Title: Export Data Frames to Excel 'xlsx' Format
Description: Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'
<https://libxlsxwriter.github.io>. Fast and no Java or Excel required.
Author: Jeroen Ooms [aut] ,
Bill Denney [aut, cre] ,
John McNamara [cph] )
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between writexl versions 1.5.4 dated 2025-04-15 and 2.0.0 dated 2026-08-05
writexl-1.5.4/writexl/NEWS |only writexl-1.5.4/writexl/src/include |only writexl-1.5.4/writexl/src/libxlsxwriter/app.c |only writexl-1.5.4/writexl/src/libxlsxwriter/chart.c |only writexl-1.5.4/writexl/src/libxlsxwriter/chartsheet.c |only writexl-1.5.4/writexl/src/libxlsxwriter/comment.c |only writexl-1.5.4/writexl/src/libxlsxwriter/content_types.c |only writexl-1.5.4/writexl/src/libxlsxwriter/core.c |only writexl-1.5.4/writexl/src/libxlsxwriter/custom.c |only writexl-1.5.4/writexl/src/libxlsxwriter/drawing.c |only writexl-1.5.4/writexl/src/libxlsxwriter/format.c |only writexl-1.5.4/writexl/src/libxlsxwriter/hash_table.c |only writexl-1.5.4/writexl/src/libxlsxwriter/metadata.c |only writexl-1.5.4/writexl/src/libxlsxwriter/packager.c |only writexl-1.5.4/writexl/src/libxlsxwriter/relationships.c |only writexl-1.5.4/writexl/src/libxlsxwriter/shared_strings.c |only writexl-1.5.4/writexl/src/libxlsxwriter/styles.c |only writexl-1.5.4/writexl/src/libxlsxwriter/table.c |only writexl-1.5.4/writexl/src/libxlsxwriter/theme.c |only writexl-1.5.4/writexl/src/libxlsxwriter/utility.c |only writexl-1.5.4/writexl/src/libxlsxwriter/vml.c |only writexl-1.5.4/writexl/src/libxlsxwriter/workbook.c |only writexl-1.5.4/writexl/src/libxlsxwriter/worksheet.c |only writexl-1.5.4/writexl/src/libxlsxwriter/xmlwriter.c |only writexl-1.5.4/writexl/src/md5 |only writexl-1.5.4/writexl/src/minizip |only writexl-1.5.4/writexl/src/tmpfileplus |only writexl-2.0.0/writexl/DESCRIPTION | 25 writexl-2.0.0/writexl/LICENSE | 4 writexl-2.0.0/writexl/MD5 | 285 - writexl-2.0.0/writexl/NAMESPACE | 112 writexl-2.0.0/writexl/NEWS.md |only writexl-2.0.0/writexl/R/excel_types.R | 228 writexl-2.0.0/writexl/R/sheet_names.R |only writexl-2.0.0/writexl/R/sheet_visibility.R |only writexl-2.0.0/writexl/R/split_panes.R |only writexl-2.0.0/writexl/R/version.R | 33 writexl-2.0.0/writexl/R/write_xlsx.R | 493 +- writexl-2.0.0/writexl/R/xl_cell_general.R |only writexl-2.0.0/writexl/R/xl_chart.R |only writexl-2.0.0/writexl/R/xl_chart_axis.R |only writexl-2.0.0/writexl/R/xl_chart_extras.R |only writexl-2.0.0/writexl/R/xl_chart_format.R |only writexl-2.0.0/writexl/R/xl_chart_parts.R |only writexl-2.0.0/writexl/R/xl_chartsheet.R |only writexl-2.0.0/writexl/R/xl_comment.R |only writexl-2.0.0/writexl/R/xl_conditional.R |only writexl-2.0.0/writexl/R/xl_filter.R |only writexl-2.0.0/writexl/R/xl_format.R |only writexl-2.0.0/writexl/R/xl_image.R |only writexl-2.0.0/writexl/R/xl_merge.R |only writexl-2.0.0/writexl/R/xl_outline.R |only writexl-2.0.0/writexl/R/xl_page_setup.R |only writexl-2.0.0/writexl/R/xl_range.R |only writexl-2.0.0/writexl/R/xl_rich_string.R |only writexl-2.0.0/writexl/R/xl_sheet.R |only writexl-2.0.0/writexl/R/xl_sheet_view.R |only writexl-2.0.0/writexl/R/xl_table.R |only writexl-2.0.0/writexl/R/xl_validation.R |only writexl-2.0.0/writexl/R/xl_workbook.R |only writexl-2.0.0/writexl/build |only writexl-2.0.0/writexl/inst/AUTHORS | 10 writexl-2.0.0/writexl/inst/COPYRIGHT | 142 writexl-2.0.0/writexl/inst/WORDLIST | 92 writexl-2.0.0/writexl/inst/doc |only writexl-2.0.0/writexl/man/is_xl_comment.Rd |only writexl-2.0.0/writexl/man/is_xl_format.Rd |only writexl-2.0.0/writexl/man/write_xlsx.Rd | 132 writexl-2.0.0/writexl/man/writexl.Rd | 22 writexl-2.0.0/writexl/man/xl_cell_general.Rd |only writexl-2.0.0/writexl/man/xl_chart.Rd |only writexl-2.0.0/writexl/man/xl_chart_axis.Rd |only writexl-2.0.0/writexl/man/xl_chart_error_bars.Rd |only writexl-2.0.0/writexl/man/xl_chart_labels.Rd |only writexl-2.0.0/writexl/man/xl_chart_legend.Rd |only writexl-2.0.0/writexl/man/xl_chart_marker.Rd |only writexl-2.0.0/writexl/man/xl_chart_series.Rd |only writexl-2.0.0/writexl/man/xl_chart_table.Rd |only writexl-2.0.0/writexl/man/xl_chart_trendline.Rd |only writexl-2.0.0/writexl/man/xl_chartsheet.Rd |only writexl-2.0.0/writexl/man/xl_color.Rd |only writexl-2.0.0/writexl/man/xl_colrow_spec.Rd |only writexl-2.0.0/writexl/man/xl_comment.Rd |only writexl-2.0.0/writexl/man/xl_conditional.Rd |only writexl-2.0.0/writexl/man/xl_filter.Rd |only writexl-2.0.0/writexl/man/xl_filter_keep.Rd |only writexl-2.0.0/writexl/man/xl_format.Rd |only writexl-2.0.0/writexl/man/xl_format_groups.Rd |only writexl-2.0.0/writexl/man/xl_formula.Rd | 122 writexl-2.0.0/writexl/man/xl_image.Rd |only writexl-2.0.0/writexl/man/xl_merge.Rd |only writexl-2.0.0/writexl/man/xl_outline.Rd |only writexl-2.0.0/writexl/man/xl_page_setup.Rd |only writexl-2.0.0/writexl/man/xl_properties.Rd |only writexl-2.0.0/writexl/man/xl_rich_run.Rd |only writexl-2.0.0/writexl/man/xl_rich_string.Rd |only writexl-2.0.0/writexl/man/xl_sheet.Rd |only writexl-2.0.0/writexl/man/xl_sheet_view.Rd |only writexl-2.0.0/writexl/man/xl_table.Rd |only writexl-2.0.0/writexl/man/xl_table_column.Rd |only writexl-2.0.0/writexl/man/xl_validation.Rd |only writexl-2.0.0/writexl/man/xl_workbook.Rd |only writexl-2.0.0/writexl/src/Makevars | 31 writexl-2.0.0/writexl/src/libxlsxwriter/License.txt |only writexl-2.0.0/writexl/src/libxlsxwriter/include |only writexl-2.0.0/writexl/src/libxlsxwriter/src |only writexl-2.0.0/writexl/src/libxlsxwriter/third_party |only writexl-2.0.0/writexl/src/write_xlsx.c | 2309 +++++++++- writexl-2.0.0/writexl/tests/spelling.R | 2 writexl-2.0.0/writexl/tests/testthat.R | 16 writexl-2.0.0/writexl/tests/testthat/helper-xlsx.R |only writexl-2.0.0/writexl/tests/testthat/test-api-consistency.R |only writexl-2.0.0/writexl/tests/testthat/test-cell-general.R |only writexl-2.0.0/writexl/tests/testthat/test-cell-vector.R |only writexl-2.0.0/writexl/tests/testthat/test-format-cell.R |only writexl-2.0.0/writexl/tests/testthat/test-format-protect.R |only writexl-2.0.0/writexl/tests/testthat/test-format-workbook.R |only writexl-2.0.0/writexl/tests/testthat/test-format-worksheet.R |only writexl-2.0.0/writexl/tests/testthat/test-integration.R |only writexl-2.0.0/writexl/tests/testthat/test-libxlsxwriter-coverage.R |only writexl-2.0.0/writexl/tests/testthat/test-limits.R |only writexl-2.0.0/writexl/tests/testthat/test-na.R |only writexl-2.0.0/writexl/tests/testthat/test-performance.R | 25 writexl-2.0.0/writexl/tests/testthat/test-print.R |only writexl-2.0.0/writexl/tests/testthat/test-sheet-names.R |only writexl-2.0.0/writexl/tests/testthat/test-sheet-view.R |only writexl-2.0.0/writexl/tests/testthat/test-types.R | 327 + writexl-2.0.0/writexl/tests/testthat/test-xl_chart.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_axis.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_extras.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_format.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_parts.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chartsheet.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_comment.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_conditional.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_filter.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_format.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_image.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_merge.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_outline.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_page_setup.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_range.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_rich_string.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_table.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_validation.R |only writexl-2.0.0/writexl/vignettes |only 146 files changed, 3736 insertions(+), 674 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-06 1.0.1
2024-10-25 1.0.0
Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: John Elizarraras [aut],
Jing Wang [aut],
Yuxing Liao [aut],
Eric Jaehnig [ctb],
Zhiao Shi [aut, cre],
Quanhu Sheng [ctb]
Maintainer: Zhiao Shi <zhiao.shi@gmail.com>
Diff between WebGestaltR versions 1.0.0 dated 2026-07-30 and 1.0.1 dated 2026-08-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 11 +++++++++++ src/Makevars.in | 11 +++++++++-- src/Makevars.win.in | 2 +- 5 files changed, 29 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-16 3.7.2
2025-12-04 3.7.1.2
2025-10-22 3.7.1
2025-10-14 3.7
2025-10-10 3.6.2
2022-11-16 3.6.1
2022-01-27 3.6.0
Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides methods for metabolomics and spectral data analysis,
including data import, preprocessing, visualization, univariate and
multivariate analysis, machine learning, feature selection, and pathway
analysis. The package supports analytical workflows for different data
types used in metabolomics and spectroscopy. Some optional functionality
uses the suggested packages 'cyjShiny' and 'specmine.datasets'. The package
'specmine.datasets' is maintained separately at
<https://github.com/PedroFontao/specmine.datasets>.
