Title: | Download and Process Data from the Paleobiology Database |
---|---|
Description: | Includes functions to wrap most endpoints of the 'PaleobioDB' API and functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>. |
Authors: | Sara Varela [aut] |
Maintainer: | Adrián Castro Insua <[email protected]> |
License: | GPL-2 |
Version: | 1.0.0 |
Built: | 2024-08-29 23:16:53 UTC |
Source: | https://github.com/ropensci/paleobioDB |
Returns information about a single collection record from the Paleobiology Database.
pbdb_collection(id, ...)
pbdb_collection(id, ...)
id |
Identifier of the collection. This parameter is required. |
... |
Additional arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/colls/single. E.g.:
|
Go to pbdb_occurrences()
to see an explanation about
the main parameters.
A data frame with a single occurrence.
## Not run: pbdb_collection(id = 1003, vocab = "pbdb", show = c("loc", "stratext")) ## End(Not run)
## Not run: pbdb_collection(id = 1003, vocab = "pbdb", show = c("loc", "stratext")) ## End(Not run)
Returns information about multiple collections, selected according to the parameters you provide.
pbdb_collections(...)
pbdb_collections(...)
... |
Additional arguments passed to the API. See all
available arguments at
https://paleobiodb.org/data1.2/colls/list. Go to
|
A data frame with the collections that match the query.
## Not run: pbdb_collections(base_name = "Cetacea", interval = "Miocene") ## End(Not run)
## Not run: pbdb_collections(base_name = "Cetacea", interval = "Miocene") ## End(Not run)
This path returns information about geographic clusters of collections from the Paleobiology Database. These clusters are defined in order to facilitate the generation of maps at low resolutions. You can make a config request via https://paleobiodb.org/data1.2/config in order to get a list of the available summary levels.
pbdb_collections_geo(level, ...)
pbdb_collections_geo(level, ...)
level |
An integer specifying a cluster level. Refer to https://paleobiodb.org/data1.2/config.txt?show=clusters for a list of available resolution levels ("cluster_level" column). |
... |
Documentation for all the parameters is available at
https://paleobiodb.org/data1.2/colls/summary. Go to
|
A data frame with the collections that match the query.
## Not run: pbdb_collections_geo( level = 2, vocab = "pbdb", lngmin = 0.0, lngmax = 15.0, latmin = 0.0, latmax = 15.0 ) ## End(Not run)
## Not run: pbdb_collections_geo( level = 2, vocab = "pbdb", lngmin = 0.0, lngmax = 15.0, latmin = 0.0, latmax = 15.0 ) ## End(Not run)
Returns information about a single interval, selected by identifier.
pbdb_interval(...)
pbdb_interval(...)
... |
Additional arguments passed to the API. See
documentation for accepted parameters at
https://paleobiodb.org/data1.2/intervals/single. Either
|
A data frame with information from a single temporal interval.
## Not run: pbdb_interval(id = 1, vocab = "pbdb") ## End(Not run)
## Not run: pbdb_interval(id = 1, vocab = "pbdb") ## End(Not run)
Returns information about multiple intervals, selected according to the parameters you provide.
pbdb_intervals(...)
pbdb_intervals(...)
... |
arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/intervals/list. E.g.:
|
A data frame with information from several temporal intervals.
## Not run: pbdb_intervals(min_ma = 0, max_ma = 2, vocab = "pbdb") ## End(Not run)
## Not run: pbdb_intervals(min_ma = 0, max_ma = 2, vocab = "pbdb") ## End(Not run)
The function opens a new window with a map showing the distribution of the fossil records as points. These points are coloured according to the number of occurrences per cell.
pbdb_map( data, col_int = "white", pch = 19, col_ocean = "black", main = NULL, col_point = c("light blue", "blue"), do_plot = TRUE, ... )
pbdb_map( data, col_int = "white", pch = 19, col_ocean = "black", main = NULL, col_point = c("light blue", "blue"), do_plot = TRUE, ... )
data |
Input data frame. This data frame is the output of the
|
col_int |
The colour of the mainland. |
pch |
See |
col_ocean |
The colour of the ocean. |
main |
Title of the map. See |
col_point |
Two or more colours that are used to generate the colour gradient showing the number of occurrences per coordinate in the map. |
do_plot |
Logical. If |
... |
The argument show = "coords"
in the pbdb_occurrences()
function is required. We recommend the use of a cairo device
(X11()
) for better visualization of the maps. See Examples.
