Code

sync Armadillo #168

Code

Merged

KlausVigo merged 218 commits intoArmadilloKlausVigo/phangorn:Armadillofrom masterKlausVigo/phangorn:masterCopy head branch name to clipboardJun 19, 2024

+4,470-1,995

Commits

Commits on Apr 27, 2023

• allow DNAbin/AAbin objects,

  Show description for a29255d
  KlausVigo

  committed
  a29255d

• simplify code

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  5b2474d

Commits on May 5, 2023

• add tip.dates to allow nicer labeling with tip dated phylogenies

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  bef9f53

• clean up

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  6a88c1a

• root tree if necessary

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  adafd66

Commits on May 9, 2023

• add reference

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  81c2994

• use ape functions

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  57fb661

• add MCC option to plotBS. Small improvements

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  8895b92

• Small improvements

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  ecf476f

• print rate for tipdated tree

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  cdbf6db

• uncomment uneeded functions

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• updates

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  137361f

• better defaults, check if trees are rooted

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  990d3ec

• clean up

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  b60878b

• bugfix

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  5edb485

Commits on May 30, 2023

• allow to return vector

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  b6c1f59

• fix man page

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  f4cd79c

• allow clade credibilities

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  00a7970

Commits on Jun 2, 2023

• fix spelling

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  b06c0cb

Commits on Jun 7, 2023

• small

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  9e2e1db

Commits on Jun 16, 2023

• fix spelling

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  84df1d2

• simplify

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  83c3be8

• allow character vectors

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  5b22e63

• Improve manual

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  48a0245

• bug fix

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  c151435

• bugfix

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  5b0d695

Commits on Jun 20, 2023

• clean up

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  3efcf6d

• update

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  7b93863

Commits on Jun 22, 2023

• improve rbind.phyDat

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  367961b

Commits on Jul 4, 2023

• reorganize code

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  6174f0d

• allow direction and rotating the plot

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  d44c9b3

• add keep.as.tip

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• small improvements

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  4e29500

• bugfix

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  97c9e24

• bug fix

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  f09bcbd

• bugfix

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  992eb18

• use experimental ape

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  f98a1cf

Commits on Jul 6, 2023

• change to ape develoment

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  0f70a4e

Commits on Jul 11, 2023

• update

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  e5b05e8

• noicer printing

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  3ed5baf

Commits on Jul 17, 2023

• consensus trees might not be

  Show description for ec9d8cb
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  ec9d8cb

• direct conversion of AAbin objects, uses less memory

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  30ffef7

Commits on Jul 18, 2023

• use node labels or add them

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  732e37a

• bugfix

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  9b04b5a

• no unnecessary output

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  dba93cc

• bugfix

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  2250b13

• update

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  8bf0d2f

Commits on Jul 24, 2023

• change URL

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  3a62282

• allow plotAnc to use proper phyDat arguments

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  09db6f8

Commits on Aug 1, 2023

• handle ancestral states better

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  df2bb82

• distinguish unrooted plots

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  229d9a1

Commits on Aug 4, 2023

• reorganize code

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  947252e

• add colorschemes

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  ec581fc

• bugfix

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  5db2474

• update

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  d1a46cc

• bugfix

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  f2724fe

• bugfix

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  5db5fcb

Commits on Aug 21, 2023

• bug fix

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  2a6aba5

• update

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  d050425

Commits on Aug 28, 2023

• clean up code

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  eb1f429

Commits on Aug 29, 2023

• speed up candidate tree

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  14e039b

• improve indexNNI to allow for different porpuses

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  8280af9

Commits on Sep 6, 2023

• add several support values to a tree

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  5a99179

• small improvements to color schemes

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  c871d71

Commits on Sep 7, 2023

• avoid warning

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  858967d

Commits on Sep 13, 2023

• improve man page

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  cac1415

• improve plot.networx

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  5adee6e

Commits on Oct 3, 2023

• bug fix if duplicated sequences exist

  KlausVigo

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  7b4e8e0

Commits on Oct 16, 2023

• improve examples

  KlausVigo

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  abb6663

• bug fix

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  committed
  dfef4ea

Commits on Oct 17, 2023

• add experimental function write.ancestral, interface might change

  KlausVigo

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  8647726

• update man page

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  71dd002

• add as.phyDat.AAStringset, as.phyDat.DNAStringset going via AAbin/DNAbin objects

