Code

Update to v1.2.5#153

Code

Merged

shwilks merged 163 commits intoacorg:masteracorg/Racmacs:masterfrom shwilks:mastershwilks/Racmacs:masterCopy head branch name to clipboardSep 27, 2023

+6,209-41,914

Commits

Commits on Mar 16, 2022

• Fix error in reoptimized-merge

  shwilks

  committed
  c78185b

• logtiterTableLayers() function exported

  shwilks

  committed
  081fc60

• Fix error when blobs are smaller than grid-spacing used to calculate them

  shwilks

  committed
  5b7e6f9

Commits on Mar 17, 2022

• * Add the blobsize() function for calculating the area/volume of uncertainty blobs

  Show description for a3185cb
  shwilks

  committed
  a3185cb

• Correct news

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  96c9521

Commits on Mar 18, 2022

• Correct docs for deprecated functions

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  ab7eb03

• Link to deprecated_functions

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  5693dee

Commits on Apr 19, 2022

• Fix error where serum column base label would remain after turning titer labels off

  shwilks

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  09c46f0

Commits on Apr 21, 2022

• Set default margins of 0.5 inches when plotting a map

  shwilks

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  7eafb24

Commits on Apr 25, 2022

• Changes and additions to js api

  shwilks

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  23e0e97

• Add support for insertions in amino acids sequences

  shwilks

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  1844df7

Commits on May 13, 2022

• Deal with missing blobs

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  df1634b

Commits on May 19, 2022

• Add option to specify a subset of antigens and sera for which to calculate blobs in the bootstrapBlobs() function

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  d68d8cc

Commits on May 28, 2022

• Update tests

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  ef067f4

• Add method for plotting a map using ggplot i.e. ggplot(map), also slight refactoring of C++ code

  shwilks

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  12c0b79

• When coloring by sequence use a more distinct color pallette

  shwilks

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  62748a2

• Add row and column names to sequence matrices

  shwilks

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  0d79588

• slight code refactoring

  shwilks

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  49bc70e

• Update warning message

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  eb69840

• Add text aesthetic

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  d59adf3

Commits on May 30, 2022

• Remove unwanted save reference

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  8e9b3b2

• Update docs and imports

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  a7a4d22

• Remove outlier arrow col from documentation

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  4ef2e36

Commits on May 31, 2022

• Return stress as part of ac_bootstrap_map

  shwilks

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  ab658ac

• Add outline width and alpha parameters

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  72841af

• Ignore .code-workspace files

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  8d2c446

• Ignore .code-workspace

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  5b3ffd1

Commits on Jun 8, 2022

• Add ability to plot procrustes lines

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  51f1df1

Commits on Jun 14, 2022

• Move r3js from remotes

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  1d6ac8b

• Add options to control arrow appearance

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  7fd8802

• Correct indentation

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  5f0451d

• Correct triangles

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  d5c5d8b

• Update date and dependencies

  shwilks

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  9c94bac

• Tidy up imports and dependencies

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  2e07307

• Update documentation

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  f1d8055

• Remove unnecessary curly braces in documentation

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  a4040b9

• Make description title case

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  c5c2a41

Commits on Jun 16, 2022

• Remove trailing whitespace

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  aabd872

Commits on Jun 22, 2022

• Add new binary build for v1.1.38

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  0869641

Commits on Jun 23, 2022

• Do not use \( syntax

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  2770b24

Commits on Aug 10, 2022

• Correct error when plotting cases where blobs were calculated for only 1 antigen / serum

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  42a743a

• Only show plot outlier arrowheads if point is marked as shown

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  969655c

• Numeric table distances account for dilution stepsize setting of map

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  d2c00eb

• Increment to 1.1.39

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  9f96c26

Commits on Oct 28, 2022

• Return more helpful error message

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  15d79df

Commits on Nov 17, 2022

• Run pkgdown on mac

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  9fd1720

• Allow for missing match cases

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  b08f180

• Deal with cases where legend groups do not contain any members

  shwilks

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  8cca419

• Update r3js lib

  shwilks

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  9e56aa3

• Set dilution stepsize when calculating numeric_min_tabledists

  shwilks

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  5285421

• Correct segments argument for new r3js library

  shwilks

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  1c19199

• Add hack to resize points

  shwilks

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  6431ffa

• Correct shape descriptions for new r3js library

  shwilks

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  6a1f5ec

• consolidate testdata path

  shwilks

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  e49d949

• Add some options to view.acmap to set the starting viewer translation, rotation and zoom