A data frame with the number of occurrences per coordinate.
See pbdb_occurrences()
, map()
, par()
and colors()
help pages.
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canis", show = "coords" ) X11(width = 12, height = 8) pbdb_map(data) pbdb_map(data, pch = 1) pbdb_map( data, pch = 19, col_point = c("pink", "red"), col_ocean = "light blue", main = "Canis" ) ## End(Not run)
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canis", show = "coords" ) X11(width = 12, height = 8) pbdb_map(data) pbdb_map(data, pch = 1) pbdb_map( data, pch = 19, col_point = c("pink", "red"), col_ocean = "light blue", main = "Canis" ) ## End(Not run)
Creates a SpatRaster
object and a plot of the sampling
effort (number of fossil records per cell).
pbdb_map_occur( data, res = 5, col_int = "white", col_ocean = "black", col_eff = c("light blue", "blue"), do_plot = TRUE, ... )
pbdb_map_occur( data, res = 5, col_int = "white", col_ocean = "black", col_eff = c("light blue", "blue"), do_plot = TRUE, ... )
data |
Input data frame. This data frame is the output of the
|
res |
The resolution of the |
col_int |
The colour of the mainland. |
col_ocean |
The colour of the ocean. |
col_eff |
Two or more colours that are used to generate the colour gradient showing the number of occurrences per cell in the map. |
do_plot |
Logical. If |
... |
The argument show = "coords"
in the pbdb_occurrences()
function is required. We recommend the use of a cairo device
(X11()
) for better visualization of the maps. See Examples.
A SpatRaster
object with the sampling effort (number of
fossil records per cell). This SpatRaster
object has the
resolution that was specified in the res
argument. The default
is res = 5
. Users that wish to work with objects of this type
should load package terra
.
See pbdb_occurrences()
, map()
, par()
and colors()
help pages
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canis", show = "coords" ) X11(width = 13, height = 7.8) pbdb_map_occur(data, res = 2) ## Get the raster object without plotting it pbdb_map_occur(data, res = 3, do_plot = FALSE) ## End(Not run)
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canis", show = "coords" ) X11(width = 13, height = 7.8) pbdb_map_occur(data, res = 2) ## Get the raster object without plotting it pbdb_map_occur(data, res = 3, do_plot = FALSE) ## End(Not run)
Creates a SpatRaster
object and a plot with richness of
species, genera, families, etc. per cell.
pbdb_map_richness( data, rank = c("species", "genus", "family", "order", "class", "phylum"), do_plot = TRUE, res = 5, col_int = "white", col_ocean = "black", col_rich = c("light blue", "blue"), title = "Taxonomic richness", ... )
pbdb_map_richness( data, rank = c("species", "genus", "family", "order", "class", "phylum"), do_plot = TRUE, res = 5, col_int = "white", col_ocean = "black", col_rich = c("light blue", "blue"), title = "Taxonomic richness", ... )
data |
Input data frame. This data frame is the output of the
|
rank |
Taxon rank for which richness is calculated. The
options are: |
do_plot |
Logical. If |
res |
The resolution of the |
col_int |
The colour of the mainland. |
col_ocean |
The colour of the ocean. |
col_rich |
Two or more colours that are used to generate the colour gradient showing the richness per cell in the map. |
title |
A title for the plot, to be positioned to the right of the legend. |
... |
The argument show = c("coords", "classext")
in the
pbdb_occurrences()
function is required. We recommend the use
of a cairo device (X11()
) for better visualization of the
graphs. See Examples.
