mapast
About
mapast is a package that combines paleomaps from different models with fossil records from Paleobiology Database. It can be used to download shapefiles with reconstructions of the past configuration of the continents, and to generate paleodiversity maps.
Available models can be found at https://github.com/GPlates/gplates_web_service_doc/wiki/Reconstruction-Models .
Quick start
Install
Install mapast from CRAN (not on CRAN yet)
install.packages("mapast")
library(mapast)Install mapast developing version from github
install.packages("devtools")
library(devtools)
install_github("macroecology/mapast")
library(mapast)General overview
mapast version 0.1 has 3 functions for getting and visualising paleogeographical maps and fossil data, 4 functions for constructing diversity rasters (paleorichness and Shannon paleodiversity) and 2 functions for creating diversity matrix (based on localities or cells) and 2 functions for getting latitudinal paleodiversity gradients.
Get and visualise paleogeograhical maps and fossil data
formatdata returns a data.frame with the data from the Paleobiology Database in the correct format for further analysis.
> data <- base::data.frame(paleobioDB::pbdb_occurrences(limit = "all",
+ base_name = "testudinata",
+ min_ma = 0, max_ma = 201.3,
+ show = c("coords", "phylo"),
+ vocab = "pbdb"))
> head(data)
occurrence_no record_type reid_no collection_no taxon_name taxon_rank taxon_no matched_name
1:1 30259 occurrence 29799 2225 Tropidemys sp. genus 37701 Tropidemys
1:2 30260 occurrence NA 2225 Trachyaspis sanctae-crucis species 37663 Trachyaspis
1:3 40165 occurrence NA 3113 Peritresius ornatus species 173397 Peritresius ornatus
1:4 40166 occurrence NA 3113 Rhetechelys platyops species 128351 Rhetechelys platyops
1:5 41525 occurrence NA 3257 Chelone sp. genus 80566 Chelone
1:6 41581 occurrence NA 3256 Chelone sp. genus 80566 Chelone
matched_rank matched_no early_interval early_age late_age reference_no lng lat genus genus_no
1:1 genus 37701 Valanginian 139.8 132.9 50311;50311 6.516667 46.83333 Tropidemys 37701
1:2 genus 37663 Valanginian 139.8 132.9 66;66 6.516667 46.83333 Trachyaspis 37663
1:3 species 173397 Thanetian 59.2 56.0 140;140 -74.683334 39.97194 Peritresius 36360
1:4 species 128351 Thanetian 59.2 56.0 140;140 -74.683334 39.97194 Rhetechelys 128349
1:5 genus 80566 Early Eocene 55.8 37.2 149;149 -1.166667 51.08333 Chelone 80566
1:6 genus 80566 Early Eocene 55.8 37.2 149;149 -1.166667 51.08333 Chelone 80566
family family_no order order_no class class_no phylum phylum_no late_interval
1:1 Plesiochelyidae 37686 Testudines 56475 Reptilia 36322 Chordata 33815 <NA>
1:2 Cheloniidae 37695 Testudines 56475 Reptilia 36322 Chordata 33815 <NA>
1:3 Chelydridae 37704 Testudines 56475 Reptilia 36322 Chordata 33815 <NA>
1:4 Pancheloniidae 165650 Testudines 56475 Reptilia 36322 Chordata 33815 <NA>
1:5 Testudinidae 37739 Testudines 56475 Reptilia 36322 Chordata 33815 Middle Eocene
1:6 Testudinidae 37739 Testudines 56475 Reptilia 36322 Chordata 33815 Middle Eocene
> df <- formatdata(data)
> head(df)
occurrence_no record_type reid_no collection_no taxon_name taxon_rank taxon_no
1:3059 829847 occurrence NA 52986 Helcura caudata species 156017
1:3060 829848 occurrence NA 52986 Helcura surgens n. sp. species 156018
1:3061 829849 occurrence NA 52986 Helcura anguinea n. sp. species 156015
1:1929 520205 occurrence NA 52994 Ancyropus heteroclitus ? species 156085
1:1930 520266 occurrence NA 52996 Amblypus n. gen. dextratus n. sp. species 156013
1:1931 520268 occurrence NA 52996 Helcura anguinea species 156015
matched_name matched_rank matched_no early_interval early_age late_age reference_no lng lat genus
1:3059 Helcura littoralis species 156016 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:3060 Helcura surgens species 156018 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:3061 Helcura anguinea species 156015 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:1929 Ancyropus heteroclitus species 156085 Hettangian 201.3 190.8 30862;30862 -72.55917 42.28056 Ancyropus
1:1930 Amblypus dextratus species 156013 Hettangian 201.3 190.8 15230;15230 -72.55286 42.61120 Amblypus
1:1931 Helcura anguinea species 156015 Hettangian 201.3 190.8 29531;29531 -72.55286 42.61120 Helcura
genus_no family family_no order order_no class class_no phylum phylum_no late_interval species avg_age
1:3059 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura littoralis 200.30
1:3060 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura surgens 200.30
1:3061 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura anguinea 200.30
1:1929 156007 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Ancyropus heteroclitus 196.05
1:1930 156012 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Amblypus dextratus 196.05
1:1931 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Helcura anguinea 196.05paleocoords Function getting the paleocoordinates of the fossils which are calculated with the model the user chooses.
