Package: tidypaleo 0.1.3.9000
tidypaleo: Tidy Tools for Paleoenvironmental Archives
Provides a set of functions with a common framework for age-depth model management, stratigraphic visualization, and common statistical transformations. The focus of the package is stratigraphic visualization, for which 'ggplot2' components are provided to reproduce the scales, geometries, facets, and theme elements commonly used in publication-quality stratigraphic diagrams. Helpers are also provided to reproduce the exploratory statistical summaries that are frequently included on stratigraphic diagrams. See Dunnington et al. (2021) <doi:10.18637/jss.v101.i07>.
Authors:
tidypaleo_0.1.3.9000.tar.gz
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tidypaleo.pdf |tidypaleo.html✨
tidypaleo/json (API)
NEWS
| # Install 'tidypaleo' in R: |
| install.packages('tidypaleo', repos = c('https://paleolimbot.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/paleolimbot/tidypaleo/issues
- alta_lake_14C_ages - Alta Lake Lead-210 and Carbon-14 Ages
- alta_lake_210Pb_ages - Alta Lake Lead-210 and Carbon-14 Ages
- alta_lake_bacon_ages - Alta Lake Lead-210 and Carbon-14 Ages
- alta_lake_geochem - Alta Lake Lead-210 and Carbon-14 Ages
- halifax_lakes_plottable - Halifax lakes water chemistry and top/bottom diatom counts
- keji_lakes_plottable - Keji lakes core diatom counts
- kellys_lake_ages - Kellys Lake Data
- kellys_lake_cladocera - Kellys Lake Data
- kellys_lake_geochem - Kellys Lake Data
- long_lake_14C_ages - Long Lake Carbon-14 Ages
- long_lake_bacon_ages - Long Lake Carbon-14 Ages
- long_lake_plottable - Long Lake Carbon-14 Ages
Last updated 2 years agofrom:4c51140261. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 07 2024 |
| R-4.5-win | OK | Sep 07 2024 |
| R-4.5-linux | OK | Sep 07 2024 |
| R-4.4-win | OK | Sep 07 2024 |
| R-4.4-mac | OK | Sep 07 2024 |
| R-4.3-win | OK | Sep 07 2024 |
| R-4.3-mac | OK | Sep 07 2024 |
Exports:age_depth_as_sec_axisage_depth_exactage_depth_extrapolateage_depth_interpolateage_depth_modelage_depth_naas_trans_factoryfacet_abundancefacet_abundancehfacet_geochem_gridfacet_geochem_gridhfacet_geochem_wrapfacet_geochem_wraphfirstgeom_area_exaggerategeom_areahgeom_areah_exaggerategeom_col_segsgeom_col_segshgeom_colhgeom_line_exaggerategeom_linehgeom_lineh_exaggerategeom_point_exaggerategeom_ribbonhGeomAreahGeomColhGeomColSegsGeomColSegshGeomLinehGeomRibbonhlabel_geochemlabel_specieslastlayer_dendrogramlayer_scoreslayer_zone_boundariesnested_analysisnested_chclust_conissnested_chclust_conslinknested_datanested_hclustnested_prcompplot_layer_dendrogramplot_layer_scoresplot_nested_analysisposition_dodge2vposition_dodgevposition_fillvposition_stackvPositionDodge2vPositionDodgevPositionFillvPositionStackvpredict_agepredict_depthrotated_axis_labelsrotated_facet_labelsscale_x_abundancescale_x_age_depthscale_x_depth_agescale_y_abundancescale_y_age_depthscale_y_depth_agesequential_layer_facetsstat_nested_hclustStatNestedHclusttheme_paleounnested_datavalidate_transvalidate_trans_factoryvars
Dependencies:cliclustercolorspacecpp11digestdplyrfansifarvergenericsggplot2ggstancegluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigplyrpurrrR.cacheR.methodsS3R.ooR.utilsR6RColorBrewerRcppriojarlangrprojrootscalesstringistringrstylertibbletidyrtidyselectutf8vctrsveganviridisLitewithr
Age-depth models
Rendered fromage_depth.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2019-12-07
Started: 2018-07-19
Nested analyses
Rendered fromnested_analysis.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2021-03-27
Started: 2018-08-06
Stratigraphic diagrams
Rendered fromstrat_diagrams.Rmdusingknitr::rmarkdownon Sep 07 2024.Last update: 2023-01-18
Started: 2018-07-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Use an age depth model as a second ggplot axis | age_depth_as_sec_axis |
| Age-depth model interpolators/extrapolators | age_depth_exact age_depth_extrapolate age_depth_interpolate age_depth_na |
| Create age depth models | age_depth_model |
| Alta Lake Lead-210 and Carbon-14 Ages | alta_lake_14C_ages alta_lake_210Pb_ages alta_lake_bacon_ages alta_lake_geochem |
| Coerce and validate transforms and functions that produce them | as_trans_factory validate_trans validate_trans_factory |
| Facet for relative abundance data | facet_abundance facet_abundanceh facet_geochem_grid facet_geochem_gridh facet_geochem_wrap facet_geochem_wraph |
| Useful geometries for strat diagrams | GeomColSegs GeomColSegsh GeomLineh geom_col_segs geom_col_segsh |
| Connect observations in the vertical direction | geom_lineh |
| Exaggerated geometries that do not train scales | geom_areah_exaggerate geom_area_exaggerate geom_lineh_exaggerate geom_line_exaggerate geom_point_exaggerate |
| Vertical ribbons and area plots | GeomAreah GeomRibbonh geom_areah geom_ribbonh |
| Halifax lakes water chemistry and top/bottom diatom counts | halifax_lakes_plottable |
| Keji lakes core diatom counts | keji_lakes_plottable |
| Kellys Lake Data | kellys_lake_ages kellys_lake_cladocera kellys_lake_geochem |
| Geochem facet labelers | label_geochem |
| Species facet labellers | label_species |
| Add a dendrogram as a layer or facet | layer_dendrogram layer_zone_boundaries plot_layer_dendrogram |
| Add scores to a plot | layer_scores plot_layer_scores |
| Long Lake Carbon-14 Ages | long_lake_14C_ages long_lake_bacon_ages long_lake_plottable |
| Perform an analysis on a nested data matrix | nested_analysis |
| Prepare a parameter-long data frame for statistical analysis | nested_data unnested_data |
| Nested (Constrained) hierarchical clustering | nested_chclust_coniss nested_chclust_conslink nested_hclust |
| Nested Principal Components Analysis (PCA) | nested_prcomp |
| Plot an age depth model using base graphics | plot.age_depth_model |
| Plot a nested analysis | biplot.nested_prcomp plot.nested_analysis plot_nested_analysis |
| Predict age and depth values | predict.age_depth_model predict_age predict_depth |
| Common plot modifications for stratigraphic plots | rotated_axis_labels rotated_facet_labels |
| Scales for relative abundance values | scale_x_abundance scale_y_abundance |
| Age-depth scales | scale_x_age_depth scale_x_depth_age scale_y_age_depth scale_y_depth_age |
| Change facet ordering behaviour | sequential_layer_facets |
| Display a dendrogram as a ggplot2 layer | StatNestedHclust stat_nested_hclust |
| A Paleo-friendly ggplot2 theme | theme_paleo |
