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base repository: wincowgerDEV/OpenSpecy-package
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base: v1.0.2
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head repository: wincowgerDEV/OpenSpecy-package
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Commits on Sep 13, 2023

  1. Better tests and interactive plots (#140)

    * better tests
    * better plotting, split and rel
    * add a couple other errors to `check_OpenSpecy()`
    * add contributors
    * submit v1.0.3
    
    ---------
    
    Co-authored-by: Zacharias Steinmetz <git@zsteinmetz.de>
    wincowgerDEV and zsteinmetz authored Sep 13, 2023
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Commits on Oct 2, 2023

  1. Various bug fixes (#147)

    * Add `showlegend` option
    * Add dots option for `plotly_spec()`
    * Fix bug with `match_spec()`
    * Improve syntax
    * Fix NA as top by removing NA, also faster logic.
    * Force col_id to equal names of the spectra
    * Add contributors
    * Prepare CRAN submission
    
    ---------
    
    Co-authored-by: Zacharias Steinmetz <git@zsteinmetz.de>
    wincowgerDEV and zsteinmetz authored Oct 2, 2023
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Commits on Oct 20, 2023

  1. Support .tsv files (#155)

    Fixes #153
    zsteinmetz authored Oct 20, 2023
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Commits on Oct 31, 2023

  1. Flip xy coordinates in ENVI files (#156)

    * Test flip
    * Update tests
    
    ---------
    
    Co-authored-by: Win Cowger, PhD <wincowger@gmail.com>
    zsteinmetz and wincowgerDEV authored Oct 31, 2023
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  2. Prepare v1.0.5 for CRAN

    zsteinmetz committed Oct 31, 2023
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  11. add tests

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  2. update tests

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Commits on Nov 25, 2023

  1. Streamlining identification (#157)

    * make it easier to do matches, this way many will be able to bypass the preprocessing.
    * updates to sig_noise make it more flexible
    * add attributes
    * new CRAN submission
    
    ---------
    
    Co-authored-by: Zacharias Steinmetz <git@zsteinmetz.de>
    wincowgerDEV and zsteinmetz authored Nov 25, 2023
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Commits on Dec 7, 2023