A SpatRaster
object with the richness of the specified
taxon rank per cell. This SpatRaster
object has the resolution
that was specified in the res
argument. The default is res = 5
. Users that wish to work with objects of this type should load
package terra
.
See pbdb_occurrences()
, map()
, par()
and colors()
help pages.
## Not run: data <- pbdb_occurrences( limit = 1000, vocab = "pbdb", base_name = "mammalia", show = c("classext", "coords") ) X11(width = 13, height = 7.8) pbdb_map_richness(data, res = 8, rank = "genus") pbdb_map_richness(data, res = 8, rank = "family") ## Get the raster object without plotting the map pbdb_map_richness(data, res = 8, rank = "family", do_plot = FALSE) ## End(Not run)
## Not run: data <- pbdb_occurrences( limit = 1000, vocab = "pbdb", base_name = "mammalia", show = c("classext", "coords") ) X11(width = 13, height = 7.8) pbdb_map_richness(data, res = 8, rank = "genus") pbdb_map_richness(data, res = 8, rank = "family") ## Get the raster object without plotting the map pbdb_map_richness(data, res = 8, rank = "family", do_plot = FALSE) ## End(Not run)
Returns information about the measurements associated with the selected fossil specimens.
pbdb_measurements(...)
pbdb_measurements(...)
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/specs/measurements. The following parameters can be used to retrieve measurements from a known list of specimens, occurrences, or collections. Only the records matching all specified parameters will be returned:
It is possible to return additional information along with the basic record with the following parameter:
See the |
A data frame with information about the measurements that match the query.
## Not run: pbdb_measurements( spec_id = c(1505, 30050), show = c("spec", "class", "methods"), vocab = "pbdb" ) ## End(Not run)
## Not run: pbdb_measurements( spec_id = c(1505, 30050), show = c("spec", "class", "methods"), vocab = "pbdb" ) ## End(Not run)
Returns information about a single occurrence record from the Paleobiology Database.
pbdb_occurrence(id, ...)
pbdb_occurrence(id, ...)
id |
Identifier of the occurrence. This parameter is required. |
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/occs/single. E.g.:
|
Documentation for all the parameters is available at https://paleobiodb.org/data1.2/occs/single. In the parameter list above, we describe the most common filters that paleontologists and ecologists might use.
A data frame with a single occurrence.
## Not run: pbdb_occurrence(id = 1001) pbdb_occurrence(id = 1001, vocab = "pbdb", show = c("class", "coords")) ## End(Not run)
## Not run: pbdb_occurrence(id = 1001) pbdb_occurrence(id = 1001, vocab = "pbdb", show = c("class", "coords")) ## End(Not run)
Returns information about fossil occurrence records stored in the Paleobiology Database.
pbdb_occurrences(...)
pbdb_occurrences(...)
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/occs/list.
|
Documentation for all the parameters is available at https://paleobiodb.org/data1.2/occs/list. We describe the most common filters that paleontologists and ecologists might use in the parameter list above.
Be aware that depending on the query, some columns may not be returned by the API if those are empty across all the rows.
A data frame with the fossil occurrences.
## Not run: pbdb_occurrences(id = c(10, 11), show = c("coords", "classext", "ident")) pbdb_occurrences( limit = "all", vocab = "pbdb", taxon_name = "Canis", show = c("coords", "classext", "ident") ) pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = c("coords", "classext", "ident") ) ## End(Not run)
## Not run: pbdb_occurrences(id = c(10, 11), show = c("coords", "classext", "ident")) pbdb_occurrences( limit = "all", vocab = "pbdb", taxon_name = "Canis", show = c("coords", "classext", "ident") ) pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = c("coords", "classext", "ident") ) ## End(Not run)
Returns information about a single taxonomic opinion, selected by identifier.
pbdb_opinion(id, ...)
pbdb_opinion(id, ...)
id |
Identifier of the opinion. This parameter is required. |
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/opinions/single. E.g.:
|
A data frame with a single taxonomic opinion.