Author: Christopher Costa [aut],
Marcelo Maraschin [aut],
Miguel Rocha [aut],
Sara Cardoso [aut],
Telma Afonso [aut],
Bruno Pereira [aut],
Pedro Fontao [aut, cre],
C. Beleites [cph],
Jie Hao [cph]
Maintainer: Pedro Fontao <pedrofontao812004@gmail.com>
This is a re-admission after prior archival of version 3.1.6 dated 2021-09-21
Diff between specmine versions 3.1.6 dated 2021-09-21 and 3.1.8 dated 2026-08-05
specmine-3.1.6/specmine/README.md |only specmine-3.1.6/specmine/man/MAIT_identify_metabolites.Rd |only specmine-3.1.6/specmine/man/absorbance_to_transmittance.Rd |only specmine-3.1.6/specmine/man/apply_by_sample.Rd |only specmine-3.1.6/specmine/man/apply_by_variable.Rd |only specmine-3.1.6/specmine/man/background_correction.Rd |only specmine-3.1.6/specmine/man/boxplot_variables.Rd |only specmine-3.1.6/specmine/man/boxplot_vars_factor.Rd |only specmine-3.1.6/specmine/man/check_2d_dataset.Rd |only specmine-3.1.6/specmine/man/check_dataset.Rd |only specmine-3.1.6/specmine/man/clustering.Rd |only specmine-3.1.6/specmine/man/compare_regions_by_sample.Rd |only specmine-3.1.6/specmine/man/convert_to_factor.Rd |only specmine-3.1.6/specmine/man/correlation_test.Rd |only specmine-3.1.6/specmine/man/correlations_dataset.Rd |only specmine-3.1.6/specmine/man/correlations_test.Rd |only specmine-3.1.6/specmine/man/create_2d_dataset.Rd |only specmine-3.1.6/specmine/man/cubic_root_transform.Rd |only specmine-3.1.6/specmine/man/data_correction.Rd |only specmine-3.1.6/specmine/man/dendrogram_plot.Rd |only specmine-3.1.6/specmine/man/dendrogram_plot_col.Rd |only specmine-3.1.6/specmine/man/detect_nmr_peaks_from_dataset.Rd |only specmine-3.1.6/specmine/man/find_equal_samples.Rd |only specmine-3.1.6/specmine/man/first_derivative.Rd |only specmine-3.1.6/specmine/man/fold_change.Rd |only specmine-3.1.6/specmine/man/fold_change_var.Rd |only specmine-3.1.6/specmine/man/get_data.Rd |only specmine-3.1.6/specmine/man/get_data_as_df.Rd |only specmine-3.1.6/specmine/man/get_data_value.Rd |only specmine-3.1.6/specmine/man/get_data_values.Rd |only specmine-3.1.6/specmine/man/get_files_list_assay.Rd |only specmine-3.1.6/specmine/man/get_metadata.Rd |only specmine-3.1.6/specmine/man/get_metadata_value.Rd |only specmine-3.1.6/specmine/man/get_metadata_var.Rd |only specmine-3.1.6/specmine/man/get_sample_2d_data.Rd |only specmine-3.1.6/specmine/man/get_sample_names.Rd |only specmine-3.1.6/specmine/man/get_samples_names_spc.Rd |only specmine-3.1.6/specmine/man/get_type.Rd |only specmine-3.1.6/specmine/man/get_value_label.Rd |only specmine-3.1.6/specmine/man/get_x_values_as_num.Rd |only specmine-3.1.6/specmine/man/group_peaks.Rd |only specmine-3.1.6/specmine/man/heatmap_correlations.Rd |only specmine-3.1.6/specmine/man/hierarchical_clustering.Rd |only specmine-3.1.6/specmine/man/impute_nas_linapprox.Rd |only specmine-3.1.6/specmine/man/indexes_to_xvalue_interval.Rd |only specmine-3.1.6/specmine/man/is_spectra.Rd |only specmine-3.1.6/specmine/man/kmeans_clustering.Rd |only specmine-3.1.6/specmine/man/kmeans_plot.Rd |only specmine-3.1.6/specmine/man/kmeans_result_df.Rd |only specmine-3.1.6/specmine/man/kruskalTest_dataset.Rd |only specmine-3.1.6/specmine/man/ksTest_dataset.Rd |only specmine-3.1.6/specmine/man/linreg_all_vars.Rd |only specmine-3.1.6/specmine/man/linreg_coef_table.Rd |only specmine-3.1.6/specmine/man/linreg_pvalue_table.Rd |only specmine-3.1.6/specmine/man/linreg_rsquared.Rd |only specmine-3.1.6/specmine/man/linregression_onevar.Rd |only specmine-3.1.6/specmine/man/log_transform.Rd |only specmine-3.1.6/specmine/man/low_level_fusion.Rd |only specmine-3.1.6/specmine/man/mean_centering.Rd |only specmine-3.1.6/specmine/man/merge_datasets.Rd |only specmine-3.1.6/specmine/man/metadata_as_variables.Rd |only specmine-3.1.6/specmine/man/msc_correction.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_all_vars.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_pvalues_table.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_varexp_table.Rd |only specmine-3.1.6/specmine/man/multiplot.Rd |only specmine-3.1.6/specmine/man/nmr_identification.Rd |only specmine-3.1.6/specmine/man/normalize.Rd |only specmine-3.1.6/specmine/man/normalize_samples.Rd |only specmine-3.1.6/specmine/man/num_samples.Rd |only specmine-3.1.6/specmine/man/num_x_values.Rd |only specmine-3.1.6/specmine/man/offset_correction.Rd |only specmine-3.1.6/specmine/man/pca_importance.Rd |only specmine-3.1.6/specmine/man/peaks_per_sample.Rd |only specmine-3.1.6/specmine/man/peaks_per_samples.Rd |only specmine-3.1.6/specmine/man/plot_2d_spectra.Rd |only specmine-3.1.6/specmine/man/plot_anova.Rd |only specmine-3.1.6/specmine/man/plot_fold_change.Rd |only specmine-3.1.6/specmine/man/plot_kruskaltest.Rd |only specmine-3.1.6/specmine/man/plot_kstest.Rd |only specmine-3.1.6/specmine/man/plot_peaks.Rd |only specmine-3.1.6/specmine/man/plot_regression_coefs_pvalues.Rd |only specmine-3.1.6/specmine/man/plot_spectra.Rd |only specmine-3.1.6/specmine/man/plot_spectra_simple.Rd |only specmine-3.1.6/specmine/man/plot_ttests.Rd |only specmine-3.1.6/specmine/man/plotvar_twofactor.Rd |only specmine-3.1.6/specmine/man/predict_samples.Rd |only specmine-3.1.6/specmine/man/read_Bruker_files.Rd |only specmine-3.1.6/specmine/man/read_Bruker_files_2d.Rd |only specmine-3.1.6/specmine/man/read_data_spc.Rd |only specmine-3.1.6/specmine/man/read_dataset_spc.Rd |only specmine-3.1.6/specmine/man/read_varian_2dspectra_raw.Rd |only specmine-3.1.6/specmine/man/read_varian_spectra_raw.Rd |only specmine-3.1.6/specmine/man/remove_peaks_interval.Rd |only specmine-3.1.6/specmine/man/remove_peaks_interval_sample_list.Rd |only specmine-3.1.6/specmine/man/replace_data_value.Rd |only specmine-3.1.6/specmine/man/replace_metadata_value.Rd |only specmine-3.1.6/specmine/man/savitzky_golay.Rd |only specmine-3.1.6/specmine/man/scaling.Rd |only specmine-3.1.6/specmine/man/scaling_samples.Rd |only specmine-3.1.6/specmine/man/set_metadata.Rd |only specmine-3.1.6/specmine/man/set_sample_names.Rd |only specmine-3.1.6/specmine/man/set_value_label.Rd |only specmine-3.1.6/specmine/man/set_x_label.Rd |only specmine-3.1.6/specmine/man/set_x_values.Rd |only specmine-3.1.6/specmine/man/shift_correction.Rd |only specmine-3.1.6/specmine/man/smoothing_interpolation.Rd |only specmine-3.1.6/specmine/man/snv_dataset.Rd |only specmine-3.1.6/specmine/man/stats_by_sample.Rd |only specmine-3.1.6/specmine/man/stats_by_variable.Rd |only specmine-3.1.6/specmine/man/sum_2d_dataset.Rd |only specmine-3.1.6/specmine/man/sum_dataset.Rd |only specmine-3.1.6/specmine/man/tTests_dataset.Rd |only specmine-3.1.6/specmine/man/transform_data.Rd |only specmine-3.1.6/specmine/man/transmittance_to_absorbance.Rd |only specmine-3.1.6/specmine/man/values_per_peak.Rd |only specmine-3.1.6/specmine/man/values_per_sample.Rd |only specmine-3.1.6/specmine/man/variables_as_metadata.Rd |only specmine-3.1.6/specmine/man/volcano_plot_fc_tt.Rd |only specmine-3.1.6/specmine/man/x_values_to_indexes.Rd |only specmine-3.1.6/specmine/man/xvalue_interval_to_indexes.Rd |only specmine-3.1.8/specmine/DESCRIPTION | 84 specmine-3.1.8/specmine/MD5 | 372 +--- specmine-3.1.8/specmine/NAMESPACE | 322 +-- specmine-3.1.8/specmine/NEWS.md |only specmine-3.1.8/specmine/R/DBSCAN_HDBSCAN.R |only specmine-3.1.8/specmine/R/GMM.R |only specmine-3.1.8/specmine/R/ICA.R |only specmine-3.1.8/specmine/R/MAIT_metabolite_identification.R | 267 +-- specmine-3.1.8/specmine/R/NMR_metabolite_identification.R | 235 +- specmine-3.1.8/specmine/R/PATHWAY_ANALYSIS.R | 649 ++++--- specmine-3.1.8/specmine/R/cluster_quality.R |only specmine-3.1.8/specmine/R/clustering.R | 238 +- specmine-3.1.8/specmine/R/compare_embeddings.R |only specmine-3.1.8/specmine/R/convert_chemospec.R | 19 specmine-3.1.8/specmine/R/feature_selection.R | 117 + specmine-3.1.8/specmine/R/filter_dataset.R | 598 ++++++ specmine-3.1.8/specmine/R/filters_flat.R | 138 - specmine-3.1.8/specmine/R/get_metabolights_study.R | 418 +++- specmine-3.1.8/specmine/R/globals.R |only specmine-3.1.8/specmine/R/graphics.R | 358 +--- specmine-3.1.8/specmine/R/init.R | 2 specmine-3.1.8/specmine/R/machinelearning.R | 694 +++++-- specmine-3.1.8/specmine/R/missing_values.R | 196 +- specmine-3.1.8/specmine/R/ms_functions.R | 110 - specmine-3.1.8/specmine/R/mzmatch_metabolite_identification.R |only specmine-3.1.8/specmine/R/nmr_id_utils.R | 2 specmine-3.1.8/specmine/R/pca.R | 730 ++++++-- specmine-3.1.8/specmine/R/peaklists.R | 116 + specmine-3.1.8/specmine/R/preprocessing.R | 169 + specmine-3.1.8/specmine/R/read.spc.modifed.R | 844 +-------- specmine-3.1.8/specmine/R/read_NMR_spectra.R | 873 +--------- specmine-3.1.8/specmine/R/read_dx.R | 110 + specmine-3.1.8/specmine/R/read_spc.R | 119 - specmine-3.1.8/specmine/R/reading_data.R | 230 ++ specmine-3.1.8/specmine/R/regression.R | 81 specmine-3.1.8/specmine/R/specmine-package.R |only specmine-3.1.8/specmine/R/spectra_options.R |only specmine-3.1.8/specmine/R/stats.R | 98 - specmine-3.1.8/specmine/R/structure.R | 519 +++-- specmine-3.1.8/specmine/R/t-sne.R |only specmine-3.1.8/specmine/R/umap.R |only specmine-3.1.8/specmine/R/univariate.R | 511 +++-- specmine-3.1.8/specmine/R/utils.R | 2 specmine-3.1.8/specmine/build/vignette.rds |binary specmine-3.1.8/specmine/inst/doc/dataset_2d_analysis.R | 90 - specmine-3.1.8/specmine/inst/doc/dataset_2d_analysis.html | 536 ++++-- specmine-3.1.8/specmine/man/aggregate_samples.Rd | 77 specmine-3.1.8/specmine/man/aov_all_vars.Rd | 78 specmine-3.1.8/specmine/man/aov_one_var.Rd |only specmine-3.1.8/specmine/man/apply_by_group.Rd | 62 specmine-3.1.8/specmine/man/apply_by_groups.Rd | 76 specmine-3.1.8/specmine/man/baseline_correction.Rd | 79 specmine-3.1.8/specmine/man/convert_chebi_to_kegg.Rd | 29 specmine-3.1.8/specmine/man/convert_from_chemospec.Rd | 46 specmine-3.1.8/specmine/man/convert_hmdb_to_kegg.Rd | 28 specmine-3.1.8/specmine/man/convert_keggpathway_2_reactiongraph.Rd | 28 specmine-3.1.8/specmine/man/convert_multiple_spcmnm_to_kegg.Rd | 29 specmine-3.1.8/specmine/man/count_missing_values.Rd | 39 specmine-3.1.8/specmine/man/count_missing_values_per_sample.Rd | 47 specmine-3.1.8/specmine/man/count_missing_values_per_variable.Rd | 47 specmine-3.1.8/specmine/man/create_dataset.Rd | 121 - specmine-3.1.8/specmine/man/create_pathway_with_reactions.Rd | 70 specmine-3.1.8/specmine/man/dataset_from_peaks.Rd | 65 specmine-3.1.8/specmine/man/feature_selection.Rd | 84 specmine-3.1.8/specmine/man/filter_feature_selection.Rd | 71 specmine-3.1.8/specmine/man/flat_pattern_filter.Rd | 83 specmine-3.1.8/specmine/man/get_MetabolitePath.Rd | 28 specmine-3.1.8/specmine/man/get_OrganismsCodes.Rd | 23 specmine-3.1.8/specmine/man/get_cpd_names.Rd | 27 specmine-3.1.8/specmine/man/get_files_list_per_assay.Rd |only specmine-3.1.8/specmine/man/get_metabPaths_org.Rd | 25 specmine-3.1.8/specmine/man/get_metabolights_study.Rd | 44 specmine-3.1.8/specmine/man/get_metabolights_study_files_assay.Rd | 42 specmine-3.1.8/specmine/man/get_metabolights_study_metadata_assay.Rd | 39 specmine-3.1.8/specmine/man/get_metabolights_study_samples_files.Rd | 35 specmine-3.1.8/specmine/man/get_paths_with_cpds_org.Rd | 43 specmine-3.1.8/specmine/man/get_peak_values.Rd | 43 specmine-3.1.8/specmine/man/get_samples_names_dx.Rd | 34 specmine-3.1.8/specmine/man/get_x_label.Rd | 47 specmine-3.1.8/specmine/man/get_x_values_as_text.Rd | 47 specmine-3.1.8/specmine/man/impute_nas_knn.Rd | 55 specmine-3.1.8/specmine/man/impute_nas_mean.Rd | 41 specmine-3.1.8/specmine/man/impute_nas_median.Rd | 41 specmine-3.1.8/specmine/man/impute_nas_value.Rd | 46 specmine-3.1.8/specmine/man/merge_data_metadata.Rd | 73 specmine-3.1.8/specmine/man/metabolights_studies_list.Rd | 21 specmine-3.1.8/specmine/man/missingvalues_imputation.Rd | 66 specmine-3.1.8/specmine/man/multiClassSummary.Rd | 49 specmine-3.1.8/specmine/man/pathway_analysis.Rd | 69 specmine-3.1.8/specmine/man/pca_analysis_dataset.Rd | 77 specmine-3.1.8/specmine/man/pca_biplot.Rd | 84 specmine-3.1.8/specmine/man/pca_biplot3D.Rd | 59 specmine-3.1.8/specmine/man/pca_kmeans_plot2D.Rd | 103 - specmine-3.1.8/specmine/man/pca_kmeans_plot3D.Rd | 90 - specmine-3.1.8/specmine/man/pca_pairs_kmeans_plot.Rd | 68 specmine-3.1.8/specmine/man/pca_pairs_plot.Rd | 68 specmine-3.1.8/specmine/man/pca_plot_3d.Rd | 81 specmine-3.1.8/specmine/man/pca_robust.Rd | 81 specmine-3.1.8/specmine/man/pca_scoresplot2D.Rd | 106 - specmine-3.1.8/specmine/man/pca_scoresplot3D.Rd | 59 specmine-3.1.8/specmine/man/pca_scoresplot3D_rgl.Rd | 78 specmine-3.1.8/specmine/man/pca_screeplot.Rd | 92 - specmine-3.1.8/specmine/man/peak_detection2d.Rd | 79 specmine-3.1.8/specmine/man/read-spc.Rd | 79 specmine-3.1.8/specmine/man/read_csvs_folder.Rd | 41 specmine-3.1.8/specmine/man/read_data_csv.Rd | 71 specmine-3.1.8/specmine/man/read_data_dx.Rd | 38 specmine-3.1.8/specmine/man/read_dataset_csv.Rd | 141 - specmine-3.1.8/specmine/man/read_dataset_dx.Rd | 91 - specmine-3.1.8/specmine/man/read_metadata.Rd | 52 specmine-3.1.8/specmine/man/read_ms_spectra.Rd | 104 - specmine-3.1.8/specmine/man/read_multiple_csvs.Rd | 44 specmine-3.1.8/specmine/man/recursive_feature_elimination.Rd | 84 specmine-3.1.8/specmine/man/remove_data.Rd | 77 specmine-3.1.8/specmine/man/remove_data_variables.Rd | 55 specmine-3.1.8/specmine/man/remove_metadata_variables.Rd | 52 specmine-3.1.8/specmine/man/remove_samples.Rd | 54 specmine-3.1.8/specmine/man/remove_samples_by_na_metadata.Rd | 49 specmine-3.1.8/specmine/man/remove_samples_by_nas.Rd | 53 specmine-3.1.8/specmine/man/remove_variables_by_nas.Rd | 53 specmine-3.1.8/specmine/man/remove_x_values_by_interval.Rd | 45 specmine-3.1.8/specmine/man/specmine-package.Rd |only specmine-3.1.8/specmine/man/spectra_options.Rd | 34 specmine-3.1.8/specmine/man/subset_by_samples_and_xvalues.Rd | 84 specmine-3.1.8/specmine/man/subset_metadata.Rd | 49 specmine-3.1.8/specmine/man/subset_random_samples.Rd | 49 specmine-3.1.8/specmine/man/subset_samples.Rd | 54 specmine-3.1.8/specmine/man/subset_samples_by_metadata_values.Rd | 57 specmine-3.1.8/specmine/man/subset_x_values.Rd | 50 specmine-3.1.8/specmine/man/subset_x_values_by_interval.Rd | 51 specmine-3.1.8/specmine/man/summary_var_importance.Rd | 47 specmine-3.1.8/specmine/man/train_and_predict.Rd | 115 - specmine-3.1.8/specmine/man/train_classifier.Rd | 110 - specmine-3.1.8/specmine/man/train_models_performance.Rd | 129 - 255 files changed, 8188 insertions(+), 6893 deletions(-)
Title: Rank-Clustered Estimation for Network Meta-Analysis
Description: An implementation of the RaCE-NMA (Rank-Clustered
Estimation for Network Meta-Analysis) model for post-hoc clustering
of treatments or interventions by rank in network meta-analysis
data. Functions for model estimation, assessment, and displaying
results are provided. For more details, see Pearce and Zhou (2025)
<doi:10.1017/rsm.2025.10049>.
