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 Chordata
pm_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,] 0
pm_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 0
pm_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 0
pm_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 0.000000
Please 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},
}