> df_coords_SETON2012 <- paleocoords(data = df, time = "timevector",
+ timevector = c(0, 2.58, 23.02, 66, 145, 201.3),
+ model = "SETON2012")
[1] "You can not plot all of these points in a single map. You have 5 different maps, which are 173.15mya , 105.5mya , 44.51mya , 12.8mya , 1.29mya ."
> head(df_coords_SETON2012)
occurrence_no record_type reid_no collection_no taxon_name taxon_rank taxon_no
1:3059 829847 occurrence NA 52986 Helcura caudata species 156017
1:3060 829848 occurrence NA 52986 Helcura surgens n. sp. species 156018
1:3061 829849 occurrence NA 52986 Helcura anguinea n. sp. species 156015
1:1929 520205 occurrence NA 52994 Ancyropus heteroclitus ? species 156085
1:1930 520266 occurrence NA 52996 Amblypus n. gen. dextratus n. sp. species 156013
1:1931 520268 occurrence NA 52996 Helcura anguinea species 156015
matched_name matched_rank matched_no early_interval early_age late_age reference_no lng lat genus
1:3059 Helcura littoralis species 156016 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:3060 Helcura surgens species 156018 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:3061 Helcura anguinea species 156015 Hettangian 201.3 199.3 29531;29531 -72.53095 42.60677 Helcura
1:1929 Ancyropus heteroclitus species 156085 Hettangian 201.3 190.8 30862;30862 -72.55917 42.28056 Ancyropus
1:1930 Amblypus dextratus species 156013 Hettangian 201.3 190.8 15230;15230 -72.55286 42.61120 Amblypus
1:1931 Helcura anguinea species 156015 Hettangian 201.3 190.8 29531;29531 -72.55286 42.61120 Helcura
genus_no family family_no order order_no class class_no phylum phylum_no late_interval species avg_age
1:3059 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura littoralis 200.30
1:3060 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura surgens 200.30
1:3061 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 <NA> Helcura anguinea 200.30
1:1929 156007 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Ancyropus heteroclitus 196.05
1:1930 156012 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Amblypus dextratus 196.05
1:1931 156014 <NA> NA <NA> NA Reptilia 36322 Chordata 33815 Sinemurian Helcura anguinea 196.05
recon_age paleolng paleolat
1:3059 173.15 -9.79 23.44
1:3060 173.15 -9.79 23.44
1:3061 173.15 -9.79 23.44
1:1929 173.15 -9.90 23.13
1:1930 173.15 -9.80 23.45
1:1931 173.15 -9.80 23.45getmap returns a SpatialPolygonsDataFrame or a list of SpatialPolygonsDataFrames of the maps of the requested model.
> maps_SETON2012 <- getmap(ma = c(1.29, 12.80, 44.51, 105.50, 173.15), model = "SETON2012")
> maps_SETON2012
[[1]]
class : SpatialPolygonsDataFrame
features : 597
extent : -180, 180, -90, 83.44 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
variables : 3
names : FID, age, model
min values : 0, 1.29, SETON2012
max values : 596, 1.29, SETON2012
[[2]]
class : SpatialPolygonsDataFrame
features : 574
extent : -180, 180, -90, 82.42 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
variables : 3
names : FID, age, model
min values : 0, 12.8, SETON2012
max values : 573, 12.8, SETON2012
[[3]]
class : SpatialPolygonsDataFrame
features : 539
extent : -180, 180, -90, 84.24 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
variables : 3
names : FID, age, model
min values : 0, 44.51, SETON2012
max values : 538, 44.51, SETON2012
[[4]]
class : SpatialPolygonsDataFrame
features : 468
extent : -180, 180, -90, 87.61 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
variables : 3
names : FID, age, model
min values : 0, 105.5, SETON2012
max values : 467, 105.5, SETON2012
[[5]]
class : SpatialPolygonsDataFrame
features : 403
extent : -180, 180, -88.36, 89.2 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
variables : 3
names : FID, age, model
min values : 0, 173.15, SETON2012
max values : 402, 173.15, SETON2012 
mapast Returns a plot with the fossil occurrences plotted on their corresponding paleogeographical map.