  1. add similarity

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Showing with 3,793 additions and 4,542 deletions.
  1. +1 −0 .Rbuildignore
  2. +22 −0 .github/workflows/deploy-cran-repo.yml
  3. +6 −3 .github/workflows/pkgdown.yaml
  4. +17 −0 .github/workflows/release-file-system-image.yml
  5. +3 −3 CRAN-SUBMISSION
  6. +27 −17 DESCRIPTION
  7. +39 −9 NAMESPACE
  8. +99 −0 NEWS.md
  9. +1 −1 R/OpenSpecy-package.R
  10. +41 −13 R/adj_intens.R
  11. +44 −0 R/adj_wave.R
  12. +143 −91 R/as_OpenSpecy.R
  13. +32 −6 R/conform_spec.R
  14. +203 −84 R/def_features.R
  15. +171 −79 R/interactive_plots.R
  16. +20 −11 R/io_spec.R
  17. +159 −41 R/manage_lib.R
  18. +107 −0 R/manage_na.R
  19. +93 −8 R/manage_spec.R
  20. +229 −31 R/match_spec.R
  21. +4 −4 R/process_spec.R
  22. +44 −11 R/read_envi.R
  23. +101 −60 R/read_ext.R
  24. +59 −24 R/read_multi.R
  25. +1 −5 R/read_opus.R
  26. +2 −2 R/run_app.R
  27. +0 −126 R/share_spec.R
  28. +86 −24 R/sig_noise.R
  29. +113 −11 R/smooth_intens.R
  30. +139 −0 R/spatial_smooth.R
  31. +1 −2 R/spec_res.R
  32. +52 −0 R/split_spec.R
  33. +230 −90 R/subtr_baseline.R
  34. +27 −7 README.md
  35. +0 −2 _pkgdown.yml
  36. +8 −5 cran-comments.md
  37. +2 −0 inst/extdata/raman_hdpe_os.csv
  38. +10 −3 man/OpenSpecy-package.Rd
  39. +8 −4 man/adj_intens.Rd
  40. +40 −0 man/adj_wave.Rd
  41. +76 −63 man/as_OpenSpecy.Rd
  42. +8 −2 man/conform_spec.Rd
  43. +62 −4 man/def_features.Rd
  44. +17 −2 man/interactive_plots.Rd
  45. +4 −5 man/io_spec.Rd
  46. +119 −25 man/manage_lib.Rd
  47. +58 −0 man/manage_na.Rd
  48. +16 −1 man/manage_spec.Rd
  49. +45 −1 man/match_spec.Rd
  50. +1 −1 man/process_spec.Rd
  51. +10 −3 man/read_envi.Rd
  52. +1 −9 man/read_ext.Rd
  53. +17 −5 man/read_multi.Rd
  54. +0 −4 man/read_opus.Rd
  55. +0 −62 man/share_spec.Rd
  56. +53 −3 man/sig_noise.Rd
  57. +37 −5 man/smooth_intens.Rd
  58. +34 −0 man/spatial_smooth.Rd
  59. +40 −0 man/split_spec.Rd
  60. +79 −16 man/subtr_baseline.Rd
  61. +1 −0 packages
  62. +6 −1 tests/testthat/test-adj_intens.R
  63. +3 −4 tests/testthat/test-adj_range.R
  64. +17 −0 tests/testthat/test-adj_wave.R
  65. +19 −7 tests/testthat/test-as_OpenSpecy.R
  66. +13 −1 tests/testthat/test-conform_spec.R
  67. +157 −20 tests/testthat/test-def_features.R
  68. +12 −8 tests/testthat/test-interactive_plots.R
  69. +31 −14 tests/testthat/test-io_spec.R
  70. +1 −56 tests/testthat/test-manage_lib.R
  71. +41 −0 tests/testthat/test-manage_na.R
  72. +17 −1 tests/testthat/test-manage_spec.R
  73. +191 −20 tests/testthat/test-match_spec.R
  74. +4 −3 tests/testthat/test-read_envi.R
  75. +10 −17 tests/testthat/test-read_ext.R
  76. +8 −4 tests/testthat/test-read_multi.R
  77. +0 −2 tests/testthat/test-read_opus.R
  78. +0 −56 tests/testthat/test-share_spec.R
  79. +38 −0 tests/testthat/test-sig_noise.R
  80. +23 −0 tests/testthat/test-smooth_intens.R
  81. +1 −1 tests/testthat/test-spec_res.R
  82. +12 −0 tests/testthat/test-split_spec.R
  83. +29 −1 tests/testthat/test-subtr_baseline.R
  84. +0 −82 tests/testthat/test-workflows.R
  85. +1 −0 vignettes/.gitignore
  86. +1 −1 vignettes/advanced.Rmd
  87. +22 −17 vignettes/app.Rmd
  88. +74 −76 vignettes/sop.Rmd
  89. +0 −3,162 vignettes/sop.html
1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -16,3 +16,4 @@
^vignettes/advanced.*
^vignettes/app.*
^vignettes/spectragryph.*
^packages$
22 changes: 22 additions & 0 deletions .github/workflows/deploy-cran-repo.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
# Workflow derived from https://github.com/r-wasm/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
# Only build on main or master branch
branches: [main, master]
# Or when triggered manually
workflow_dispatch: {}

name: Build and deploy wasm R package repository

jobs:
# Reads `./packages` for package references to put
# into a CRAN-like repository hosted on GitHub pages
deploy-cran-repo:
uses: r-wasm/actions/.github/workflows/deploy-cran-repo.yml@v2
permissions:
# To download GitHub Packages within action
repository-projects: read
# For publishing to pages environment
pages: write
id-token: write
9 changes: 6 additions & 3 deletions .github/workflows/pkgdown.yaml
Original file line number Diff line number Diff line change
@@ -36,13 +36,16 @@ jobs:
needs: website

- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, dest_dir = "docs/pkgdown")
shell: Rscript {0}

- name: List built site
run: ls -R docs/pkgdown

- name: Deploy to GitHub pages 🚀
- name: Deploy pkgdown to GitHub Pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/github-pages-deploy-action@v4.4.1
with:
clean: false
branch: gh-pages
folder: docs
folder: docs/pkgdown
17 changes: 17 additions & 0 deletions .github/workflows/release-file-system-image.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
# Workflow derived from https://github.com/r-wasm/actions/tree/v1/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
release:
# Must republish release to update assets
types: [ published ]