## Not run: pbdb_opinion(id = 1000, vocab = "pbdb", show = "full") ## End(Not run)
## Not run: pbdb_opinion(id = 1000, vocab = "pbdb", show = "full") ## End(Not run)
Returns information about multiple taxonomic opinions, selected according to criteria other than taxon name. This function could be used to query for all of the opinions attributed to a particular author, or to show all of the recently entered opinions.
pbdb_opinions(...)
pbdb_opinions(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/opinions/list. E.g.:
|
A data frame with information about the taxonomic opinions that match the query.
## Not run: pbdb_opinions(op_pubyr = 1818) ## End(Not run)
## Not run: pbdb_opinions(op_pubyr = 1818) ## End(Not run)
Returns information about the taxonomic opinions used to build the taxonomic hierarchy. From all of the opinions entered into the database about a particular taxon, the most recent opinion that is stated with the most evidence is used to classify that taxon. The others are considered to be superseded and are ignored.
pbdb_opinions_taxa(...)
pbdb_opinions_taxa(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/taxa/opinions. |
A data frame with information about the taxonomic opinions that match the query.
## Not run: pbdb_opinions_taxa(base_name = "Canis") ## End(Not run)
## Not run: pbdb_opinions_taxa(base_name = "Canis") ## End(Not run)
Returns a data frame with the appearance of new taxa and their last appearances across time in the provided data and optionally produces a plot from it, showing the new appearances or last appearances.
pbdb_orig_ext( data, rank = c("species", "genus", "family", "order", "class", "phylum"), temporal_extent, res, orig_ext = 1, colour = "#0000FF30", bord = "#0000FF", ylab = NULL, do_plot = TRUE )
pbdb_orig_ext( data, rank = c("species", "genus", "family", "order", "class", "phylum"), temporal_extent, res, orig_ext = 1, colour = "#0000FF30", bord = "#0000FF", ylab = NULL, do_plot = TRUE )
data |
Data frame from a query to PaleobioDB as returned by
|
rank |
The taxon rank to be analyzed. Its default value is
|
temporal_extent |
Vector to set the temporal extent (min, max) |
res |
Numeric. Sets the intervals of the temporal extent. |
orig_ext |
Set to 1 to plot the number new appearances, or to 2 to plot the number of extinctions. |
colour |
Colour of the area of the polygon in the plot. |
bord |
Colour of the border of the polygon. |
ylab |
A label for the y axis. |
do_plot |
Logical value indicating whether to produce a plot
( |
A data frame with the number of first appearances and extinctions of the selected taxon rank across time.
## Not run: canidae <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = "classext" ) # Plot of the evolutionary rates pbdb_orig_ext( canidae, rank = "genus", orig_ext = 1, temporal_extent = c(0, 10), res = 1 ) # Plot of the extinction rates pbdb_orig_ext( canidae, rank = "genus", orig_ext = 2, temporal_extent = c(0, 10), res = 1 ) ## End(Not run)
## Not run: canidae <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = "classext" ) # Plot of the evolutionary rates pbdb_orig_ext( canidae, rank = "genus", orig_ext = 1, temporal_extent = c(0, 10), res = 1 ) # Plot of the extinction rates pbdb_orig_ext( canidae, rank = "genus", orig_ext = 2, temporal_extent = c(0, 10), res = 1 ) ## End(Not run)
Returns information about the references from which the selected collection data were entered.
pbdb_ref_collections(...)
pbdb_ref_collections(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/colls/refs. E.g.:
|
A data frame with the information about the references that match the query.
## Not run: pbdb_ref_collections( base_name = "Canidae", interval = "Quaternary", cc = "ASI" ) ## End(Not run)
## Not run: pbdb_ref_collections( base_name = "Canidae", interval = "Quaternary", cc = "ASI" ) ## End(Not run)
Returns information about the bibliographic references associated with fossil occurrences from the database.
pbdb_ref_occurrences(...)
pbdb_ref_occurrences(...)
... |
arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/occs/refs
|
Go to pbdb_occurrences()
to see an explanation about
the main filtering parameters.
A data frame with the information about the references that match the query.