  shwilks

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  07f7352

• Add option to copy viewer rotation etc. settings

  shwilks

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  d48e190

• Try and fix gl point size problem

  shwilks

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  9e0b390

• minor edits

  shwilks

  committed
  0b2eb75

• Update to v1.1.40

  shwilks

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  b96b1e1

Commits on Nov 28, 2022

• Update line segments argument

  shwilks

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  d3904e9

• Correct line segments argument

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  ac6f12a

Commits on Dec 21, 2022

• Fix the implementation of glarrow

  shwilks

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  697fd05

• Update documentation

  shwilks

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  f45e36f

• Descrease number of external packages required

  shwilks

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  d73cce0

• Remove unneccessary files

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  c52cdd4

Commits on Dec 22, 2022

• Update description

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  5765fd1

• Update R-CMD-check

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  c83daad

• Update pkgdown action

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  8bde4c8

Commits on Dec 23, 2022

• Remove usage of sprintf

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  4828ac6

• Use linewidth instead of size

  shwilks

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  e95199f

• Remove map diagnostics vignette

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  cdc5742

• Require ggplot >= v3

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  570f637

• Use .data keyword

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  5f20137

• Use .data keyword

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  0cd09d1

• set seed

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  91413fd

• Import .data from ggplot2

  shwilks

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  207b309

• Update fortran compiler installation instructions

  shwilks

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  2c0c43f

Commits on Dec 28, 2022

• Change setup file

  shwilks

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  588b1bf

Commits on Dec 29, 2022

• Reduce size of hemisphering arrows

  shwilks

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  595ab62

• Correct maxpointsize for pixel ratio size

  shwilks

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  afb5a15

• Remove duplicated shader code

  shwilks

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  5861e59

• Change arrow linewidth depending on the number of dimensions

  shwilks

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  c2ac2ae

• Correct sequence change information

  shwilks

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  9278fd8

• Do not export test viewers by default

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  f8b98f5

Commits on Jan 3, 2023

• Update .gitignore

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  ac32b9d

• Remove previous builds

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  28503fe

• Remove .afdesign file

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  b6d4c95

• Decrease image sizes

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  636d8b4

Commits on Jan 31, 2023

• Return null array for NA points

  shwilks

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  53eb9f0

• Correct argument for updated r3js library

  shwilks

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  2dd16a7

• Remove legend for outline width when doing ggplot.acmap

  shwilks

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  656744b

• Deal with missing blob cases

  shwilks

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  1355ac6

• Increase size of boostrap point blobs in 2D

  shwilks

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  e2248a8

• Correct hemisphering error and add test

  shwilks

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  b599385

Commits on Feb 6, 2023

• Remove unnecessary readme breaks

  shwilks

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  d2d09fb

• Correct typo

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  cd166ed

Commits on Feb 24, 2023

• Update roxygen version

  shwilks

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  884ee8d

• Add grid.lwd option to control grid linewidth in ggplot(map)

  shwilks

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  bb47e93

• Add antigen and sera names to vector when retreiving antigen and sera attributes like agFill()

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  6446388

Commits on Apr 24, 2023

• Add new options and default methods to use when merging titers as described for RacMerge.options()

  

  Sam Wilks

  committed
  3bcbdd4

• Return a more useful error if bootstrapBlobs() is run on a map where bootstrapMap() has not yet been performed.