Author: Michael Pearce [aut, cre, cph] ,
Shouhao Zhou [aut]
Maintainer: Michael Pearce <michaelpearce@reed.edu>
Diff between RaCE.NMA versions 1.1.0 dated 2026-07-29 and 1.2.0 dated 2026-08-05
DESCRIPTION | 8 - MD5 | 87 +++++++++++--------- NEWS.md | 6 + R/calculate_Rhat.R | 4 R/calculate_SUCRA_MNBT.R | 8 + R/clusterplot_ranks.R | 4 R/cumulativeprobplot_ranks.R | 4 R/fit_raceNMA.R | 39 ++++++--- R/forestplot_muhat.R | 4 R/make_logdmvnorm.R |only R/mcmc_raceNMA.R | 84 +++++++++++++++----- R/sample_partition_correlation.R | 12 +- R/sample_partition_independence.R | 1 R/toy_data.R | 2 R/traceplot_K.R | 2 inst/doc/overview.Rmd | 2 inst/doc/overview.html | 2 inst/doc/reproducibility.R | 6 - inst/doc/reproducibility.Rmd | 8 - inst/doc/reproducibility.html | 8 - inst/doc/tutorial.R | 8 - inst/doc/tutorial.Rmd | 15 +-- inst/doc/tutorial.html | 104 ++++++++++++------------- man/calculate_Rhat.Rd | 4 man/calculate_SUCRA_MNBT.Rd | 2 man/clusterplot_ranks.Rd | 2 man/cumulativeprobplot_ranks.Rd | 2 man/fit_raceNMA.Rd | 2 man/forestplot_muhat.Rd | 2 man/make_logdmvnorm.Rd |only man/mcmc_raceNMA.Rd | 15 ++- man/sample_partition_correlation.Rd | 9 +- man/sample_partition_independence.Rd | 1 man/toy_data.Rd | 2 man/traceplot_K.Rd | 2 tests/testthat/test-calculate_Rhat.R | 10 ++ tests/testthat/test-calculate_SUCRA_MNBT.R | 43 ++++++++++ tests/testthat/test-clusterplot_ranks.R | 26 ++++++ tests/testthat/test-cumulativeprobplot_ranks.R | 18 ++++ tests/testthat/test-datasets.R |only tests/testthat/test-fit_raceNMA.R |only tests/testthat/test-forestplot_muhat.R | 26 ++++++ tests/testthat/test-mcmc_raceNMA.R | 36 +++++++- tests/testthat/test-sample_partition.R |only vignettes/overview.Rmd | 2 vignettes/reproducibility.Rmd | 8 - vignettes/tutorial.Rmd | 15 +-- 47 files changed, 450 insertions(+), 195 deletions(-)
Title: AI Agent Runtime
Description: An agent runtime that gives Large Language Models (LLMs)
from 'Anthropic' <https://www.anthropic.com/>, 'OpenAI'
<https://openai.com/>, 'Moonshot' <https://www.moonshot.ai/>, and
'Ollama' <https://ollama.com/> direct access to a live R session with
managed workspace state. Tools execute as R function calls with
provenance tracking, and a deterministic retrieval system keeps
relevant objects in context across turns. Three entry points: a
shell command-line interface (CLI), a console read-eval-print-loop
via chat(), and a Model Context Protocol (MCP) server via serve()
for external clients.
Author: Troy Hernandez [aut, cre] ,
Grant McDermott [ctb] ,
Jorge Krzyzaniak [ctb],
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between corteza versions 0.7.0 dated 2026-06-26 and 0.7.1 dated 2026-08-05
DESCRIPTION | 12 MD5 | 139 +++--- NEWS.md | 117 +++++ R/agent_context.R | 1 R/archival-history-shim.R | 1 R/archival.R | 1 R/banner.R | 77 ++- R/chat-slash.R | 3 R/chat.R | 10 R/chunk.R | 1 R/cli-colors.R | 1 R/cli-ui.R | 32 - R/compact-turn.R | 1 R/config.R | 1 R/context-budget.R | 1 R/context-engine.R | 1 R/context-meter.R | 1 R/context.R | 1 R/deny.R | 1 R/diff-render.R | 1 R/dispatch.R | 1 R/format-elapsed.R | 1 R/handles.R | 1 R/heartbeat.R | 1 R/install-cli.R | 1 R/interrupt.R | 1 R/log.R | 1 R/matrix.R | 676 +++++++++++++++++++++++++---- R/matrix_crypto.R | 20 R/mcp-handler.R | 1 R/mcp-transport.R | 1 R/package-tools.R | 1 R/paths.R | 1 R/permissions.R | 1 R/plan-mode.R | 1 R/policy.R | 1 R/rate-limit.R | 1 R/registry.R | 1 R/render-md-ansi.R | 1 R/repl.R | 1 R/retrieval.R | 1 R/rstudio-addin.R | 1 R/schema.R | 1 R/serve.R | 1 R/session.R | 1 R/session_setup.R | 39 + R/skill.R | 5 R/spend.R | 1 R/subagent.R | 1 R/tasks.R | 1 R/tool-buffer.R | 1 R/tool-impl.R | 5 R/tools.R | 1 R/turn.R | 105 ++++ R/utils.R | 1 R/workspace.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/bin/corteza | 30 + inst/doc/configuration.html | 170 ++++--- inst/doc/configuration.md | 50 ++ inst/tinytest/test_banner.R | 27 - inst/tinytest/test_matrix.R | 851 +++++++++++++++++++++++++++++++++++-- inst/tinytest/test_session_setup.R | 75 +++ inst/tinytest/test_turn.R | 23 + inst/tinytest/test_web_search.R |only man/chat.Rd | 7 man/matrix_configure.Rd | 15 man/new_session.Rd | 17 man/session_setup.Rd | 11 vignettes/configuration.md | 50 ++ 71 files changed, 2225 insertions(+), 384 deletions(-)
Title: Neo4j to R
Description: The aim of neo2R is to provide simple and low level connectors
for querying neo4j graph databases (<https://neo4j.com/>).
The objects returned by the query functions are either lists or data.frames
with very little post-processing.
It allows fast processing of queries returning many records.
And it let the users handle post-processing according to the data model
and their needs.
Author: Patrice Godard [aut, cre, cph] ,
Eusebiu Marcu [ctb]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between neo2R versions 3.0.0 dated 2026-05-18 and 3.1.1 dated 2026-08-05
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/cypher.R | 125 ++++++++++++++++++++++++++++++++++++----------------- R/import_from_df.R | 29 +----------- R/startGraph.R | 23 ++++++++- man/cypher.Rd | 6 +- man/multicypher.Rd | 6 +- man/startGraph.Rd | 6 ++ 8 files changed, 133 insertions(+), 84 deletions(-)
Title: Morphological Analysis for Japanese
Description: Supports morphological analysis for Japanese by using
'MeCab' <https://taku910.github.io/mecab/>,
'Sudachi' <https://github.com/WorksApplications/Sudachi>,
'Chamame' <https://chamame.ninjal.ac.jp/>,
or 'Ginza' <https://github.com/megagonlabs/ginza>.
Can input a data.frame and obtain all results of 'MeCab' and the row
number of the original data.frame as a text id.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
This is a re-admission after prior archival of version 0.9.7 dated 2024-08-01
Diff between moranajp versions 0.9.7 dated 2024-08-01 and 0.9.8 dated 2026-08-05
moranajp-0.9.7/moranajp/man/text_id_with_break.Rd |only moranajp-0.9.8/moranajp/DESCRIPTION | 10 moranajp-0.9.8/moranajp/MD5 | 42 +- moranajp-0.9.8/moranajp/NAMESPACE | 2 moranajp-0.9.8/moranajp/NEWS.md | 25 + moranajp-0.9.8/moranajp/R/clean_up.R | 5 moranajp-0.9.8/moranajp/R/make_group.R | 11 moranajp-0.9.8/moranajp/R/moranajp.R | 249 ++++++++++++++--- moranajp-0.9.8/moranajp/R/utils_id.R | 121 ++------ moranajp-0.9.8/moranajp/build/vignette.rds |binary moranajp-0.9.8/moranajp/inst/doc/bigram.R | 56 +-- moranajp-0.9.8/moranajp/inst/doc/bigram.html | 7 moranajp-0.9.8/moranajp/inst/doc/moranajp.R | 30 +- moranajp-0.9.8/moranajp/inst/doc/moranajp.html | 7 moranajp-0.9.8/moranajp/man/add_group.Rd | 6 moranajp-0.9.8/moranajp/man/add_sentence_no.Rd | 4 moranajp-0.9.8/moranajp/man/add_text_id.Rd | 6 moranajp-0.9.8/moranajp/man/eval_str.Rd |only moranajp-0.9.8/moranajp/man/make_groups.Rd | 17 - moranajp-0.9.8/moranajp/man/moranajp_all.Rd | 26 + moranajp-0.9.8/moranajp/man/remove_brk.Rd | 2 moranajp-0.9.8/moranajp/man/web_chamame.Rd | 90 ++++++ moranajp-0.9.8/moranajp/tests/testthat/test-moranajp.R | 10 23 files changed, 496 insertions(+), 230 deletions(-)
Title: Lookup for IP Address Information
Description: Enables the user to find the country, region, district, city, coordinates, zip code, time zone, ISP, domain name, connection type, area code, weather, Mobile Country Codes (MCC), Mobile Network Code (MNC), mobile brand name, elevation, usage type, address type, IAB category and Autonomous system number (ASN) that any IP address or hostname originates from. Supported IPv4 and IPv6.