## Not run: pbdb_ref_occurrences(vocab = "pbdb", base_name = "Canis", ref_pubyr = 2000) ## End(Not run)
## Not run: pbdb_ref_occurrences(vocab = "pbdb", base_name = "Canis", ref_pubyr = 2000) ## End(Not run)
Returns information about the bibliographic references associated with the selected fossil specimens.
pbdb_ref_specimens(...)
pbdb_ref_specimens(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/specs/refs. E.g.:
|
A data frame with the information about the references that match the query.
## Not run: pbdb_ref_specimens(spec_id = c(1505, 30050)) ## End(Not run)
## Not run: pbdb_ref_specimens(spec_id = c(1505, 30050)) ## End(Not run)
Returns information about the source references associated with
taxa in the Paleobiology Database. You can use the same parameters
that are available with pbdb_taxa
, but reference records are
returned instead of taxon records. One record is returned per
reference, even if it is associated with multiple taxa.
pbdb_ref_taxa(...)
pbdb_ref_taxa(...)
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/taxa/refs
|
A data frame with references from a list of taxa.
## Not run: pbdb_ref_taxa( name = "Canidae", vocab = "pbdb", show = c("both", "comments") ) ## End(Not run)
## Not run: pbdb_ref_taxa( name = "Canidae", vocab = "pbdb", show = c("both", "comments") ) ## End(Not run)
Returns information about a single reference, selected by identifier.
pbdb_reference(id, ...)
pbdb_reference(id, ...)
id |
Identifier of the reference. This parameter is required. |
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/refs/single. E.g.:
|
A data frame with a single reference.
## Not run: pbdb_reference(id = 1003, vocab = "pbdb", show = "both") ## End(Not run)
## Not run: pbdb_reference(id = 1003, vocab = "pbdb", show = "both") ## End(Not run)
Returns information about multiple references, selected according to the parameters you provide.
pbdb_references(...)
pbdb_references(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/refs/list. E.g.:
|
A data frame with the information about the references that match the query.
## Not run: pbdb_references(ref_author = "Polly") ## End(Not run)
## Not run: pbdb_references(ref_author = "Polly") ## End(Not run)
Returns a data frame of temporal variation in taxon richness in the indicated temporal extent and resolution from the provided occurrence data and optionally produces a plot from it.
pbdb_richness( data, rank = c("species", "genus", "family", "order", "class", "phylum"), res = 1, temporal_extent = c(0, 10), colour = "#0000FF30", bord = "#0000FF", ylab = "Richness", do_plot = TRUE )
pbdb_richness( data, rank = c("species", "genus", "family", "order", "class", "phylum"), res = 1, temporal_extent = c(0, 10), colour = "#0000FF30", bord = "#0000FF", ylab = "Richness", do_plot = TRUE )
data |
Data frame from a query to PaleobioDB as returned by
|
rank |
The taxon rank to be analyzed. The default value is
|
res |
Numeric. Sets the duration of the intervals in the temporal extent. |
temporal_extent |
Numeric vector to set the temporal extent (min, max). |
colour |
Colour of the area of the polygon in the plot. |
bord |
Colour of the border of the polygon. |
ylab |
A label for the y axis. |
do_plot |
Logical indicating whether to produce a plot ( |
A data frame with the richness aggregated by the taxon rank in the specified temporal extent and resolution.
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = "class" ) pbdb_richness(data, rank = "species", res = 0.2, temporal_extent = c(0, 3)) ## End(Not run)
## Not run: data <- pbdb_occurrences( limit = "all", vocab = "pbdb", base_name = "Canidae", show = "class" ) pbdb_richness(data, rank = "species", res = 0.2, temporal_extent = c(0, 3)) ## End(Not run)
Returns information about a single time scale, selected by identifier.
pbdb_scale(id, ...)
pbdb_scale(id, ...)
id |
Identifier of the temporal interval. This parameter is required. |
... |
Additional arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/scales/single. E.g.:
|
A data frame with information from a single scale.