> data <- base::data.frame(paleobioDB::pbdb_occurrences(limit = "all",
+ base_name = "testudinata",
+ min_ma = 0, max_ma = 201.3,
+ show = c("coords", "phylo"),
+ vocab = "pbdb"))
> #format the data so it has the columns needed for further analysis
> df <- formatdata(data)
>
> #get the coordinates
> df_coords_SETON2012 <- paleocoords(data = df, time = "timevector",
+ timevector = c(0, 2.58, 23.02, 66, 145, 201.3),
+ model = "SETON2012")
[1] "You can not plot all of these points in a single map. You have 5 different maps, which are 173.15mya , 105.5mya , 44.51mya , 12.8mya , 1.29mya ."
> mapast(data = df_coords_SETON2012, map = maps_SETON2012)
Functions for paleogeographical analyses
mapocc Returns a RasterLayer of the sampling effort and a map with the raster on it.
> data <- base::data.frame(paleobioDB::pbdb_occurrences(limit = "all",
+ base_name = "testudinata",
+ min_ma = 0, max_ma = 201.3,
+ show = c("coords", "phylo"),
+ vocab = "pbdb"))
> #format the data so it has the columns needed for further analysis
> df <- formatdata(data)
>
> #get the coordinates
> df_coords_SETON2012 <- paleocoords(data = df, time = "timevector",
+ timevector = c(0, 2.58, 23.02, 66, 145, 201.3),
+ model = "SETON2012")
[1] "You can not plot all of these points in a single map. You have 5 different maps, which are 173.15mya , 105.5mya , 44.51mya , 12.8mya , 1.29mya ."
> mapocc_SETON2012 <- mapocc(df_coords_SETON2012, model = "SETON2012", rank = "genus", map = maps_SETON2012, res = 10)
> mapocc_SETON2012
class : RasterStack
dimensions : 18, 36, 648, 5 (nrow, ncol, ncell, nlayers)
resolution : 10, 10 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : NA
names : layer.1, layer.2, layer.3, layer.4, layer.5
min values : 1, 1, 1, 1, 1
max values : 82, 387, 475, 150, 102 
maprich Returns a RasterLayer of richness and a map with the raster on it.
> maprich_SETON2012 <- maprich(df_coords_SETON2012, model = "SETON2012", rank = "genus", map = maps_SETON2012, res = 10)
> maprich_SETON2012
class : RasterStack
dimensions : 18, 36, 648, 5 (nrow, ncol, ncell, nlayers)
resolution : 10, 10 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : NA
names : layer.1, layer.2, layer.3, layer.4, layer.5
min values : 1, 1, 1, 1, 1
max values : 82, 387, 475, 150, 102
Paleodiversity
spsite Returns a dataframe of taxa occurrences vs. localities (unity="fossilsite) or cells(unity="cell") (~ sites/cells per taxa matrix)
> fossilsite_SETON2012 <- spsite(data = df_coords_SETON2012, unity = "fossilsite", rank = "genus")
> fossilsite_SETON2012[1][[1]][1:2,]
paleolng paleolat Helcura Ancyropus Amblypus Episcopopus Australochelys Kayentachelys Indochelys
1 -9.79 23.44 3 0 0 0 0 0 0
4 -9.90 23.13 0 1 0 0 0 0 0
Condorchelys Xinjiangchelys Plesiochelys Siamochelys Heckerochelys Bashuchelys Chengyuchelys
1 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0
Protoxinjiangchelys Chuannanchelys Sichuanchelys Eileanchelys Annemys Toxocheloides Sinaspideretes
1 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0
Tienfuchelys Notoemys Yaxartemys Glyptops Chelonipus Thalassemys Tropidemys Platychelys Peltochelys
1 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0
Undjulemys Hongkongochelys Chelonichnium Solnhofia Selenemys Craspedochelys Jurassichelon Chelonides
1 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0
Eurysternum Idiochelys Enaliochelys Portlandemys Achelonia Hydropelta Stylemys Pelobatochelys Dinochelys
1 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0
Dorsetochelys Uluops Pleurosternon Palaeomedusa Neusticemys Hylaeochelys Owadowia Parachelys Acichelys
1 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0