  

  Sam Wilks

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  83aecc1

• Add grid.margin.lwd option to control grid margin linewidth in ggplot(map)

  

  Sam Wilks

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  41049e6

• Add internal function to lower point drawing order in a map plot

  

  Sam Wilks

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  6cf6e13

• Ignore .vscode

  

  Sam Wilks

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  5604160

• Ignore .vscode

  

  Sam Wilks

  committed
  5fdd870

• Update docs

  

  Sam Wilks

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  98c1440

• Improve user interruption of map optimization runs

  

  Sam Wilks

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  3fbc080

• Add test for bootstrap map with no bootstrapping done

  

  Sam Wilks

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  f2a7b47

• Account for the fact that the vectors are named

  

  Sam Wilks

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  d84c82a

• Add titer tables

  

  Sam Wilks

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  7c647f9

• Account for warning

  

  Sam Wilks

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  a890d3c

• Update docs

  

  Sam Wilks

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  f92a8aa

• Update version

  

  Sam Wilks

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  849ef3b

Commits on Apr 25, 2023

• Make headings consistent

  

  Sam Wilks

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  12ab217

• Remove unnecessary Racmacs:::

  

  Sam Wilks

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  6d26ebd

Commits on May 12, 2023

• Titer merge method changed so that sd limit is implemented before any merging to < values and add additional tests

  shwilks

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  dc5fadd

• Expose further optimization options as user controllable options

  shwilks

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  9032f1b

• Add the option to set lighting using the r3js::light3js() function

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  b69c06a

• Add the option to set the viewer background color

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  1981b62

• Update documentation

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  41f55b8

Commits on May 14, 2023

• Add argument in view.acmap to control set viewer background color

  shwilks

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  5a968ae

• Match up arguments and documentation with generic method

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  0e7bada

Commits on May 16, 2023

• Fix error where light was not being added to the viewer properly

  shwilks

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  a4ea0ca

Commits on Jun 14, 2023

• Add arguments to control procrustes arrow appearance in plot.acmap()

  shwilks

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  8d53681

Commits on Aug 29, 2023

• Allow for shorthand description of shapes e.g. "C" for "CIRCLE" in map .ace files

  shwilks

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  7c80ac2

• Add unexported functions to get map data in a long table format

  shwilks

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  ad8d18d

• Add unexported functions to get agExtra and srExtra information in a matrix format

  shwilks

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  97bc81f

• Use R value color encoding for named colors

  shwilks

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  e76401a

• Update to version 1.2.5

  shwilks

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  c53fb49

• Add preliminary vignette describing styling a map

  shwilks

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  5badadb

• Update animation function

  shwilks

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  5b90034

• Add customising map appearance vignette

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  eedfa70

• Add tidyr

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  8a2490b

• Add additional imports

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  29fd09c

• Update Date

  shwilks

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  9e201e5

• Correct URL

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  eee790d

Commits on Aug 30, 2023

• Add CRAN submission notes

  shwilks

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  840c305

• Remove C++11 requirement

  shwilks

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  4e09543

• Set the default number of cores to use as 2 unless otherwise specified

  shwilks

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  794df31

• Update to version 1.2.6

  shwilks

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  09cea7a

Commits on Sep 1, 2023

• on.exit() calls added to code in R/map_plot.R and inst/shinyapps/RacmacsGUI/app.R where changes to graphical parameters and user options are made.

  shwilks

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  9b053cc

• Remove unused files

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  9eef23d

• snapshotMap() function removed.

  shwilks

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  f0216ae

• Removed unused files

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  e47d869

• Make sure user options are restored on exit

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  5f79bbb

• Remove test

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  d97f47e

• Comment out benchmarking code

  shwilks

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  cfa3173

• Remove benchmarking code

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  de6758c

• Use testmap_large for tests instead of 2004 map

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  00a13dd

• Update function documentation to make sure each function has a documented return value

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  415e6ca

• Ignore the vignettes/figures directory and the vignettes/intro-to-antigenic-cartography directory

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  73d73b0

• Update version and expand author and description

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  08b9c55

• Update documentation

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  16f7d92

• Update news

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  de47ece

• Add CRAN resubmission comments

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  6d2cd24

• Update submission info

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  6c1c5a9

• Update CRAN-SUBMISSION

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  28ec8d0

• Remove redundant author categories

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  6ff8b8c

• specify graphics::par and add another on.exit call

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  427a0fc

Commits on Sep 4, 2023

• Add documentation for the return value for the view() and keepOptimizations() functions

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  5ffb2c1

• Remove unnecessary additional spaces in Description

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  fc41c6a

• Update cran-comments for new submission

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  68f1d63

• Update cran submission file

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  2196763