paleoMap is a package for downloading, visualizing and processing data from Paleobiology Database combined with maps from GPlates.
Install
Install paleoMap from CRAN
install.packages("paleoMap")
library(paleoMap)Install paleoMap developing version from github
install.packages("devtools")
library(devtools)
install_github("sonjaleo/paleoMap")
library(paleoMap)General overview
paleoMap version xx has 3 functions for getting and visualising paleogeographical maps and fossil data,
5 functions for doing paleogeographical analyses and 2 functions for biodversity analyses.
pm_getmap returns the shapefile of a choosen paleogeographical time interval
> shape <- pm_getmap(interval="Jurassic", do.plot=TRUE)
> shape##class : SpatialPolygonsDataFrame
##features : 77
##extent : -180, 180, -82.9491, 89.0674 (xmin, xmax, ymin, ymax)
##coord. ref. : NA
##variables : 13
##names : PLATEID1, GPGIM_TYPE, TYPE, FROMAGE, TOAGE, NAME, DESCR, FEATURE_ID, PLATEID2, L_PLATE, R_PLATE, RECON_METH, SPREAD_ASY
##min values : 0, gpml:UnclassifiedFeature, NA, 0, 0, NA, NA, GPlates-049b54d5-0c8d-4c48-ab2c-c01af79bb31f, 0, 0, 0, NA, 0
##max values : 0, gpml:UnclassifiedFeature, NA, 0, 0, NA, NA, GPlates-f6cb6ad6-6c48-42f0-a1c2-52badd007c73, 0, 0, 0, NA, 0 
pm_getdata returns the needed parameter of the fossil record
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> head(data) matched_name matched_rank early_interval late_interval paleolng paleolat geoplate
##1 Chaoyangsaurus youngi species Late Tithonian Valanginian 127.48 50.66 604
##2 Chaoyangsaurus youngi species Late Tithonian Valanginian 127.48 50.66 604
##3 Theropoda unranked clade Hettangian Sinemurian -9.08 21.08 101
##4 Theropoda unranked clade Hettangian Sinemurian -9.08 21.08 101
##5 Amygdalodon patagonicus species Late Toarcian Early Aalenian -16.23 -44.08 291
##6 Amygdalodon patagonicus species Late Toarcian Early Aalenian -16.23 -44.08 291
## genus family order class phylum
##1 Chaoyangsaurus Chaoyangsauridae <NA> Ornithischia Chordata
##2 Chaoyangsaurus Chaoyangsauridae <NA> Ornithischia Chordata
##3 <NA> <NA> Theropoda Saurischia Chordata
##4 <NA> <NA> Theropoda Saurischia Chordata
##5 Amygdalodon <NA> <NA> Saurischia Chordata
##6 Amygdalodon <NA> <NA> Saurischia Chordatapm_plot Returns a map with the fossil occurrences.
> pm_plot (interval="Jurassic", base_name= "Reptilia", limit=50)
pm_occraster Returns a RasterLayer of the sampling effort and a map with the raster on it.
> shape <- pm_getmap(interval="Jurassic")
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> pm_occraster (shape, data)##class : RasterLayer
##dimensions : 17, 36, 612 (nrow, ncol, ncell)
##resolution : 10, 10 (x, y)
##extent : -180, 180, -80.9326, 89.0674 (xmin, xmax, ymin, ymax)
##coord. ref. : NA
##data source : in memory
##names : layer
##values : 3, 1405 (min, max)
pm_richraster Returns a RasterLayer of richness and a map with the raster on it.
> shape <- pm_getmap(interval="Jurassic")
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> pm_richraster (shape, data, rank="genus")##class : RasterLayer
##dimensions : 17, 36, 612 (nrow, ncol, ncell)
##resolution : 10, 10 (x, y)
##extent : -180, 180, -80.9326, 89.0674 (xmin, xmax, ymin, ymax)
##coord. ref. : NA
##data source : in memory
##names : layer
##values : 1, 69 (min, max)
pm_corrichraster Returns a corrected RasterLayer of richness and a map with the raster on it.
> shape <- pm_getmap(interval="Jurassic")
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> ngl_data <- pm_ngl(data)
> pm_corrichraster (shape, ngl_data)##class : RasterLayer
##dimensions : 17, 36, 612 (nrow, ncol, ncell)
##resolution : 10, 10 (x, y)
##extent : -180, 180, -80.9326, 89.0674 (xmin, xmax, ymin, ymax)
##coord. ref. : NA
##data source : in memory
##names : layer
##values : 1, 145291 (min, max)
pm_ngl Calculates the number of genera per locality.
