Package: paleoDiv 0.4.0

Darius Nau

paleoDiv: Extracting and Visualizing Paleobiodiversity

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

Authors:Darius Nau [aut, cre]

paleoDiv_0.4.0.tar.gz
paleoDiv_0.4.0.tar.gz(r-4.5-noble)paleoDiv_0.4.0.tar.gz(r-4.4-noble)
paleoDiv_0.4.0.tgz(r-4.4-emscripten)paleoDiv_0.4.0.tgz(r-4.3-emscripten)
paleoDiv.pdf |paleoDiv.html✨
paleoDiv/json (API)
NEWS

# Install 'paleoDiv' in R:

install.packages('paleoDiv', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ages_archosauria - Ages_archosauria
archosauria - Archosauria
diversity_table - Diversity_table
tree_archosauria - Tree_archosauria

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.78 score 2 stars 180 downloads 31 exports 13 dependencies

Last updated 6 days agofrom:b5465b0df4. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 18 2024
R-4.5-linux	OK	Oct 18 2024

Exports:ab.gg abdistr_add.alpha convert.sptab darken div.gg divdistr_divdistr_int ggcol jitterp mk.sptab multijitter occ.cleanup pdb pdb.autodiv pdb.diff pdb.union phylo.spindles redraw.phylo rmean rmeana stax.sel synonymize tree.age.combine tree.ages tree.ages.spp ts.periods ts.stages tsconv viol violins

Dependencies:ape cli digest glue lattice lifecycle magrittr nlme Rcpp rlang stringi stringr vctrs

Paleobiodiversity Analysis

Rendered fromPaleobiodiversity_analysis.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-05-03
Started: 2024-03-07

Citation

Readme and manuals

Help Manual

Help page	Topics
Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2	ab.gg
Count number of entries in occurrence or collection data.frame for specific points in geological time	abdistr_
Add transparency to any color	add.alpha
ages_archosauria	ages_archosauria
archosauria	archosauria
Convert geological ages in taxon-range tables as constructed by mk.sptab() for plotting alongside a time-calibrated phylogeny.	convert.sptab
Darken or lighten colors by adding/subtracting to or hsv channel values	darken
Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2	div.gg
Calculate total species diversity for any point in time based on a taxon-range table	divdistr_
Count number of taxon records overlapping a specific time interval.	divdistr_int
diversity_table	diversity_table
Replicate the standard color scheme from ggplot2	ggcol
plot data as a jitter-plot	jitterp
Generate a taxon-range table based on an occurrence dataset.	mk.sptab
Wrapper around jitterp that plots multiple jitter plots on the same plotting device (analogous to violins())	multijitter
Clean up occurrence dataset by removing commonly used character combinations in the identified name that will result in different factor levels for the same taxon.	occ.cleanup
Download data from the paleobiology database.	pdb
A wrapper around pdb(), occ.cleanup() and mk.sptab() to automatically download and clean occurrence data from the paleobiology database and build species-level taxon-range tables for multiple taxa in one step.	pdb.autodiv
Subtract one occurrence data.frame from another, for disentangling overlapping taxonomies or quantifying stem-lineage diversity.	pdb.diff
Form the union of two occurrence data.frames or remove duplicates from occurrence data.frame. Useful if parts of a clade are not included in the downloaded dataset and need to be added separately.	pdb.union
Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.	phylo.spindles
Redraw the lines of a phylogenetic tree.	redraw.phylo
Calculate a rolling mean for a vector x.	rmean
Calculate a rolling mean based on distance within a second variable.	rmeana
Extract subsets of an occurrence data.frame.	stax.sel
Combine selected entries in a taxon-range table to remove duplicates	synonymize
tree_archosauria	tree_archosauria
Combine two calibration matrixes and fill in NA values in one with values from another	tree.age.combine
Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.	tree.ages
Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.	tree.ages.spp
Add a horizontal, period-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.	ts.periods
Add a horizontal, stage-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.	ts.stages
Convert geological ages for accurate plotting alongside a calibrated phylogeny	tsconv
Generate a violin plot	viol
Wrapper around viol() to conveniently plot multiple violins on a single plot, analogous to the behavior of boxplot()	violins