name: Build and deploy wasm R package image

jobs:
release-file-system-image:
uses: r-wasm/actions/.github/workflows/release-file-system-image.yml@v1
permissions:
# For publishing artifact files to the release
contents: write
# To download GitHub Packages within action
repository-projects: read
6 changes: 3 additions & 3 deletions CRAN-SUBMISSION
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
Version: 1.0.2
Date: 2023-09-05 13:16:55 UTC
SHA: 92ce663a7883e3c9886fb7c2ada24fd7deb4c49b
Version: 1.1.0
Date: 2024-06-13 22:34:19 UTC
SHA: f29e66336db09ef70e6ab6dc6a3a95523980a4a9
44 changes: 27 additions & 17 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,23 +1,28 @@
Package: OpenSpecy
Type: Package
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Version: 1.0.2
Date: 2023-09-05
Version: 1.4.0
Date: 2024-11-04
Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
email = "wincowger@gmail.com",
comment = c(ORCID = "0000-0001-9226-3104")),
person("Zacharias", "Steinmetz", role = c("aut"),
email = "z.steinmetz@rptu.de",
comment = c(ORCID = "0000-0001-6675-5033")),
person("Hazel", "Vaquero", role = c("aut"),
email = "hvaquero98@gmail.com",
comment = c(ORCID = "0009-0001-5468-2049")),
person("Nick", "Leong", role = c("aut"),
comment = c(ORCID = "0009-0008-3313-4132")),
person("Andrea","Faltynkova", role = c("aut", "dtc"),
person("Andrea", "Faltynkova", role = c("aut", "dtc"),
comment = c(ORCID = "0000-0003-2523-3137")),
person("Hannah", "Sherrod", role = c("aut"),
comment = c(ORCID = "0009-0001-0497-8693")),
person("Andrew B", "Gray", role = c("ctb"),
comment = c(ORCID = "0000-0003-2252-7367")),
person("Hannah", "Hapich", role = c("ctb"),
comment = c(ORCID = "0000-0003-0000-6632")),
person("Jennifer", "Lynch", role = c("ctb","dtc"),
person("Jennifer", "Lynch", role = c("ctb", "dtc"),
comment = c(ORCID = "0000-0003-3572-8782")),
person("Hannah", "De Frond", role = c("ctb", "dtc"),
comment = c(ORCID = "0000-0003-1199-0727")),
@@ -38,7 +43,18 @@ Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
person("Laura A. T.", "Markley", role = c("ctb"),
comment = c(ORCID = "0000-0003-0620-8366")),
person("Shreyas", "Patankar", role = c("ctb", "dtc")),
person("Rachel", "Kozloski", role = c("ctb", "dtc"),
comment = c(ORCID = "0000-0003-1211-9351")),
person("Samiksha", "Singh", role = c("ctb")),
person("Katherine", "Lasdin", role = c("ctb")),
person("Cristiane", "Vidal", role = c("ctb"),
comment = c(ORCID = "0000-0001-6363-9475")),
person("Clare", "Murphy-Hagan", role = c("ctb"),
comment = c(ORCID = "0009-0009-9629-2856")),
person("Philipp", "Baumann", role = c("ctb"),
email = "info@spectral-cockpit.space",
comment = c(ORCID = "0000-0002-3194-8975")),
person("Pierre", "Roudier", role = c("ctb")),
person("National Renewable Energy Laboratory", role = c("fnd")),
person("Possibility Lab", role = c("fnd")))
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
@@ -53,7 +69,7 @@ Description: Raman and (FT)IR spectral analysis tool for plastic particles and
<doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available
via run_app() or online at <https://openanalysis.org/openspecy/>.
URL: https://github.com/wincowgerDEV/OpenSpecy-package/,
http://wincowger.com/OpenSpecy-package/
https://wincowger.com/OpenSpecy-package/
BugReports: https://github.com/wincowgerDEV/OpenSpecy-package/issues/
License: CC BY 4.0
Encoding: UTF-8
@@ -67,31 +83,25 @@ Imports:
data.table,
jsonlite,
yaml,
osfr,
caTools,
hyperSpec,
imager,
mmand,
plotly,
digest,
signal,
glmnet,
jpeg,
shiny
Suggests:
knitr,
rmarkdown,
testthat (>= 3.1.9),
config,
qs,
shinyjs,
shinyjs,
shinyWidgets,
bs4Dash,
dplyr,
ggplot2,
dplyr,
DT,
curl,
aws.s3,
mongolite,
loggit
RoxygenNote: 7.2.3
ggplot2
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
48 changes: 39 additions & 9 deletions NAMESPACE
Original file line number Diff line number Diff line change
@@ -2,6 +2,8 @@