## Not run: pbdb_scale(id = 1, vocab = "pbdb") ## End(Not run)
## Not run: pbdb_scale(id = 1, vocab = "pbdb") ## End(Not run)
Returns information about multiple time scales.
pbdb_scales(...)
pbdb_scales(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/scales/list. E.g.:
|
A data frame with information from the selected scales.
## Not run: ## Get a data frame with all the scales available in PBDB ## by setting no ids pbdb_scales() ## End(Not run)
## Not run: ## Get a data frame with all the scales available in PBDB ## by setting no ids pbdb_scales() ## End(Not run)
Returns information about a single fossil specimen, identified either by name or by identifier.
pbdb_specimen(id, ...)
pbdb_specimen(id, ...)
id |
The identifier of the specimen. This parameter is required. |
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/specs/single.
|
A data frame with information about a single specimen.
## Not run: pbdb_specimen(id = 30050, show = c("class", "loc", "refattr")) ## End(Not run)
## Not run: pbdb_specimen(id = 30050, show = c("class", "loc", "refattr")) ## End(Not run)
Returns information about multiple fossil specimens, selected
according to the parameters you provide. Depending upon which
output blocks you select (show
parameter), the response will
contain some fields describing the specimens and some describing
the occurrences and collections (if any) with which they are
associated.
pbdb_specimens(...)
pbdb_specimens(...)
... |
Arguments passed to the API. See all available
arguments at https://paleobiodb.org/data1.2/specs/list. See the
|
A data frame with the fossil specimens that match the query.
## Not run: pbdb_specimens(base_name = "Cetacea", interval = "Miocene", vocab = "pbdb") ## End(Not run)
## Not run: pbdb_specimens(base_name = "Cetacea", interval = "Miocene", vocab = "pbdb") ## End(Not run)
Returns information about geological strata, selected by name, rank, and/or geographic location.
pbdb_strata(...)
pbdb_strata(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/strata/list. E.g.:
|
A data frame with information from the selected strata.
## Not run: pbdb_strata( lngmin = 0, lngmax = 15, latmin = 0, latmax = 15, rank = "formation", vocab = "pbdb" ) ## End(Not run)
## Not run: pbdb_strata( lngmin = 0, lngmax = 15, latmin = 0, latmax = 15, rank = "formation", vocab = "pbdb" ) ## End(Not run)
Returns a list of strata matching the given prefix or partial name. This can be used to implement auto-completion for strata names, and can be limited by geographic location if desired.
pbdb_strata_auto(...)
pbdb_strata_auto(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/strata/auto. E.g.:
|
A data frame with information from the strata that match
the name
parameter.
## Not run: pbdb_strata_auto(name = "Pin", vocab = "pbdb") ## End(Not run)
## Not run: pbdb_strata_auto(name = "Pin", vocab = "pbdb") ## End(Not run)
Count the number of taxa (species, genera, families, orders, classes, and phyla) in an occurrence data frame.
pbdb_subtaxa(data, do_plot = TRUE, col = "#0000FF")
pbdb_subtaxa(data, do_plot = TRUE, col = "#0000FF")
data |
Data frame from a query to PaleobioDB as returned by
the |
do_plot |
Logical indicating whether to produce a plot ( |
col |
Colour of the histogram. |
A data frame with the number of subtaxa in the data.
## Not run: canidae_quat <- pbdb_occurrences( limit = "all", base_name = "Canidae", interval = "Quaternary", show = c("coords", "classext", "ident"), vocab = "pbdb" ) pbdb_subtaxa(canidae_quat) ## End(Not run)
## Not run: canidae_quat <- pbdb_occurrences( limit = "all", base_name = "Canidae", interval = "Quaternary", show = c("coords", "classext", "ident"), vocab = "pbdb" ) pbdb_subtaxa(canidae_quat) ## End(Not run)
Returns information about multiple taxonomic names. This function can be used to query for all of the children or parents of a given taxon, among other operations.
pbdb_taxa(...)
pbdb_taxa(...)
... |
Arguments passed to the API. See all available arguments at https://paleobiodb.org/data1.2/taxa/list.
|
A data frame with information from a list of taxa.