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  aa8c9c6

Commits on Oct 20, 2023

• change scalebar and suport values with cex

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  44d350a

Commits on Oct 24, 2023

• set trace=0 by default

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  5cacdbb

Commits on Nov 14, 2023

• improve as.data.frame.ancestral

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  975d23a

• simplify code

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  ba3c44f

Commits on Dec 5, 2023

• fix documentation

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  2a375c6

• more ratchet iterations

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  ea381f1

Commits on Dec 13, 2023

• several bug fies and improvements

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  f001d48

Commits on Dec 18, 2023

• improve man page

  KlausVigo

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  486af8b

• cleaning up, improve ratchet

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  1d65575

Commits on Jan 11, 2024

• bug fix reported by John Rhodes

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  98e09d7

Commits on Jan 12, 2024

• Improve man page

  KlausVigo

  committed
  5709e0b

• add references

  KlausVigo

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  37d76ef

• small improvements

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  committed
  9d091b3

Commits on Jan 15, 2024

• Fix phylip webpage

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  b34fc4a

• reorganise code

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  819ace8

• update

  KlausVigo

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  8a6a848

• try to avoid errors

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  3dbe65e

• try to avoid errors

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  95456b0

• test

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  8d32c6c

• test if tests work now again

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  927a461

Commits on Jan 16, 2024

• add_edge_length assign now also edge length to an splits graph (networx)

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  ebd9d80

Commits on Jan 25, 2024

• fix bug reported by @amizeranschi

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  2f66600

• don't depend on apex

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  5c3aeba

Commits on Jan 31, 2024

• remove duplicated code

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  7a6c2d9

• speed up example

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  1cd2373

• bugfix

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  6687277

Commits on Feb 7, 2024

• apex is back on CRAN

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  312b127

• cleaning up

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  d821bd6

• bug fix

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  committed
  54f6361

Commits on Feb 8, 2024

• add apex support

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  636b78c

Commits on Feb 9, 2024

• new tests

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  680329f

Commits on Feb 14, 2024

• clean up

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  committed
  f142b40

• improve error messages

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  0ef34aa

• small API change

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  717f47d

• bugfix

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  88fa224

• bugfix

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  5e53e16

Commits on Feb 16, 2024

• use shared ape data

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  998c93f

Commits on Feb 21, 2024

• fixed esoteric error for invariant sites

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  4b07aac

Commits on Feb 23, 2024

• small updates

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  ad14693

• small improvement

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  20a83c5

• add immproved lower bound by default

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  1c6606c

Commits on Mar 5, 2024

• clean up

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  ee876f7

• nicer plots

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  68fd4b5

• improve image (allow gaps as states)