Please visit <https://www.ip2location.com> to learn more. You may also want to visit <https://lite.ip2location.com> for free database download.
This package requires 'IP2Location Python' module. At the terminal, please run 'pip install IP2Location' to install the module.
Author: Kai Wen Ooi [aut, cre],
IP2Location [cph]
Maintainer: Kai Wen Ooi <support@ip2location.com>
Diff between ip2location versions 8.1.3 dated 2023-05-02 and 8.1.4 dated 2026-08-05
DESCRIPTION | 14 ++--- LICENSE | 4 - MD5 | 16 +++--- NAMESPACE | 22 ++++---- R/IP2Location.R | 32 ++++++++---- README.md | 145 ++++++++++---------------------------------------------- man/get_all.Rd | 46 ++++++++--------- man/open.Rd | 40 +++++++-------- man/plot_map.Rd | 40 +++++++-------- 9 files changed, 140 insertions(+), 219 deletions(-)
Title: Predicting Invasion Probabilities from Phylogenetic Data and
Species Traits
Description: A phylogenetic modelling approach for predicting species invasion risk, out of
a given pool of local species where a subset is known to be invasive elsewhere.
The package uses phylogenetic signal estimation and phylogenetic linear and logistic models
to estimate probabilities of being invasive based on phylogeny and any set of additional
predictors. A ranking method is implemented to evaluate prioritisation strategies. A manuscript
describing these methods, by Shahar Dubiner and Tamar Guy-Haim, is in preparation.
Author: Shahar Dubiner [aut, cre]
Maintainer: Shahar Dubiner <dubiner@mail.tau.ac.il>
This is a re-admission after prior archival of version 0.1.0 dated 2026-07-21
Diff between invasible versions 0.1.0 dated 2026-07-21 and 0.1.1 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/predict_invasible.R | 8 +++++--- R/prepare_invasible.R | 2 +- man/predict_invasible.Rd | 8 +++++--- man/prepare_invasible.Rd | 2 +- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Convert Engineering 'DWG' Drawings to Auditable 'GeoJSON'
Description: Converts engineering 'DWG' drawings ('AutoCAD' 2013+ format) to
'GeoJSON' entirely in-process, with no 'CAD' software, 'LibreDWG', or
'GDAL' required. Wraps the pure-Rust 'dwg2geo' conversion core
<https://github.com/milkway/dwg2geo>: every feature carries resolved
'CAD' style metadata (layer, colour, line weight, text), skipped and
failed entities are reported with reasons, and the output is
deterministic: the same bytes always produce byte-identical 'GeoJSON'.
Coordinates are kept in the drawing's local system; the package never
guesses a coordinate reference system.
Author: Andre Leite [aut, cre]
Maintainer: Andre Leite <leite@castlab.org>
Diff between dwg2geo versions 0.2.3 dated 2026-08-04 and 0.2.4 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ src/Makevars | 8 ++++++-- src/Makevars.win | 6 +++++- src/rust/Cargo.lock | 4 ++-- src/rust/src/lib.rs | 4 +++- src/rust/vendor.tar.xz |binary 8 files changed, 36 insertions(+), 16 deletions(-)
Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.8.2 dated 2026-03-19 and 1.9.0 dated 2026-08-05
campsis-1.8.2/campsis/R/results_processing.R |only campsis-1.8.2/campsis/man/VPC.Rd |only campsis-1.8.2/campsis/man/applyAction.Rd |only campsis-1.8.2/campsis/man/applyCompartmentCharacteristics.Rd |only campsis-1.8.2/campsis/man/applyScenario.Rd |only campsis-1.8.2/campsis/man/assignDoseNumber.Rd |only campsis-1.8.2/campsis/man/checkIIandADDL.Rd |only campsis-1.8.2/campsis/man/computeIncrementalProgress.Rd |only campsis-1.8.2/campsis/man/dosingOnly.Rd |only campsis-1.8.2/campsis/man/dropOthers.Rd |only campsis-1.8.2/campsis/man/exportDelegate.Rd |only campsis-1.8.2/campsis/man/exportTableDelegate.Rd |only campsis-1.8.2/campsis/man/factorScenarios.Rd |only campsis-1.8.2/campsis/man/generateIIV.Rd |only campsis-1.8.2/campsis/man/generateIIV_.Rd |only campsis-1.8.2/campsis/man/getAvailableTimeUnits.Rd |only campsis-1.8.2/campsis/man/getCampsisOption.Rd |only campsis-1.8.2/campsis/man/getCampsisOptions.Rd |only campsis-1.8.2/campsis/man/getColumn.Rd |only campsis-1.8.2/campsis/man/getCompartmentMapping.Rd |only campsis-1.8.2/campsis/man/getCovariates.Rd |only campsis-1.8.2/campsis/man/getEventCovariates.Rd |only campsis-1.8.2/campsis/man/getFixedCovariates.Rd |only campsis-1.8.2/campsis/man/getIOVs.Rd |only campsis-1.8.2/campsis/man/getInitialConditions.Rd |only campsis-1.8.2/campsis/man/getOccasions.Rd |only campsis-1.8.2/campsis/man/getRandomSeedValue.Rd |only campsis-1.8.2/campsis/man/getSeed.Rd |only campsis-1.8.2/campsis/man/getSeedForDatasetExport.Rd |only campsis-1.8.2/campsis/man/getSeedForIteration.Rd |only campsis-1.8.2/campsis/man/getSeedForParametersSampling.Rd |only campsis-1.8.2/campsis/man/getSimulationEngineType.Rd |only campsis-1.8.2/campsis/man/getSplittingConfiguration.Rd |only campsis-1.8.2/campsis/man/getTimeVaryingCovariates.Rd |only campsis-1.8.2/campsis/man/getTimes.Rd |only campsis-1.8.2/campsis/man/importCampsismodToNamespace.Rd |only campsis-1.8.2/campsis/man/isEmptyBootstrap.Rd |only campsis-1.8.2/campsis/man/jsonToCampsisDataset.Rd |only campsis-1.8.2/campsis/man/jsonToCampsisSettings.Rd |only campsis-1.8.2/campsis/man/leftJoinIIV.Rd |only campsis-1.8.2/campsis/man/obsOnly.Rd |only campsis-1.8.2/campsis/man/onCI.Rd |only campsis-1.8.2/campsis/man/onCran.Rd |only campsis-1.8.2/campsis/man/openJSON.Rd |only campsis-1.8.2/campsis/man/output_function-class.Rd |only campsis-1.8.2/campsis/man/preprocessArmColumn.Rd |only campsis-1.8.2/campsis/man/preprocessDest.Rd |only campsis-1.8.2/campsis/man/preprocessDosing.Rd |only campsis-1.8.2/campsis/man/preprocessEvents.Rd |only campsis-1.8.2/campsis/man/preprocessIds.Rd |only campsis-1.8.2/campsis/man/preprocessOutfun.Rd |only campsis-1.8.2/campsis/man/preprocessOutvars.Rd |only campsis-1.8.2/campsis/man/preprocessReplicates.Rd |only campsis-1.8.2/campsis/man/preprocessScenarios.Rd |only campsis-1.8.2/campsis/man/preprocessSettings.Rd |only campsis-1.8.2/campsis/man/preprocessSlices.Rd |only campsis-1.8.2/campsis/man/preprocessTablefun.Rd |only campsis-1.8.2/campsis/man/processArmLabels.Rd |only campsis-1.8.2/campsis/man/processDropOthers.Rd |only campsis-1.8.2/campsis/man/processSimulateArguments.Rd |only campsis-1.8.2/campsis/man/removeInitialConditions.Rd |only campsis-1.8.2/campsis/man/reorderColumns.Rd |only campsis-1.8.2/campsis/man/repeatSchedule.Rd |only campsis-1.8.2/campsis/man/retrieveParameterValue.Rd |only campsis-1.8.2/campsis/man/sampleCovariatesList.Rd |only campsis-1.8.2/campsis/man/sampleDistributionAsTibble.Rd |only campsis-1.8.2/campsis/man/setSeed.Rd |only campsis-1.8.2/campsis/man/simulateDelegate.Rd |only campsis-1.8.2/campsis/man/simulateDelegateCore.Rd |only campsis-1.8.2/campsis/man/simulateScenarios.Rd |only campsis-1.8.2/campsis/man/standardiseTime.Rd |only campsis-1.8.2/campsis/man/toExplicitDistribution.Rd |only campsis-1.8.2/campsis/man/uniteColumns.Rd |only campsis-1.8.2/campsis/man/unwrapTreatment.Rd |only campsis-1.8.2/campsis/man/updateADDL.Rd |only campsis-1.8.2/campsis/man/updateAmount.Rd |only campsis-1.8.2/campsis/man/updateII.Rd |only campsis-1.8.2/campsis/man/updateRepeat.Rd |only campsis-1.8.2/campsis/tests/testthat/_snaps/testDefaultPlots |only campsis-1.8.2/campsis/tests/testthat/_snaps/testSimulateReplicates |only campsis-1.8.2/campsis/tests/testthat/testArm.R |only campsis-1.8.2/campsis/tests/testthat/testArms.R |only campsis-1.8.2/campsis/tests/testthat/testBootstrap.R |only campsis-1.8.2/campsis/tests/testthat/testCompilationError.R |only campsis-1.8.2/campsis/tests/testthat/testCovariate.R |only campsis-1.8.2/campsis/tests/testthat/testCovariates.R |only campsis-1.8.2/campsis/tests/testthat/testDataset.R |only campsis-1.8.2/campsis/tests/testthat/testDatasetExportParallelisation.R |only campsis-1.8.2/campsis/tests/testthat/testDefaultPlots.R |only campsis-1.8.2/campsis/tests/testthat/testDistribution.R |only campsis-1.8.2/campsis/tests/testthat/testDoseAdaptation.R |only campsis-1.8.2/campsis/tests/testthat/testEvent.R |only campsis-1.8.2/campsis/tests/testthat/testEvents.R |only campsis-1.8.2/campsis/tests/testthat/testJSONInterface.R |only campsis-1.8.2/campsis/tests/testthat/testObservations.R |only campsis-1.8.2/campsis/tests/testthat/testOccasion.R |only campsis-1.8.2/campsis/tests/testthat/testOccasions.R |only campsis-1.8.2/campsis/tests/testthat/testRepeatedSchedule.R |only campsis-1.8.2/campsis/tests/testthat/testScenario.R |only campsis-1.8.2/campsis/tests/testthat/testScenarios.R |only campsis-1.8.2/campsis/tests/testthat/testSeed.R |only campsis-1.8.2/campsis/tests/testthat/testSettings.R |only campsis-1.8.2/campsis/tests/testthat/testShowMethod.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateArguments.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBioavailability.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBolus.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBolusInfusionSameCmt.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDeclare.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDoseAdaptation.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDosingInfo.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateEvents.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateEventsLogic.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateIOV.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateInfusion.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateInit.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateLagTime.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateMinimalistModel.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateNoOmega.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateNocbLocf.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateOutvars.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateRUV.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateReplicates.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateScenarios.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTSLD.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTTEModels.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTable.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTimeVaryingCovariates.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateWeirdCases.R |only campsis-1.8.2/campsis/tests/testthat/testTimeUtilities.R |only campsis-1.8.2/campsis/tests/testthat/testTreatment.R |only campsis-1.8.2/campsis/tests/testthat/testTreatmentEntry.R |only campsis-1.8.2/campsis/tests/testthat/testUtils.R |only campsis-1.9.0/campsis/DESCRIPTION | 33 campsis-1.9.0/campsis/MD5 | 894 +++---- campsis-1.9.0/campsis/NAMESPACE | 107 campsis-1.9.0/campsis/NEWS.md | 19 campsis-1.9.0/campsis/R/all_classes.R |only campsis-1.9.0/campsis/R/arm.R | 190 - campsis-1.9.0/campsis/R/arms.R | 126 - campsis-1.9.0/campsis/R/bootstrap.R | 94 campsis-1.9.0/campsis/R/campsis_metadata.R |only campsis-1.9.0/campsis/R/campsis_plot_helpers.R |only campsis-1.9.0/campsis/R/check.R | 93 campsis-1.9.0/campsis/R/covariate.R | 139 - campsis-1.9.0/campsis/R/covariates.R | 61 campsis-1.9.0/campsis/R/data.R | 1 campsis-1.9.0/campsis/R/dataset.R | 921 ++++--- campsis-1.9.0/campsis/R/dataset_config.R | 69 campsis-1.9.0/campsis/R/dataset_summary.R | 32 campsis-1.9.0/campsis/R/declare_settings.R | 18 campsis-1.9.0/campsis/R/default_plot.R | 251 +- campsis-1.9.0/campsis/R/default_settings.R | 115 campsis-1.9.0/campsis/R/deprecated_methods.R |only campsis-1.9.0/campsis/R/distribution.R | 365 +- campsis-1.9.0/campsis/R/dose_adaptation.R | 37 campsis-1.9.0/campsis/R/dose_adaptations.R | 11 campsis-1.9.0/campsis/R/event.R | 35 campsis-1.9.0/campsis/R/event_logic.R | 60 campsis-1.9.0/campsis/R/events.R | 26 campsis-1.9.0/campsis/R/generic.R | 249 +- campsis-1.9.0/campsis/R/global.R | 9 campsis-1.9.0/campsis/R/hardware_settings.R | 94 campsis-1.9.0/campsis/R/internal_settings.R | 11 campsis-1.9.0/campsis/R/json_interface.R | 100 campsis-1.9.0/campsis/R/nocb_settings.R | 25 campsis-1.9.0/campsis/R/observations.R | 104 campsis-1.9.0/campsis/R/observations_set.R | 26 campsis-1.9.0/campsis/R/occasion.R | 27 campsis-1.9.0/campsis/R/occasions.R | 24 campsis-1.9.0/campsis/R/outfun.R | 377 ++- campsis-1.9.0/campsis/R/outfun_core.R |only campsis-1.9.0/campsis/R/outfuns.R |only campsis-1.9.0/campsis/R/plan_setup.R | 28 campsis-1.9.0/campsis/R/progress_settings.R | 16 campsis-1.9.0/campsis/R/protocol.R | 18 campsis-1.9.0/campsis/R/repeated_schedule.R | 95 campsis-1.9.0/campsis/R/scatter_plot.R |only campsis-1.9.0/campsis/R/scenario.R | 79 campsis-1.9.0/campsis/R/scenario_action.R | 43 campsis-1.9.0/campsis/R/scenario_actions.R | 18 campsis-1.9.0/campsis/R/scenarios.R | 38 campsis-1.9.0/campsis/R/seed.R | 51 campsis-1.9.0/campsis/R/shaded_plot.R |only campsis-1.9.0/campsis/R/simulate.R | 1231 ++++++---- campsis-1.9.0/campsis/R/simulate_preprocess.R | 207 - campsis-1.9.0/campsis/R/simulation_engine.R | 28 campsis-1.9.0/campsis/R/simulation_progress.R | 114 campsis-1.9.0/campsis/R/simulation_settings.R | 123 campsis-1.9.0/campsis/R/solver_settings.R | 46 campsis-1.9.0/campsis/R/spaghetti_plot.R |only campsis-1.9.0/campsis/R/time_entry.R | 10 campsis-1.9.0/campsis/R/time_utilities.R | 64 campsis-1.9.0/campsis/R/time_vector.R | 48 campsis-1.9.0/campsis/R/treatment.R | 175 - campsis-1.9.0/campsis/R/treatment_entry.R | 579 ++-- campsis-1.9.0/campsis/R/treatment_iov.R | 28 campsis-1.9.0/campsis/R/treatment_iovs.R | 16 campsis-1.9.0/campsis/R/utilities.R | 54 campsis-1.9.0/campsis/R/vpc_plot.R |only campsis-1.9.0/campsis/README.md | 8 campsis-1.9.0/campsis/build/vignette.rds |binary campsis-1.9.0/campsis/inst/doc/campsis.R | 10 campsis-1.9.0/campsis/inst/doc/campsis.Rmd | 18 campsis-1.9.0/campsis/inst/doc/campsis.html | 38 campsis-1.9.0/campsis/inst/doc/v01_dataset.R | 6 campsis-1.9.0/campsis/inst/doc/v01_dataset.Rmd | 42 campsis-1.9.0/campsis/inst/doc/v02_uncertainties.R | 6 campsis-1.9.0/campsis/inst/doc/v02_uncertainties.Rmd | 35 campsis-1.9.0/campsis/inst/doc/v03_covariates.R | 6 campsis-1.9.0/campsis/inst/doc/v03_covariates.Rmd | 115 campsis-1.9.0/campsis/inst/doc/v04_bioavailability.R | 6 campsis-1.9.0/campsis/inst/doc/v04_bioavailability.Rmd | 61 campsis-1.9.0/campsis/inst/doc/v05_lag_time.R | 6 campsis-1.9.0/campsis/inst/doc/v05_lag_time.Rmd | 61 campsis-1.9.0/campsis/inst/doc/v06_infusions.R | 6 campsis-1.9.0/campsis/inst/doc/v06_infusions.Rmd | 53 campsis-1.9.0/campsis/inst/doc/v07_iov.R | 6 campsis-1.9.0/campsis/inst/doc/v07_iov.Rmd | 30 campsis-1.9.0/campsis/inst/doc/v08_initial_conditions.R | 6 campsis-1.9.0/campsis/inst/doc/v08_initial_conditions.Rmd | 17 campsis-1.9.0/campsis/inst/doc/v09_dose_adaptation.R | 6 campsis-1.9.0/campsis/inst/doc/v09_dose_adaptation.Rmd | 21 campsis-1.9.0/campsis/inst/doc/v10_replicate_study.R | 6 campsis-1.9.0/campsis/inst/doc/v10_replicate_study.Rmd | 22 campsis-1.9.0/campsis/inst/doc/v11_scenarios.R | 6 campsis-1.9.0/campsis/inst/doc/v11_scenarios.Rmd | 128 - campsis-1.9.0/campsis/inst/doc/v12_time_varying_covariates.R | 6 campsis-1.9.0/campsis/inst/doc/v12_time_varying_covariates.Rmd | 71 campsis-1.9.0/campsis/inst/doc/v13_events.R | 6 campsis-1.9.0/campsis/inst/doc/v13_events.Rmd | 43 campsis-1.9.0/campsis/inst/doc/v14_complex_pkpd_models.R | 6 campsis-1.9.0/campsis/inst/doc/v14_complex_pkpd_models.Rmd | 55 campsis-1.9.0/campsis/inst/doc/v15_pkpd_model_library.R | 6 campsis-1.9.0/campsis/inst/doc/v15_pkpd_model_library.Rmd | 98 campsis-1.9.0/campsis/inst/doc/v16_progress_bar.R | 6 campsis-1.9.0/campsis/inst/doc/v16_progress_bar.Rmd | 69 campsis-1.9.0/campsis/inst/doc/v17_run_simulation_in_parallel.R | 6 campsis-1.9.0/campsis/inst/doc/v17_run_simulation_in_parallel.Rmd | 224 - campsis-1.9.0/campsis/inst/extdata/campsis_settings.schema.json | 181 + campsis-1.9.0/campsis/man/Arm.Rd | 42 campsis-1.9.0/campsis/man/BinomialDistribution.Rd | 38 campsis-1.9.0/campsis/man/Bolus.Rd | 94 campsis-1.9.0/campsis/man/Bootstrap.Rd | 70 campsis-1.9.0/campsis/man/BootstrapDistribution.Rd | 46 campsis-1.9.0/campsis/man/ConstantDistribution.Rd | 34 campsis-1.9.0/campsis/man/Covariate.Rd | 38 campsis-1.9.0/campsis/man/CyclicSchedule.Rd | 38 campsis-1.9.0/campsis/man/Dataset.Rd | 42 campsis-1.9.0/campsis/man/DatasetConfig.Rd | 72 campsis-1.9.0/campsis/man/DatasetSummary.Rd | 30 campsis-1.9.0/campsis/man/Declare.Rd | 34 campsis-1.9.0/campsis/man/DefaultOutfun.Rd |only campsis-1.9.0/campsis/man/DefaultSettings.Rd | 70 campsis-1.9.0/campsis/man/DiscreteDistribution.Rd | 42 campsis-1.9.0/campsis/man/DoseAdaptation.Rd | 40 campsis-1.9.0/campsis/man/DosingSchedule.Rd | 28 campsis-1.9.0/campsis/man/EtaDistribution.Rd | 42 campsis-1.9.0/campsis/man/Event.Rd | 46 campsis-1.9.0/campsis/man/EventCovariate.Rd | 42 campsis-1.9.0/campsis/man/EventIteration.Rd | 52 campsis-1.9.0/campsis/man/EventRelatedObservations.Rd | 44 campsis-1.9.0/campsis/man/Events.Rd | 28 campsis-1.9.0/campsis/man/FixedDistribution.Rd | 38 campsis-1.9.0/campsis/man/FunctionDistribution.Rd | 50 campsis-1.9.0/campsis/man/Hardware.Rd | 80 campsis-1.9.0/campsis/man/IOV.Rd | 50 campsis-1.9.0/campsis/man/Infusion.Rd | 106 campsis-1.9.0/campsis/man/LogNormalDistribution.Rd | 38 campsis-1.9.0/campsis/man/NCATableOutfun.Rd |only campsis-1.9.0/campsis/man/NOCB.Rd | 38 campsis-1.9.0/campsis/man/NormalDistribution.Rd | 38 campsis-1.9.0/campsis/man/Observations.Rd | 46 campsis-1.9.0/campsis/man/Occasion.Rd | 46 campsis-1.9.0/campsis/man/Outfun.Rd | 63 campsis-1.9.0/campsis/man/Outfuns.Rd |only campsis-1.9.0/campsis/man/PI.Rd | 52 campsis-1.9.0/campsis/man/PIOutfun.Rd |only campsis-1.9.0/campsis/man/ParameterDistribution.Rd | 46 campsis-1.9.0/campsis/man/Progress.Rd | 38 campsis-1.9.0/campsis/man/RepeatAtSchedule.Rd | 38 campsis-1.9.0/campsis/man/ReplaceAction.Rd | 34 campsis-1.9.0/campsis/man/Scenario.Rd | 42 campsis-1.9.0/campsis/man/Scenarios.Rd | 34 campsis-1.9.0/campsis/man/Settings.Rd | 38 campsis-1.9.0/campsis/man/SimulationProgress.Rd | 56 campsis-1.9.0/campsis/man/Solver.Rd | 62 campsis-1.9.0/campsis/man/StatsOutfun.Rd |only campsis-1.9.0/campsis/man/TimeSequence.Rd | 42 campsis-1.9.0/campsis/man/TimeVaryingCovariate.Rd | 48 campsis-1.9.0/campsis/man/TimeVector.Rd | 34 campsis-1.9.0/campsis/man/UniformDistribution.Rd | 38 campsis-1.9.0/campsis/man/apply_action.Rd |only campsis-1.9.0/campsis/man/apply_compartment_characteristics.Rd |only campsis-1.9.0/campsis/man/apply_outfun.Rd |only campsis-1.9.0/campsis/man/apply_scenario.Rd |only campsis-1.9.0/campsis/man/arm-class.Rd | 50 campsis-1.9.0/campsis/man/arms-class.Rd | 18 campsis-1.9.0/campsis/man/as.numeric-time_sequence-method.Rd | 34 campsis-1.9.0/campsis/man/as.numeric-time_vector-method.Rd | 34 campsis-1.9.0/campsis/man/assign_dose_number.Rd |only campsis-1.9.0/campsis/man/binomial_distribution-class.Rd | 18 campsis-1.9.0/campsis/man/bolus-class.Rd | 18 campsis-1.9.0/campsis/man/bolus_wrapper-class.Rd | 18 campsis-1.9.0/campsis/man/bootstrap-class.Rd | 46 campsis-1.9.0/campsis/man/bootstrap_distribution-class.Rd | 38 campsis-1.9.0/campsis/man/campsis_handler.Rd | 28 campsis-1.9.0/campsis/man/campsis_metadata-class.Rd |only campsis-1.9.0/campsis/man/campsis_tbl-class.Rd |only campsis-1.9.0/campsis/man/check_ii_and_addl.Rd |only campsis-1.9.0/campsis/man/compute_incremental_progress.Rd |only campsis-1.9.0/campsis/man/compute_pi.Rd |only campsis-1.9.0/campsis/man/compute_stats.Rd |only campsis-1.9.0/campsis/man/constant_distribution-class.Rd | 30 campsis-1.9.0/campsis/man/convertTime.Rd | 46 campsis-1.9.0/campsis/man/convert_time.Rd |only campsis-1.9.0/campsis/man/counterBalanceLocfMode.Rd | 44 campsis-1.9.0/campsis/man/counterBalanceNocbMode.Rd | 44 campsis-1.9.0/campsis/man/covariate-class.Rd | 34 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campsis-1.9.0/campsis/man/minutes.Rd | 34 campsis-1.9.0/campsis/man/months.Rd | 34 campsis-1.9.0/campsis/man/mrgsolve_engine-class.Rd | 18 campsis-1.9.0/campsis/man/nca_table_outfun-class.Rd |only campsis-1.9.0/campsis/man/nhanes.Rd | 58 campsis-1.9.0/campsis/man/nocb_settings-class.Rd | 34 campsis-1.9.0/campsis/man/normal_distribution-class.Rd | 18 campsis-1.9.0/campsis/man/obs_only.Rd |only campsis-1.9.0/campsis/man/observations-class.Rd | 42 campsis-1.9.0/campsis/man/observations_set-class.Rd | 18 campsis-1.9.0/campsis/man/occasion-class.Rd | 38 campsis-1.9.0/campsis/man/occasions-class.Rd | 18 campsis-1.9.0/campsis/man/on_ci.Rd |only campsis-1.9.0/campsis/man/on_cran.Rd |only campsis-1.9.0/campsis/man/open_json.Rd |only campsis-1.9.0/campsis/man/outfun-class.Rd |only campsis-1.9.0/campsis/man/outfuns-class.Rd |only campsis-1.9.0/campsis/man/pi_campsis_tbl-class.Rd |only campsis-1.9.0/campsis/man/pi_outfun-class.Rd |only campsis-1.9.0/campsis/man/preprocessNocbvars.Rd | 30 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campsis-1.9.0/campsis/man/scenario_actions-class.Rd | 18 campsis-1.9.0/campsis/man/scenarios-class.Rd | 18 campsis-1.9.0/campsis/man/seconds.Rd | 34 campsis-1.9.0/campsis/man/setLabel.Rd | 48 campsis-1.9.0/campsis/man/setSubjects.Rd | 48 campsis-1.9.0/campsis/man/set_label.Rd |only campsis-1.9.0/campsis/man/set_seed.Rd |only campsis-1.9.0/campsis/man/set_subjects.Rd |only campsis-1.9.0/campsis/man/setupPlanDefault.Rd | 50 campsis-1.9.0/campsis/man/setupPlanSequential.Rd | 32 campsis-1.9.0/campsis/man/setup_plan_default.Rd |only campsis-1.9.0/campsis/man/setup_plan_sequential.Rd |only campsis-1.9.0/campsis/man/shadedPlot.Rd | 69 campsis-1.9.0/campsis/man/shaded_plot.Rd |only campsis-1.9.0/campsis/man/shaded_plot.std_campsis_tbl.Rd |only campsis-1.9.0/campsis/man/simulate.Rd | 296 +- campsis-1.9.0/campsis/man/simulate_delegate.Rd |only campsis-1.9.0/campsis/man/simulate_delegate_core.Rd |only campsis-1.9.0/campsis/man/simulate_scenarios.Rd |only 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campsis-1.9.0/campsis/man/treatment_iov-class.Rd | 38 campsis-1.9.0/campsis/man/treatment_iovs-class.Rd | 18 campsis-1.9.0/campsis/man/undefined_distribution-class.Rd | 26 campsis-1.9.0/campsis/man/undefined_schedule-class.Rd | 18 campsis-1.9.0/campsis/man/uniform_distribution-class.Rd | 18 campsis-1.9.0/campsis/man/unite_columns.Rd |only campsis-1.9.0/campsis/man/unwrap_treatment.Rd |only campsis-1.9.0/campsis/man/update_addl.Rd |only campsis-1.9.0/campsis/man/update_amount.Rd |only campsis-1.9.0/campsis/man/update_ii.Rd |only campsis-1.9.0/campsis/man/update_repeat.Rd |only campsis-1.9.0/campsis/man/vec_restore.campsis_tbl.Rd |only campsis-1.9.0/campsis/man/vpcPlot.Rd | 55 campsis-1.9.0/campsis/man/vpc_plot.Rd |only campsis-1.9.0/campsis/man/vpc_plot.pi_campsis_tbl.Rd |only campsis-1.9.0/campsis/man/vpc_plot.std_campsis_tbl.Rd |only campsis-1.9.0/campsis/man/weeks.Rd | 34 campsis-1.9.0/campsis/man/years.Rd | 34 campsis-1.9.0/campsis/tests/testthat/_snaps/default_plots |only 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campsis-1.9.0/campsis/vignettes/v01_dataset.Rmd | 42 campsis-1.9.0/campsis/vignettes/v02_uncertainties.Rmd | 35 campsis-1.9.0/campsis/vignettes/v03_covariates.Rmd | 115 campsis-1.9.0/campsis/vignettes/v04_bioavailability.Rmd | 61 campsis-1.9.0/campsis/vignettes/v05_lag_time.Rmd | 61 campsis-1.9.0/campsis/vignettes/v06_infusions.Rmd | 53 campsis-1.9.0/campsis/vignettes/v07_iov.Rmd | 30 campsis-1.9.0/campsis/vignettes/v08_initial_conditions.Rmd | 17 campsis-1.9.0/campsis/vignettes/v09_dose_adaptation.Rmd | 21 campsis-1.9.0/campsis/vignettes/v10_replicate_study.Rmd | 22 campsis-1.9.0/campsis/vignettes/v11_scenarios.Rmd | 128 - campsis-1.9.0/campsis/vignettes/v12_time_varying_covariates.Rmd | 71 campsis-1.9.0/campsis/vignettes/v13_events.Rmd | 43 campsis-1.9.0/campsis/vignettes/v14_complex_pkpd_models.Rmd | 55 campsis-1.9.0/campsis/vignettes/v15_pkpd_model_library.Rmd | 98 campsis-1.9.0/campsis/vignettes/v16_progress_bar.Rmd | 69 campsis-1.9.0/campsis/vignettes/v17_run_simulation_in_parallel.Rmd | 224 - 590 files changed, 9636 insertions(+), 7404 deletions(-)
Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.9.0 dated 2026-04-23 and 1.9.1 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dependencies.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about rmoriebricklayer at CRAN
Permanent link
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.3.0 dated 2026-07-02 and 1.4.0 dated 2026-08-05
btw-1.3.0/btw/inst/js/run-r/btw-icons.js |only btw-1.4.0/btw/DESCRIPTION | 44 - btw-1.4.0/btw/MD5 | 104 +-- btw-1.4.0/btw/NEWS.md | 22 btw-1.4.0/btw/R/btw-config.R |only btw-1.4.0/btw/R/btw_client.R | 24 btw-1.4.0/btw/R/btw_client_app.R | 160 +++-- btw-1.4.0/btw/R/edit_btw_md.R | 159 ++++- btw-1.4.0/btw/R/mcp.R | 2 btw-1.4.0/btw/R/task_create_btw_md.R | 2 btw-1.4.0/btw/R/tool-agent-custom.R | 19 btw-1.4.0/btw/R/tool-agent-subagent.R | 6 btw-1.4.0/btw/R/tool-docs-news.R | 2 btw-1.4.0/btw/R/tool-docs.R | 9 btw-1.4.0/btw/R/tool-env-df.R | 6 btw-1.4.0/btw/R/tool-files-edit.R | 4 btw-1.4.0/btw/R/tool-files-patch.R | 4 btw-1.4.0/btw/R/tool-files-read.R | 48 - btw-1.4.0/btw/R/tool-files-replace.R | 4 btw-1.4.0/btw/R/tool-files-search.R | 21 btw-1.4.0/btw/R/tool-files-write.R | 5 btw-1.4.0/btw/R/tool-git.R | 6 btw-1.4.0/btw/R/tool-pkg-src.R |only btw-1.4.0/btw/R/tool-run.R | 86 +- btw-1.4.0/btw/R/tool-skills.R | 38 + btw-1.4.0/btw/R/utils.R | 115 +++ btw-1.4.0/btw/exec/btw.R | 281 +++++++++ btw-1.4.0/btw/inst/cli-skill/r-btw-cli/SKILL.md | 23 btw-1.4.0/btw/inst/js/app/btw_app.css | 41 - btw-1.4.0/btw/inst/js/app/btw_app.js | 71 +- btw-1.4.0/btw/inst/js/run-r/btw-run-r.css | 508 +++++++++------- btw-1.4.0/btw/inst/js/run-r/btw-run-r.js | 514 +++-------------- btw-1.4.0/btw/man/btw-config.Rd |only btw-1.4.0/btw/man/btw_agent_tool.Rd | 6 btw-1.4.0/btw/man/btw_client.Rd | 72 ++ btw-1.4.0/btw/man/btw_skill_install_github.Rd | 3 btw-1.4.0/btw/man/btw_skill_install_package.Rd | 3 btw-1.4.0/btw/man/btw_tool_skill.Rd | 3 btw-1.4.0/btw/man/mcp.Rd | 2 btw-1.4.0/btw/man/use_btw_md.Rd | 28 btw-1.4.0/btw/tests/testthat/_snaps/btw_client.md | 4 btw-1.4.0/btw/tests/testthat/_snaps/edit_btw_md.md | 83 ++ btw-1.4.0/btw/tests/testthat/_snaps/tool-files-edit.md | 74 +- btw-1.4.0/btw/tests/testthat/_snaps/utils.md | 12 btw-1.4.0/btw/tests/testthat/helpers.R | 16 btw-1.4.0/btw/tests/testthat/test-btw_client_app.R |only btw-1.4.0/btw/tests/testthat/test-cli.R | 149 ++++ btw-1.4.0/btw/tests/testthat/test-edit_btw_md.R | 190 ++++++ btw-1.4.0/btw/tests/testthat/test-tool-agent-custom.R | 38 + btw-1.4.0/btw/tests/testthat/test-tool-docs.R | 3 btw-1.4.0/btw/tests/testthat/test-tool-files-read.R | 34 + btw-1.4.0/btw/tests/testthat/test-tool-files-write.R | 8 btw-1.4.0/btw/tests/testthat/test-tool-pkg-src.R |only btw-1.4.0/btw/tests/testthat/test-tool-run.R | 82 ++ btw-1.4.0/btw/tests/testthat/test-tool_skills.R | 82 ++ btw-1.4.0/btw/tests/testthat/test-utils.R | 187 ++++++ 56 files changed, 2413 insertions(+), 994 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-22 1.0
Title: Colour Palettes for Data
Description: Colour palettes for data, based on some well known public data
sets. Includes helper functions to map absolute values to known palettes, and
capture the work of image colour mapping as raster data sets.
Author: Michael D. Sumner [aut, cre, cph],
Abigael Proctor [ctb] ,
Tomas Remenyi [ctb] ,
R Core Team and contributors worldwide [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between palr versions 0.4.0 dated 2023-11-06 and 0.5.0 dated 2026-08-05
palr-0.4.0/palr/R/element_pal.R |only palr-0.4.0/palr/R/palr-package.r |only palr-0.5.0/palr/DESCRIPTION | 19 - palr-0.5.0/palr/MD5 | 61 ++- palr-0.5.0/palr/NAMESPACE | 8 palr-0.5.0/palr/NEWS.md | 37 ++ palr-0.5.0/palr/R/bathy.R | 20 - palr-0.5.0/palr/R/data_pal.R | 10 palr-0.5.0/palr/R/dirty.R |only palr-0.5.0/palr/R/image_hex.R |only palr-0.5.0/palr/R/image_pal.R | 1 palr-0.5.0/palr/R/palr-package.R |only palr-0.5.0/palr/R/palr.R | 376 ++++++------------------ palr-0.5.0/palr/R/stretch.R |only palr-0.5.0/palr/R/utils.R | 2 palr-0.5.0/palr/README.md | 4 palr-0.5.0/palr/build/vignette.rds |binary palr-0.5.0/palr/data/chl.rda |only palr-0.5.0/palr/inst/doc/nasa_chla.Rmd | 2 palr-0.5.0/palr/inst/doc/nasa_chla.html | 11 palr-0.5.0/palr/inst/doc/palr.R | 2 palr-0.5.0/palr/inst/doc/palr.html | 15 palr-0.5.0/palr/inst/extdata |only palr-0.5.0/palr/man/bathy_deep_pal.Rd | 2 palr-0.5.0/palr/man/chl_pal.Rd | 16 - palr-0.5.0/palr/man/d_pal.Rd | 3 palr-0.5.0/palr/man/dirty_pal.Rd |only palr-0.5.0/palr/man/ice_pal.Rd | 15 palr-0.5.0/palr/man/image_hex.Rd |only palr-0.5.0/palr/man/oisst.Rd | 9 palr-0.5.0/palr/man/palr.Rd | 28 + palr-0.5.0/palr/man/sst_pal.Rd | 2 palr-0.5.0/palr/man/stretch_linear.Rd |only palr-0.5.0/palr/tests/testthat/test-basic.R | 93 ++--- palr-0.5.0/palr/tests/testthat/test-image_hex.R |only palr-0.5.0/palr/tests/testthat/test-missing.R | 19 - palr-0.5.0/palr/tests/testthat/test-stretch.R |only palr-0.5.0/palr/vignettes/nasa_chla.Rmd | 2 38 files changed, 335 insertions(+), 422 deletions(-)