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> ngl_data <- pm_ngl (data)
> head(ngl_data) paleolat paleolng Chaoyangsaurus Amygdalodon Camarasaurus Allosaurus Diplodocus Stegosaurus
##[1,] 50.66 127.48 2 0 0 0 0 0
##[2,] -44.08 -16.23 0 2 0 0 0 0
##[3,] 26.59 -43.61 0 0 2 0 0 0
##[4,] 26.66 -42.07 0 0 2 0 0 0
##[5,] 28.58 -40.48 0 0 0 2 0 0
##[6,] 28.79 -40.71 0 0 2 6 2 2
Scutellosaurus Rhamphinion Massospondylus Apatosaurus Gigantosauropus Hispanosauropus
##[1,] 0 0 0 0 0 0
##[2,] 0 0 0 0 0 0
##[3,] 0 0 0 0 0 0
##[4,] 0 0 0 0 0 0
##[5,] 0 0 0 0 0 0
##[6,] 0 0 0 0 0 0
Brontosaurus Protosuchus Dilophosaurus Coelophysis Kotasaurus Camptosaurus Barosaurus Opisthias
##[1,] 0 0 0 0 0 0 0 0
##[2,] 0 0 0 0 0 0 0 0
##[3,] 0 0 0 0 0 0 0 0
##[4,] 0 0 0 0 0 0 0 0
##[5,] 0 0 0 0 0 0 0 0
##[6,] 0 0 0 0 0 0 0 0
Eilenodon
##[1,] 0
##[2,] 0
##[3,] 0
##[4,] 0
##[5,] 0pm_nloc Calculates the number of localities per grid cell for different genera.
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> nloc <- pm_nloc (data, res=10)
> head(nloc) -180;-170 -170;-160 -160;-150 -150;-140 -140;-130 -130;-120 -120;-110 -110;-100 -100;-90
##-90;-80 0 0 0 0 0 0 0 0 0
##-80;-70 0 0 0 0 0 0 0 0 0
##-70;-60 0 0 0 0 0 0 0 0 0
##-60;-50 0 0 0 0 0 0 0 0 0
##-50;-40 0 0 0 0 0 0 0 0 0
##-40;-30 0 0 0 0 0 0 0 0 0
-90;-80 -80;-70 -70;-60 -60;-50 -50;-40 -40;-30 -30;-20 -20;-10 -10;0 0;10 10;20 20;30 30;40
##-90;-80 0 0 0 0 0 0 0 0 0 0 0 0 0
##-80;-70 0 0 0 0 0 0 0 0 0 0 0 0 0
##-70;-60 0 0 0 0 0 0 0 0 0 0 0 0 0
##-60;-50 0 0 0 0 0 0 0 0 0 0 0 0 0
##-50;-40 0 0 0 0 0 0 0 1 0 0 2 0 0
##-40;-30 0 0 0 0 0 0 0 0 0 0 0 1 0
40;50 50;60 60;70 70;80 80;90 90;100 100;110 110;120 120;130 130;140 140;150 150;160 160;170
##-90;-80 0 0 0 0 0 0 0 0 0 0 0 0 0
##-80;-70 0 0 0 0 0 0 0 0 0 0 0 0 0
##-70;-60 0 0 0 0 0 0 0 0 0 0 0 0 0
##-60;-50 0 0 0 0 0 0 0 0 0 0 0 0 0
##-50;-40 0 0 0 0 0 0 0 0 0 0 0 0 0
##-40;-30 0 0 0 0 0 0 0 0 0 0 0 0 0
170;180
##-90;-80 0
##-80;-70 0
##-70;-60 0
##-60;-50 0
##-50;-40 0
##-40;-30 0pm_latrich Calculates the latitudinal generic richness.
> data <- pm_getdata (base_name="Reptilia", interval="Jurassic", limit=50)
> pm_latrich (data) min paleolat max paleolat richness
##1 -90 -80 0
##2 -80 -70 0
##3 -70 -60 0
##4 -60 -50 0
##5 -50 -40 3
##6 -40 -30 1
##7 -30 -20 1
##8 -20 -10 0
##9 -10 0 0
##10 0 10 0
##11 10 20 3
##12 20 30 10
##13 30 40 7
##14 40 50 0
##15 50 60 1
##16 60 70 0
##17 70 80 0
##18 80 90 0pm_corlatrich Returns the corrected latitudinal generic richness.
> data<- pm_getdata (base_name="Canis", interval="Quaternary")
> ngl_data <- pm_ngl(data)
> pm_corlatrich (ngl_data) maxlat minlat richness
##1 -90 -80 0.000000
##2 -80 -70 0.000000
##3 -70 -60 0.000000
##4 -60 -50 0.000000
##5 -50 -40 0.000000
##6 -40 -30 0.000000
##7 -30 -20 0.000000
##8 -20 -10 0.000000
##9 -10 0 0.000000
##10 0 10 0.000000
##11 10 20 0.000000
##12 20 30 4.238186
##13 30 40 3.178054
##14 40 50 0.000000
##15 50 60 0.000000
##16 60 70 0.000000
##17 70 80 0.000000
##18 80 90 0.000000Please report any issues or bugs.
License: GPL-2
To cite package paleoMap in publications use:
To cite package `paleoMap` in publications use:
Sonja Leo, Sara Varela (2015). paleoMap: An R-package for getting and using paleontoligcal maps. R package version xx. https://github.com/NonaR/paleoMap
A BibTeX entry for LaTeX users is
@Manual{,
title = {paleoMap: An R-package for getting and using paleontoligcal maps},
author = {{Sonja Leo} and {Sara Varela}},
year = {2015},
note = {R package version xx},
base = {https://github.com/sonjaleo/paleoMap},
}