Tacuarembemys Riodevemys Basilochelys Phunoichelys
1 0 0 0 0
4 0 0 0 0> cell_SETON2012 <- spsite(data = df_coords_SETON2012, unity = "cell", res = 10, rank = "genus")
> cell_SETON2012[1][[1]][1:2,]
paleolng paleolat Helcura Ancyropus Amblypus Episcopopus Australochelys Kayentachelys Indochelys
613 -175 85 0 0 0 0 0 0 0
577 -175 75 0 0 0 0 0 0 0
Condorchelys Xinjiangchelys Plesiochelys Siamochelys Heckerochelys Bashuchelys Chengyuchelys
613 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0
Protoxinjiangchelys Chuannanchelys Sichuanchelys Eileanchelys Annemys Toxocheloides Sinaspideretes
613 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0
Tienfuchelys Notoemys Yaxartemys Glyptops Chelonipus Thalassemys Tropidemys Platychelys Peltochelys
613 0 0 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0 0 0
Undjulemys Hongkongochelys Chelonichnium Solnhofia Selenemys Craspedochelys Jurassichelon Chelonides
613 0 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0 0
Eurysternum Idiochelys Enaliochelys Portlandemys Achelonia Hydropelta Stylemys Pelobatochelys Dinochelys
613 0 0 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0 0 0
Dorsetochelys Uluops Pleurosternon Palaeomedusa Neusticemys Hylaeochelys Owadowia Parachelys Acichelys
613 0 0 0 0 0 0 0 0 0
577 0 0 0 0 0 0 0 0 0
Tacuarembemys Riodevemys Basilochelys Phunoichelys
613 0 0 0 0
577 0 0 0 0mapdiv 1- calculates the Shannon diversity per unique locality (based on its coordinates), 2- makes a raster file and a plot showing mean, max, min diversity per cell, or number of unique localities per cell
> mapdiv_cell_SETON2012 <- mapdiv(data = df_coords_SETON2012, unity = "cell", map=maps_SETON2012, res = 10, rank = "genus")
> mapdiv_cell_SETON2012
class : RasterStack
dimensions : 18, 36, 648, 5 (nrow, ncol, ncell, nlayers)
resolution : 10, 10 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : NA
names : layer.1, layer.2, layer.3, layer.4, layer.5
min values : 0.6365142, 0.6931472, 0.5004024, 0.6365142, 0.6365142
max values : 2.682016, 3.575652, 4.089226, 3.218349, 3.115633 
> mapdiv_site_SETON2012 <- mapdiv(data = df_coords_SETON2012, unity = "fossilsite", map=maps_SETON2012, res = 10, rank = "genus")
> mapdiv_site_SETON2012
class : RasterStack
dimensions : 18, 36, 648, 5 (nrow, ncol, ncell, nlayers)
resolution : 10, 10 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : NA
names : layer.1, layer.2, layer.3, layer.4, layer.5
min values : 0.06931472, 0.05776227, 0.09372252, 0.08154673, 0.06931472
max values : 0.558745, 1.332179, 1.713454, 1.098612, 1.906155 
latdivgrad calculates latitudinal diversity (either shannon or richness) of taxa (species, genera, families, orders)
> latrich_SETON2012 <- latdivgrad(data = df_coords_SETON2012, method = "richness", map= maps_SETON2012, rank = "genus")
> latrich_SETON2012[[1]][1:5,]
paleolat div
180 89.5 0
179 88.5 0
178 87.5 0
177 86.5 0
176 85.5 0
> latdiv_SETON2012 <- latdivgrad(data = df_coords_SETON2012, method = "shannon", map= maps_SETON2012, rank = "genus")
> latdiv_SETON2012[[1]][1:5,]
paleolat div
180 89.5 0
179 88.5 0
178 87.5 0
177 86.5 0
176 85.5 0
Meta
Please report any issues or bugs.
License: GPL-2
To cite package mapast in publications use:
To cite package `mapast` in publications use:
Sara Varela, K. Sonja Rothkugel (2018). mapast: combine paleogeography and paleobiodiversity. R package version 0.1. https://github.com/macroecology/mapast
A BibTeX entry for LaTeX users is
@Manual{,
title = {mapast: combine paleogeography and paleobiodiversity},
author = {Sara Varela} and {Sonja Rothkugel},
year = {2018},
note = {R package version 0.1},
base = {https://github.com/macroecology/mapast},
}