Package: ferrn 0.2.0

ferrn: Facilitate Exploration of touRR optimisatioN

Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.

Authors:H. Sherry Zhang [aut, cre], Dianne Cook [aut], Ursula Laa [aut], Nicolas Langrené [aut], Patricia Menéndez [aut]

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ferrn.pdf |ferrn.html✨
ferrn/json (API)
NEWS

# Install 'ferrn' in R:
install.packages('ferrn', repos = c('https://huizezhang-sherry.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/huizezhang-sherry/ferrn/issues

Datasets:
  • boa - Simulated sine, pipe, and gaussian mixture
  • boa5 - Simulated sine, pipe, and gaussian mixture
  • boa6 - Simulated sine, pipe, and gaussian mixture
  • holes_1d_better - Data objects collected during the projection pursuit optimisation
  • holes_1d_geo - Data objects collected during the projection pursuit optimisation
  • holes_1d_jellyfish - Data objects collected during the projection pursuit optimisation
  • holes_2d_better - Data objects collected during the projection pursuit optimisation
  • holes_2d_better_max_tries - Data objects collected during the projection pursuit optimisation
  • pipe1000 - Simulated sine, pipe, and gaussian mixture
  • pipe1000_10d - Simulated sine, pipe, and gaussian mixture
  • pipe1000_12d - Simulated sine, pipe, and gaussian mixture
  • pipe1000_8d - Simulated sine, pipe, and gaussian mixture
  • sine1000 - Simulated sine, pipe, and gaussian mixture
  • sine1000_8d - Simulated sine, pipe, and gaussian mixture

On CRAN:

55 exports 6 stars 1.76 score 65 dependencies 17 scripts 242 downloads

Last updated 6 days agofrom:b2e91b29e3. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:%>%add_anchoradd_annoadd_dir_searchadd_endadd_interpadd_interp_lastadd_interruptadd_searchadd_spaceadd_startadd_theobind_randombind_random_matrixbind_theoreticalbotanical_palbotanical_palettescalc_smoothnesscalc_squintabilityclean_methodcompute_pcacompute_projectionexplore_space_endexplore_space_pcaexplore_space_startexplore_space_tourexplore_trace_interpexplore_trace_searchfit_ksfit_nlsflip_signformat_labelgeom_huberget_anchorget_basis_matrixget_bestget_dir_searchget_interpget_interp_lastget_interruptget_searchget_search_countget_space_paramget_startget_theoplot_projectionprep_huberprep_space_toursample_basesscale_color_continuous_botanicalscale_color_discrete_botanicalscale_fill_continuous_botanicalscale_fill_discrete_botanicaltheme_ferntheme_huber

Dependencies:BHclassclassIntclicolorspacecpp11crayonDBIdplyre1071fansifarverFNNgenericsgganimateggforceggplot2ggrepelglueGpGpgtablehmsisobandKernSmoothlabelinglatticelifecyclelpSolvemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpolyclipprettyunitsprogressproxypurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangs2scalessfstringistringrsystemfontstibbletidyrtidyselecttourrtransformrtweenrunitsutf8vctrsviridisLitewithrwk

Readme and manuals

Help Manual

Help pageTopics
A ggproto for drawing anchor pointsadd_anchor
A ggproto for annotating the symmetry of the starting pointsadd_anno
A ggproto for drawing directional search pointsadd_dir_search
A ggproto for drawing start pointsadd_end
A ggproto for drawing interpolation pathadd_interp
A ggproto for drawing finish pointsadd_interp_last
A ggproto for annotating the interrupted pathadd_interrupt
A ggproto for drawing search pointsadd_search
A ggproto for drawing circleadd_space
A ggproto for drawing start pointsadd_start
A ggproto for drawing the theoretical basis, if applicableadd_theo
Bind random bases in the projection bases spacebind_random
Bind random bases in the projection bases space as a matrixbind_random_matrix
Bind the theoretical best recordbind_theoretical
A customised colour palette based on Australian botaniesbotanical_pal botanical_palettes
Clean method namesclean_method
Plot the PCA projection of the projection bases spaceexplore_space_end explore_space_pca explore_space_start
Plot the grand tour animation of the bases space in high dimensionexplore_space_tour prep_space_tour
Plot the trace the search progressionexplore_trace_interp
Plot the count in each iterationexplore_trace_search
Helper functions for `explore_space_pca()`compute_pca flip_sign
Better label formatting to avoid overlappingformat_label
Create Huber plot with ggplot2geom_huber prep_huber theme_huber
Functions to get components from the data collecting objectget_anchor get_basis_matrix get_best get_dir_search get_interp get_interp_last get_interrupt get_search get_search_count get_space_param get_start get_theo
Data objects collected during the projection pursuit optimisationholes_1d_better holes_1d_geo holes_1d_jellyfish holes_2d_better holes_2d_better_max_tries
Plot the projection from the optimisation data collected from projection pursuitcompute_projection plot_projection
Function to calculate smoothness and squintabilitycalc_smoothness calc_squintability fit_ks fit_nls print.basis_df print.smoothness_res print.squintability_res sample_bases tbl_sum.basis_df tbl_sum.smoothness_res tbl_sum.squintability_res
continuous scale colour functionscale_color_continuous_botanical scale_color_discrete_botanical scale_fill_continuous_botanical scale_fill_discrete_botanical
Simulated sine, pipe, and gaussian mixtureboa boa5 boa6 pipe1000 pipe1000_10d pipe1000_12d pipe1000_8d sine1000 sine1000_8d
A specific theme for trace plotstheme_fern