary1999.nex
7.1 kB
OMeara2014.nex
21.6 kB
Rougier2012.nex
19.7 kB
Rousset2004.nex
5.4 kB
Sano2011.nex
3.4 kB
Sansom2010.nex
3.2 kB
Schulze2007.nex
5.1 kB
Shultz2007.nex
13.6 kB
Vinther2008.nex
2.0 kB
Wetterer2000.nex
11.5 kB
Wills2012.nex
7.0 kB
Wilson2003.nex
12.8 kB
Wortley2006.nex
5.4 kB
Zanol2014.nex
18.5 kB
Zhu2013.nex
20.9 kB
_data_generator.R
458 Bytes
inst
CITATION
2.4 kB
REFERENCES.bib
3.8 kB
WORDLIST
1.9 kB
_pkgdown.yml
1.9 kB
apa-old-doi-prefix.csl
25.1 kB
preamble.tex
127 Bytes
tests
benchmark_timing.R
7.5 kB
man
AllSPR.Rd
1.3 kB
AsBinary.Rd
740 Bytes
CharacterLength.Rd
1.3 kB
DoubleNNI.Rd
996 Bytes
Evaluate.Rd
567 Bytes
Fitch.Rd
1.5 kB
ICPerStep.Rd
958 Bytes
ICSteps.Rd
1.8 kB
IWScore.Rd
2.1 kB
InfoAmounts.Rd
861 Bytes
JackLabels.Rd
1.3 kB
LogisticPoints.Rd
598 Bytes
MinimumLength.Rd
2.0 kB
MorphyBootstrap.Rd
3.0 kB
MorphyErrorCheck.Rd
1.4 kB
MorphyTreeLength.Rd
2.2 kB
MorphyWeights.Rd
1.7 kB
NNI.Rd
2.5 kB
PhyDat2Morphy.Rd
1.6 kB
PrepareDataProfile.Rd
1.8 kB
ProfileScore.Rd
2.9 kB
RandomMorphyTree.Rd
603 Bytes
RandomTreeScore.Rd
541 Bytes
Ratchet.Rd
9.5 kB
RearrangeEdges.Rd
2.6 kB
SPR.Rd
3.0 kB
SetMorphyWeights.Rd
1.9 kB
SingleCharMorphy.Rd
1.7 kB
StopUnlessBifurcating.Rd
648 Bytes
Suboptimality.Rd
546 Bytes
SuccessiveApproximations.Rd
1.5 kB
SuccessiveWeights.Rd
679 Bytes
TBR.Rd
3.4 kB
TBRWarning.Rd
686 Bytes
TipsAreNames.Rd
883 Bytes
TreeSearch.Rd
5.5 kB
UniqueExceptHits.Rd
323 Bytes
UnloadMorphy.Rd
1.8 kB
WithOneExtraStep.Rd
536 Bytes
congreveLamsdellMatrices.Rd
913 Bytes
inapplicable.citations.Rd
8.2 kB
inapplicable.datasets.Rd
8.4 kB
inapplicable.phyData.Rd
8.3 kB
mpl_apply_tipdata.Rd
1.7 kB
mpl_attach_rawdata.Rd
1.8 kB
mpl_attach_symbols.Rd
2.1 kB
mpl_delete_Morphy.Rd
1.6 kB
mpl_delete_rawdata.Rd
1.6 kB
mpl_first_down_recon.Rd
2.2 kB
mpl_first_up_recon.Rd
2.2 kB
mpl_get_charac_weight.Rd
1.7 kB
mpl_get_num_charac.Rd
1.5 kB
mpl_get_num_internal_nodes.Rd
1.6 kB
mpl_get_numtaxa.Rd
1.6 kB
mpl_get_symbols.Rd
1.7 kB
mpl_init_Morphy.Rd
1.7 kB
mpl_new_Morphy.Rd
1.6 kB
mpl_second_down_recon.Rd
2.2 kB
mpl_second_up_recon.Rd
2.3 kB
mpl_set_charac_weight.Rd
1.6 kB
mpl_set_num_internal_nodes.Rd
1.7 kB
mpl_set_parsim_t.Rd
1.9 kB
mpl_translate_error.Rd
1.6 kB
mpl_update_lower_root.Rd
2.0 kB
mpl_update_tip.Rd
2.3 kB
referenceTree.Rd
646 Bytes
summary.morphyPtr.Rd
1.6 kB
man-roxygen
CleanUpDataParam.R
152 Bytes
EdgeSwapperParam.R
148 Bytes
InitializeDataParam.R
232 Bytes
MRS.R
101 Bytes
concavityParam.R
204 Bytes
dataForFunction.R
68 Bytes
datasetParam.r
214 Bytes
edgeListParam.R
374 Bytes
edgeToBreakParam.R
239 Bytes
inapplicableSources.R
9.2 kB
labelledTreeParam.R
249 Bytes
leftChildParam.R
233 Bytes
mergeEdgesParam.R
399 Bytes
morphyObjParam.R
92 Bytes
nCoresParam.R
264 Bytes
parentOfParam.R
178 Bytes
pointlessDots.R
151 Bytes
returnEdgeList.R
328 Bytes
rightChildParam.R
113 Bytes
split12Params.R
213 Bytes
split1Param.R
124 Bytes
split2Param.R
124 Bytes
splits12params.R
361 Bytes
splitsParam.R
354 Bytes
stopAtPeakParam.R
460 Bytes
stopAtPlateauParam.R
379 Bytes
stopAtScoreParam.R
74 Bytes
swappersParam.R
567 Bytes
treeChild.R
212 Bytes
treeNEdge.R
125 Bytes
treeNEdgeOptional.R
200 Bytes
treeParam.r
113 Bytes
treeParent.r
212 Bytes
treeScorerDots.r
116 Bytes
treeScorerParam.r
208 Bytes
verbosityParam.r
121 Bytes
warnParam.R
129 Bytes
src
RMorphy.c
9.7 kB
RMorphy.h
1.9 kB
RMorphyUtils.c
751 Bytes
RMorphyUtils.h
241 Bytes
TreeSearch-init.c
2.4 kB
build_postorder.h
6.4 kB
fitch.c
25.9 kB
fitch.h
2.3 kB
from_ape.c
1.4 kB
morphy.c
27.2 kB
morphy.h
2.7 kB
morphydefs.h
4.9 kB
mpl.c
24.5 kB
mpl.h
22.6 kB
mplerror.h
2.4 kB
statedata.c
17.2 kB
statedata.h
2.0 kB
wagner.c
2.7 kB
wagner.h
484 Bytes
tests
testthat
test-Fitch.R
5.6 kB
test-Jackknife.R
985 Bytes
test-RMorphy.R
314 Bytes
test-TreeSearch.R
6.7 kB
test-data-manipulation.R
1.4 kB
test-pp-ICS.R
947 Bytes
test-pp-fitch.R
579 Bytes
test-pp-random-tree.R
5.0 kB
test-zzz-tree-rearrange.R
10.0 kB
testthat.R
68 Bytes
vignettes
getting-started.Rmd
1.7 kB
inapplicable.Rmd
8.3 kB
profile-scores.Rmd
2.8 kB
profile.Rmd
13.6 kB