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  6501347

• Ancestral states of constant sites are now always this state

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  0ea5b08

Commits on Mar 6, 2024

• export glance methods

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  d016642

• add gap_as_state

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  ad9117a

• update

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  7b634b5

Commits on Mar 7, 2024

• bug fix

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  committed
  02e3193

• small improvements

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  e069e46

• add composition_test

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  4bf2863

Commits on Mar 9, 2024

• add composition_test

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  7d02ccc

• Merge branch 'master' of https://github.com/KlausVigo/phangorn

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  68061cb

Commits on Mar 18, 2024

• clean up

  KlausVigo

  committed
  b700fcc

• update man page

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  committed
  ed29611

Commits on Mar 26, 2024

• small improvement

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  20507bf

Commits on Apr 3, 2024

• get rid of note

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  20f6282

• fix ape link and add r-universe link

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  a43c136

• small improvement and new check functions

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  885dda5

• make it more robust

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  97a3925

• replace warning by message

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  0dec81b

• add example

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  b1af551

• clean up

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  20495f3

• new function dna2aa

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  8c6bb76

Commits on Apr 4, 2024

• less print out

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  1a92ed2

• clean up

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  aa3bc61

• ML support for gap as its own state

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  committed
  e1a3660

• bugfix

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  cd1adca

• small improvements

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  fa10b18

Commits on Apr 5, 2024

• bug fix

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  committed
  4cbd17e

Commits on Apr 17, 2024

• use ggseqlogo instead of seqLogo, update ape to >=5.8

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  2d56a50

• ancestral reconstruction was rewritten

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  committed
  76aa52c

• clean up

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  90f8166

• update

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  committed
  1a4e448

• small improvements

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  committed
  0fb3099

• clean up, use definition for color schemes in ape

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  committed
  93e7edf

• prevent warnings

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  c1442bc

• small improvement

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  796fed5

• scale tree

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  a929e35

Commits on Apr 18, 2024

• add links, try black gaps in plots

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  71e9307

• nicer messages, encapsulate code

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  1926499

• add rechceck workflow

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  ffbab19

Commits on Apr 19, 2024

• scale edges if necessary

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  ed09a47

• more consistent coloring

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  committed
  a7f6ca4

• simpler workflow

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  committed
  c1a80a5

• Merge branch 'master' of https://github.com/KlausVigo/phangorn

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  committed
  15261fd

Commits on Apr 23, 2024

• add supoort codons

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  29eb64f

• add suport for codons

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  c76a40d

• try avoiding nodes, add as.phyDat.ancestral

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  d8c0e9f

• add ggplot2 as import

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  8a56b70

• updates

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  6464347

• bugfix

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  0106dc5

Commits on Apr 28, 2024

• add xlim and ylim, allow more control for the plots

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  f6932e3

• improve documentation, add examples and return values to make pkgcheck happy

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  212254d

• update, add return

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  4b3186c

• don't export read.aa (use read.phyDat instead)

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  bd60ac0

• improve man page

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  committed
  90bc96e

• small improvements

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  committed
  4c7a814

Commits on Apr 29, 2024

• small improvements

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  committed
  5a77a8c

• add tests

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  committed
  8e0cbcf

• update

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  committed
  91439ab

• add examples

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  9191d98

• clean up

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  395a169

• add tests

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  729e8a4

Commits on May 1, 2024

• improve man pages add return values

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  0f27d82

Commits on May 3, 2024

• change to make_graph, pointed out by Szabolcs Horvát

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  884d31b

Commits on May 10, 2024

• Improve man pages

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  committed
  a025619

• bugfix

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  1671ae3

Commits on May 17, 2024

• avoid warning

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  committed
  82dfdbb

• add some additional test infrastructure

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  committed
  ca442e5

• updates

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  committed
  83b39c8

• add tests

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  447c641

• remove plot.ancestral for now

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  87902a6

• add tests for some plots

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  01934aa

• bug fix

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  7089787

• bug fix

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  7166ab5

Commits on May 19, 2024

• update code coverage

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  542c0f5

• add test

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  7dd4383

Commits on May 20, 2024

• remove warning

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  342fcee

• add write.pml

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  656d1dc

• add imports

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  9bbeed9

• bug fix

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  e4e1622

• add man pages

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  3be40de

Commits on May 21, 2024

• no Remotes

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  2231d74

• fix plot

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  ec88541

• clean up

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  b273a84

Commits on May 22, 2024

• avoid empty cycle attribute

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  bfc2650

Commits on May 23, 2024

• small improvements to plot functions

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  7d484b3

Commits on May 27, 2024

• return x invisible in densiTree

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  942175f

Commits on Jun 1, 2024

• reorganize networx code

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  committed
  6ffc11e

• add rate to print output

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  committed
  54a4ee5

• change defaults and experiment with early ...

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  c81e968

Commits on Jun 6, 2024

• improve ancestral (when reading ASR from iqtree), update man pages

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  committed
  57141b0

Commits on Jun 7, 2024

• update man page of plotAnc

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  a4cc7b0

• update man page

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  committed
  7cecbc0

Commits on Jun 11, 2024

• Add lt2amb the equivalent to latag2n in ape. Generic in future?

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  2a046ae

• add experimental joint reconstruction, based on Liam's phytools code.

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  committed
  5ae5761

• update NEWS

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  committed
  b1927f7

• add some links

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  committed
  ddbed49

• fix spelling

  KlausVigo

  committed
  5086adc

Commits on Jun 16, 2024

• small improvements

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  committed
  971d981

Commits on Jun 17, 2024

• bugfix

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  committed
  17ce4c1

• bugfix

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  committed
  3b52c30

• bugfix

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  committed
  ea8ca9b

Commits on Jun 19, 2024

• fix wrong links

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  committed
  5c33b58