Code

rOpenSci review by Aug24th#3

Code

Merged

cromanpa94 merged 79 commits intomasterropensci/treedata.table:masterfrom cristianropensci/treedata.table:cristianCopy head branch name to clipboardAug 25, 2020

+1,269-538

Commits

Commits on Aug 4, 2020

• REVIEW:Type field deleted

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  07746cf

  Copy full SHA for 07746cf

• REVIEW: Title case

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  ff610ad

  Copy full SHA for ff610ad

• REVIEW: LICENSE updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  8b6250e

  Copy full SHA for 8b6250e

• REVIEW:Multiline instructions removed

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  748ddde

  Copy full SHA for 748ddde

• Fix multiline as.treedata.table

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  59872e5

  Copy full SHA for 59872e5

• REVIEW:Booleans fixed in ifelse statements

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  9afe310

  Copy full SHA for 9afe310

• REVIEW:using inherits instead of class

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  1b5c188

  Copy full SHA for 1b5c188

• REVIEW:Fix seq_along

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  700e0ed

  Copy full SHA for 700e0ed

• REVIEW:message() instead of cat()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  b99ea3c

  Copy full SHA for b99ea3c

• REVIEW:paste0() within message() were removed

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  c7ebb3b

  Copy full SHA for c7ebb3b

• REVIEW:name_column argument fixed for "detect"

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  cb04cf5

  Copy full SHA for cb04cf5

• REVIEW:testthat updated to include correct column auto-detection

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  54a8559

  Copy full SHA for 54a8559

• REVIEW:Message printing the auto-detected column

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  5b1951b

  Copy full SHA for 5b1951b

• REVIEW:Changes based on style_pkg

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  d4cffa5

  Copy full SHA for d4cffa5

• Remove new testthat

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  600752d

  Copy full SHA for 600752d

Commits on Aug 5, 2020

• REVIEW:testthat updated to include correct column auto-detection (UPDATED)

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  e00fef9

  Copy full SHA for e00fef9

• Review:remove repeatsAsDiscrete from detectCharacterType() and detectAllCharacters()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  41f32f5

  Copy full SHA for 41f32f5

• REVIEW:removed as.matrix() from detectAllCharacters

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  099a0a8

  Copy full SHA for 099a0a8

• REVIEW:Test if the correct number of discrete/continuous characters are being found in the anolis dataset

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  4752e44

  Copy full SHA for 4752e44

• REVIEW:Fixing 1: in forceNames()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  96f84da

  Copy full SHA for 96f84da

• Back to e00fef9

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  d22efc2

  Copy full SHA for d22efc2

• REVIEW:Fixing additional Seq_along instead of 1:

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  9779592

  Copy full SHA for 9779592

• REVIEW:Remove as.matrix from detectAllCharacters()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  8d4b9e1

  Copy full SHA for 8d4b9e1

• Using seq_len instead of 1:

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  19a777c

  Copy full SHA for 19a777c

• REVIEW:Test if the correct number of discrete/continuous characters

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  3cd17b9

  Copy full SHA for 3cd17b9

• REVIEW:promt removed in droptreedata.table

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  a6d0b60

  Copy full SHA for a6d0b60

• remove extra line in summary.treedata.table()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  23cfafe

  Copy full SHA for 23cfafe

• REVIEW:extractVector simplified for ...

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  63a2935

  Copy full SHA for 63a2935

• REVIEW:tail() included. Additional changes-ROXIGENISE()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  9b62811

  Copy full SHA for 9b62811

• extractVector examples updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  42491d2

  Copy full SHA for 42491d2

• update vignette

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  9aca3dd

  Copy full SHA for 9aca3dd

• Update extractVector

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  0f31ded

  Copy full SHA for 0f31ded

• S3 methods updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  292295c

  Copy full SHA for 292295c

• Prev versions of tail and head

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  de8045f

  Copy full SHA for de8045f

• imports solved

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  500648a

  Copy full SHA for 500648a

• print() Updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  f662ff4

  Copy full SHA for f662ff4

Commits on Aug 6, 2020

• tests added

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  29cf0aa

  Copy full SHA for 29cf0aa

• Additional tests

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  17e940c

  Copy full SHA for 17e940c

• Coverage to >80% (local)

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  ab53e26

  Copy full SHA for ab53e26

• REVIEW:styler::style_pkg() and roxygen2md::roxygen2md()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  cd0c945

  Copy full SHA for cd0c945

• REVIEW:name_column argument to explain that "detect"

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  b5f19cb

  Copy full SHA for b5f19cb

• REVIEW:remove @return in as.treedata.table()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  10354e2