S3method(adj_intens,OpenSpecy)
S3method(adj_intens,default)
S3method(adj_wave,OpenSpecy)
S3method(adj_wave,default)
S3method(ai_classify,OpenSpecy)
S3method(ai_classify,default)
S3method(as.data.frame,OpenSpecy)
@@ -14,6 +16,8 @@ S3method(as_OpenSpecy,list)
S3method(c_spec,OpenSpecy)
S3method(c_spec,default)
S3method(c_spec,list)
S3method(calc_window_points,OpenSpecy)
S3method(calc_window_points,default)
S3method(collapse_spec,OpenSpecy)
S3method(collapse_spec,default)
S3method(conform_spec,OpenSpecy)
@@ -22,6 +26,8 @@ S3method(cor_spec,OpenSpecy)
S3method(cor_spec,default)
S3method(def_features,OpenSpecy)
S3method(def_features,default)
S3method(fill_spec,OpenSpecy)
S3method(fill_spec,default)
S3method(filter_spec,OpenSpecy)
S3method(filter_spec,default)
S3method(flatten_range,OpenSpecy)
@@ -36,8 +42,15 @@ S3method(interactive_plot,default)
S3method(lines,OpenSpecy)
S3method(make_rel,OpenSpecy)
S3method(make_rel,default)
S3method(manage_na,OpenSpecy)
S3method(manage_na,default)
S3method(match_spec,OpenSpecy)
S3method(match_spec,default)
S3method(merge_map,OpenSpecy)
S3method(merge_map,default)
S3method(merge_map,list)
S3method(os_similarity,OpenSpecy)
S3method(os_similarity,default)
S3method(plot,OpenSpecy)
S3method(plotly_spec,OpenSpecy)
S3method(plotly_spec,default)
@@ -48,8 +61,6 @@ S3method(restrict_range,OpenSpecy)
S3method(restrict_range,default)
S3method(sample_spec,OpenSpecy)
S3method(sample_spec,default)
S3method(share_spec,OpenSpecy)
S3method(share_spec,default)
S3method(sig_noise,OpenSpecy)
S3method(sig_noise,default)
S3method(smooth_intens,OpenSpecy)
@@ -65,17 +76,20 @@ export(OpenSpecy)
export(adj_intens)
export(adj_neg)
export(adj_res)
export(adj_wave)
export(ai_classify)
export(as_OpenSpecy)
export(as_hyperSpec)
export(c_spec)
export(calc_window_points)
export(check_OpenSpecy)
export(check_lib)
export(collapse_spec)
export(conform_res)
export(conform_spec)
export(cor_spec)
export(def_features)
export(fill_spec)
export(filter_spec)
export(flatten_range)
export(gen_grid)
@@ -89,16 +103,20 @@ export(is_OpenSpecy)
export(is_empty_vector)
export(load_lib)
export(make_rel)
export(manage_na)
export(match_spec)
export(max_cor_named)
export(mean_replace)
export(merge_map)
export(os_similarity)
export(plotly_spec)
export(process_spec)
export(read_any)
export(read_asp)
export(read_envi)
export(read_extdata)
export(read_jdx)
export(read_many)
export(read_opus)
export(read_opus_raw)
export(read_spa)
@@ -110,10 +128,11 @@ export(restrict_range)
export(rm_lib)
export(run_app)
export(sample_spec)
export(share_spec)
export(sig_noise)
export(smooth_intens)
export(spatial_smooth)
export(spec_res)
export(split_spec)
export(subtr_baseline)
export(write_spec)
importFrom(caTools,read.ENVI)
@@ -125,27 +144,34 @@ importFrom(data.table,dcast)
importFrom(data.table,fifelse)
importFrom(data.table,fread)
importFrom(data.table,frollapply)
importFrom(data.table,fwrite)
importFrom(data.table,is.data.table)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(data.table,transpose)
importFrom(digest,digest)
importFrom(glmnet,predict.glmnet)
importFrom(grDevices,as.raster)
importFrom(grDevices,chull)
importFrom(grDevices,col2rgb)
importFrom(grDevices,heat.colors)
importFrom(graphics,image)
importFrom(graphics,matlines)
importFrom(graphics,matplot)
importFrom(hyperSpec,read.jdx)
importFrom(hyperSpec,read.spc)
importFrom(imager,as.cimg)
importFrom(imager,label)
importFrom(jpeg,readJPEG)
importFrom(jsonlite,read_json)
importFrom(jsonlite,write_json)
importFrom(methods,new)
importFrom(osfr,osf_download)
importFrom(osfr,osf_ls_files)
importFrom(osfr,osf_retrieve_node)
importFrom(mmand,closing)
importFrom(mmand,components)
importFrom(mmand,gaussianSmooth)
importFrom(mmand,shapeKernel)
importFrom(plotly,add_markers)
importFrom(plotly,add_trace)
importFrom(plotly,layout)
@@ -155,17 +181,22 @@ importFrom(shiny,runGitHub)
importFrom(shiny,shinyOptions)
importFrom(signal,filter)
importFrom(signal,sgolay)
importFrom(stats,IQR)
importFrom(stats,approx)
importFrom(stats,ave)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.frame)
importFrom(stats,poly)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,terms)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,modifyList)
@@ -174,6 +205,5 @@ importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,sessionInfo)
importFrom(utils,unzip)
importFrom(utils,write.csv)
importFrom(yaml,read_yaml)
importFrom(yaml,write_yaml)
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