## Not run: pbdb_taxa(name = "Canidae", rel = "all_parents", vocab = "pbdb", show = c("attr", "app", "size", "class")) pbdb_taxa(id = c(10, 11), vocab = "pbdb", show = c("attr", "app", "size", "class")) pbdb_taxa( id = c(10, 11), vocab = "pbdb", show = c("attr", "app", "size", "class"), rel = "common" ) ## End(Not run)
## Not run: pbdb_taxa(name = "Canidae", rel = "all_parents", vocab = "pbdb", show = c("attr", "app", "size", "class")) pbdb_taxa(id = c(10, 11), vocab = "pbdb", show = c("attr", "app", "size", "class")) pbdb_taxa( id = c(10, 11), vocab = "pbdb", show = c("attr", "app", "size", "class"), rel = "common" ) ## End(Not run)
Returns a list of taxonomic names matching the given prefix or partial name.
pbdb_taxa_auto(...)
pbdb_taxa_auto(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/taxa/auto. E.g.:
|
A data frame with information about the matches (taxon rank and number of occurrences in the database).
## Not run: pbdb_taxa_auto(name = "Cani", limit = 10) ## End(Not run)
## Not run: pbdb_taxa_auto(name = "Cani", limit = 10) ## End(Not run)
Returns information about a single taxonomic name, identified either by name or by identifier.
pbdb_taxon(...)
pbdb_taxon(...)
... |
Arguments passed to the API. See documentation for accepted parameters at https://paleobiodb.org/data1.2/taxa/single. One of the following parameters must be specified (but not both):
|
A data frame with information from a single taxon.
## Not run: pbdb_taxon(name = "Canis", vocab = "pbdb", show = c("attr", "app", "size")) ## End(Not run)
## Not run: pbdb_taxon(name = "Canis", vocab = "pbdb", show = c("attr", "app", "size")) ## End(Not run)
Returns a data frame with the temporal range of the taxa within a selected rank (species, genera, families, etc.), and optionally generates a plot from it.
pbdb_temp_range( data, rank = c("species", "genus", "family", "order", "class", "phylum"), col = "#0000FF", names = TRUE, do_plot = TRUE )
pbdb_temp_range( data, rank = c("species", "genus", "family", "order", "class", "phylum"), col = "#0000FF", names = TRUE, do_plot = TRUE )
data |
Data frame from a query to PaleobioDB as returned by
|
rank |
The taxon rank to be analyzed. The default value is
|
col |
Colour of the bars in the plot. |
names |
Logical indicating whether to include the name of the
taxa in the plot ( |
do_plot |
Logical value indicating whether to produce a plot
( |
A data frame with the time span of the taxa selected (species, genera, etc.).
## Not run: canis_quaternary <- pbdb_occurrences( limit = "all", base_name = "Canis", interval = "Quaternary", show = c("coords", "classext"), vocab = "pbdb" ) pbdb_temp_range(canis_quaternary, rank = "species", names = FALSE) ## End(Not run)
## Not run: canis_quaternary <- pbdb_occurrences( limit = "all", base_name = "Canis", interval = "Quaternary", show = c("coords", "classext"), vocab = "pbdb" ) pbdb_temp_range(canis_quaternary, rank = "species", names = FALSE) ## End(Not run)
Shows the temporal resolution of the fossil data.
pbdb_temporal_resolution(data, do_plot = TRUE)
pbdb_temporal_resolution(data, do_plot = TRUE)
data |
Data frame from a query to PaleobioDB as returned by
|
do_plot |
Logical. If |
A list with a summary of the temporal resolution of the data (min, max, 1st and 3rd quartiles, median and mean), and the temporal resolution of each fossil record (Ma).
## Not run: data <- pbdb_occurrences(taxon_name = "Canidae", interval = "Quaternary") pbdb_temporal_resolution(data) ## End(Not run)
## Not run: data <- pbdb_occurrences(taxon_name = "Canidae", interval = "Quaternary") pbdb_temporal_resolution(data) ## End(Not run)