  Copy full SHA for 10354e2

• REVIEW:Documentation for hasNames() and forceNames() updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  2b62d02

  Copy full SHA for 2b62d02

• REVIEW:multiple column names in extractVector

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  3acb5cc

  Copy full SHA for 3acb5cc

• REVIEW:pulldata.data.table() instead of pull.data.data.table()

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  cd8fc93

  Copy full SHA for cd8fc93

Commits on Aug 7, 2020

• REVIEW:updated head and tail documentation

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  8fbaaa6

  Copy full SHA for 8fbaaa6

• REVIEW:Fixed vignette

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  07d2178

  Copy full SHA for 07d2178

• reconfigure author block so ORCIDs can be added

  wrightaprilm

  committed
  abfb2cb

  Copy full SHA for abfb2cb

• updated README per review

  wrightaprilm

  committed
  9cd075a

  Copy full SHA for 9cd075a

• added CONTRIBUTING document

  wrightaprilm

  committed
  a9a7bde

  Copy full SHA for a9a7bde

• REVIEW: long lines per gp()

  wrightaprilm

  committed
  bfb2572

  Copy full SHA for bfb2572

• REVIEW: make spaces and tabs uniform with styler()

  wrightaprilm

  committed
  016bc06

  Copy full SHA for 016bc06

• REVIEW: make tests compatible with 80-line limits

  wrightaprilm

  committed
  d860070

  Copy full SHA for d860070

Commits on Aug 8, 2020

• REVIEW:Removing charType from filterMatrix

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  3253251

  Copy full SHA for 3253251

• REVIEW:Description added to detectCharacterType, detectCharacterChanges, and filterMatrix

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  ca94642

  Copy full SHA for ca94642

• REVIEW:Vignette updated for filterMatrix, forceNames, and hasNames

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  9988f78

  Copy full SHA for 9988f78

• REVIEW:repeatsAsDiscrete removed

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  79cfcb4

  Copy full SHA for 79cfcb4

• REVIEW:more badges added

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  b38d88a

  Copy full SHA for b38d88a

• codecov updated

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  43450f1

  Copy full SHA for 43450f1

• codecov

  

  Cristian Román Palacios

  authored and

  Cristian Román Palacios

  committed
  3003e00

  Copy full SHA for 3003e00

Commits on Aug 9, 2020

• Add logo

  cromanpa94

  committed
  42b58cf

  Copy full SHA for 42b58cf

• Logo size

  cromanpa94

  committed
  2a12a7d

  Copy full SHA for 2a12a7d

• Logo resized

  cromanpa94

  committed
  7062a02

  Copy full SHA for 7062a02

• links and formatting

  cromanpa94

  committed
  22b0f18

  Copy full SHA for 22b0f18

• REVIEW:CRP to aut

  cromanpa94

  committed
  16b6fbe

  Copy full SHA for 16b6fbe

• REVIEW:Missing ORCID added

  cromanpa94

  committed
  b76f4a8

  Copy full SHA for b76f4a8

• REVIEW: Hugo and Kari

  cromanpa94

  committed
  44cceda

  Copy full SHA for 44cceda

• REVIEW:match.arg for oulltreedata.table

  cromanpa94

  committed
  9408ac3

  Copy full SHA for 9408ac3

• REVIEW:setDT removed

  cromanpa94

  committed
  92bf3c8

  Copy full SHA for 92bf3c8

• REVIEW:Information on the Default added

  cromanpa94

  committed
  fa8fd8f

  Copy full SHA for fa8fd8f

• REVIEW:Depends and Imports

  cromanpa94

  committed
  3d43122

  Copy full SHA for 3d43122

Commits on Aug 10, 2020

• Fixing tips dropped from [

  cromanpa94

  committed
  22eace9

  Copy full SHA for 22eace9

• Fixing tips dropped x2 [

  cromanpa94

  committed
  be1a218

  Copy full SHA for be1a218

Commits on Aug 14, 2020

• REVIEW:microbenchmark

  cromanpa94

  committed
  3bd6574

  Copy full SHA for 3bd6574

• FigSize

  cromanpa94

  committed
  bee6c12

  Copy full SHA for bee6c12

• FigSize

  cromanpa94

  committed
  479f04c

  Copy full SHA for 479f04c

• Figsize3

  cromanpa94

  committed
  3f308e6

  Copy full SHA for 3f308e6

Commits on Aug 24, 2020

• REVIEW:filterMatrix and droptreedata.table message

  cromanpa94

  committed
  4917b4a

  Copy full SHA for 4917b4a

• Bisaloo's comments

  cromanpa94

  committed
  73e5c14

  Copy full SHA for 73e5c14