Stratigraphic diagrams

Helpers for ggplot2-based stratigraphic diagrams.

geom_col_segsh() geom_col_segs() GeomColSegsh GeomColSegs GeomLineh

Useful geometries for strat diagrams


Connect observations in the vertical direction

geom_point_exaggerate() geom_line_exaggerate() geom_lineh_exaggerate() geom_area_exaggerate() geom_areah_exaggerate()

Exaggerated geometries that do not train scales

geom_ribbonh() GeomRibbonh geom_areah() GeomAreah

Vertical ribbons and area plots

stat_nested_hclust() StatNestedHclust

Display a dendrogram as a ggplot2 layer

scale_x_abundance() scale_y_abundance()

Scales for relative abundance values

scale_y_depth_age() scale_y_age_depth() scale_x_depth_age() scale_x_age_depth()

Age-depth scales

facet_abundanceh() facet_abundance() facet_geochem_wraph() facet_geochem_wrap() facet_geochem_grid() facet_geochem_gridh()

Facet for relative abundance data

layer_dendrogram() plot_layer_dendrogram() layer_zone_boundaries()

Add a dendrogram as a layer or facet

layer_scores() plot_layer_scores()

Add scores to a plot

rotated_facet_labels() rotated_axis_labels()

Common plot modifications for stratigraphic plots


Geochem facet labelers


Species facet labellers


A Paleo-friendly ggplot2 theme


Change facet ordering behaviour

Age-depth models

Functions to interpolate/extrapolate ages and depths given a set of paired age/depth values.


Create age depth models

predict(<age_depth_model>) predict_depth() predict_age()

Predict age and depth values


Use an age depth model as a second ggplot axis

age_depth_interpolate() age_depth_extrapolate() age_depth_exact() age_depth_na()

Age-depth model interpolators/extrapolators


Plot an age depth model using base graphics

as_trans_factory() validate_trans_factory() validate_trans()

Coerce and validate transforms and functions that produce them

Nested analyses

Helpers for clustering and ordination of stratigraphic data.


Perform an analysis on a nested data matrix

nested_data() unnested_data()

Prepare a parameter-long data frame for statistical analysis

nested_hclust() nested_chclust_conslink() nested_chclust_coniss()

Nested (Constrained) hierarchical clustering


Nested Principal Components Analysis (PCA)

plot(<nested_analysis>) plot_nested_analysis() biplot(<nested_prcomp>)

Plot a nested analysis

Example data

Real data sets to test and document this package.

alta_lake_210Pb_ages alta_lake_14C_ages alta_lake_bacon_ages alta_lake_geochem

Alta Lake Lead-210 and Carbon-14 Ages


Halifax lakes water chemistry and top/bottom diatom counts


Keji lakes core diatom counts

long_lake_14C_ages long_lake_bacon_ages long_lake_plottable

Long Lake Carbon-14 Ages

kellys_lake_cladocera kellys_lake_geochem kellys_lake_ages

Kellys Lake Data