Occurrence data on bivalves from the Ypresian Data from the Paleobiology Database via the velociraptr package on May 17th, 2017

Description

Occurrence data on bivalves from the Ypresian Data from the Paleobiology Database via the velociraptr package on May 17th, 2017

Usage

data(BivalvePBDB)

Format

A csv file

Examples

data(BivalvePBDB)

Performs Convex Hull area calculation

Description

Performs Convex Hull area calculation

Usage

CHullArea(longs, lats)

Arguments

Details

Uses the cylindrical equal area projection in order to check if the minimum convex hull wraps around the prime meridian

Value

Returns area of a set of coordinates

Note

Relies on the 'sp' package for the Polygon and chull function

Examples

longs<-c(-12,23,55)
lats<-c(34,22,30)
CHullArea(longs,lats)

Performs convex hull area calculation from coordinate sets on the Earth's surface

Description

Performs convex hull area calculation from coordinate sets on the Earth's surface

Usage

CHullAreaEarth(longs, lats)

Arguments

Details

Uses the cylindrical equal area projection in order to check if the minimum convex hull wraps around the prime meridian

Value

Returns the convex hull area is square kilometers

Note

Relies on the 'sp' package for the Polygon and chull function. Assumes latitude and longitude coordinates use the WGS84 datum

Examples

longs<-c(-133,-101,56)
lats<-c(33,12,-2)
CHullAreaEarth(longs,lats)

Calculates degree x degree cell counts of a specified size

Description

Calculates degree x degree cell counts of a specified size

Usage

CellCount(longs, lats, CellSize = 5, longBounds = c(-180, 180),
  latBounds = c(-90, 90))

Arguments

Value

Returns the number of cells occupied, specified cell size, and coordinate list

Note

This method uses grids cells constructed by equal degrees not area. So high latitude cells will have smaller areas than those at low latitude

Examples

longs<-c(22,55,-144)
lats<-c(-12,22,-12)
CellCount(longs,lats,CellSize=5,longBounds=c(-180,180),latBounds=c(-90,90))

Removes duplicate geographic locations and binds coordinates into a single element

Description

Removes duplicate geographic locations and binds coordinates into a single element

Usage

CoordCollapse(longs, lats)

Arguments

Value

Returns a 2-column array of coordinates without any duplicate locations

Note

Points are truncated to the hundredths place before checking for duplicates

Examples

longs<-c(34,133,-45)
lats<-c(-12,44,76)
CoordCollapse(longs,lats)

Creates an occurrence matrix of taxa by coordinates from the Paleobiology Database

Description

Creates an occurrence matrix of taxa by coordinates from the Paleobiology Database

Usage

CoordList_PBDB(pbdb_data)

Arguments

Details

Cuts out records for which there is no paleogeographic information known

Value

Returns a taxa by coordinates matrix of occurrences

See Also

See the velociraptr package for more details on downloading PBDB data

Examples

data(BivalvePBDB)
CoordList_PBDB(BivalvePBDB)

Create a rectangular shaped distribution with equal area to a given area

Description

Create a rectangular shaped distribution with equal area to a given area

Usage

EqualAreaRectangle(center = c(0, 0), TargetArea, error = 0.001)

Arguments

Value

Returns a 2-dimensional array of decimal degree coordinates outlining a rectangular shaped distribution

Note

This returns 100 evenly spaced points along each corner of the rectangle, in addition to the corners themselves

Examples

HorseShoeTest<-PtsAlgHorseShoe(z=2000,spacing=1,endAngles=c(-90,90))
HorseShoePts<-RandHorseShoe(center=c(0,0),npts=100,HorseShoeShape=HorseShoeTest)
EqualAreaRectangle(TargetArea=as.numeric(HorseShoePts$TotalArea_km2),error=0.001)

Calculates the maximum pairwise great circle distance from a set of decimal degree coordinates

Description

Calculates the maximum pairwise great circle distance from a set of decimal degree coordinates

Usage

GCD(longs, lats)

Arguments

Details

Because this function does not account for the possibility that a taxa may wrap around more than half the Earth the maximum value is half the circumference of the Earth, approximately 20,038 kilometers.

Value

Returns the maximum great circle distance in kilometers

Note

The great circle distance can be extracted from the result of a minium spanning tree calcualation MSTDist() if available to avoid redundant calculations

Examples

longs<-c(34,156,-78)
lats<-c(45,12,9)
GCD(longs,lats)

Function to calculate the correlation coefficient for pairwise comparisons between geographic range measures

Description

Function to calculate the correlation coefficient for pairwise comparisons between geographic range measures

Usage

GeoCor(GeoRange, Start = 1, method = "pearson")

Arguments

Value

Returns a sparse pairwsie matrix of correlation coefficients

Note

The correlation calculation uses the "pairwise.complete.obs" option from the cor function so that only complete pairs of observations are used, pairs containing an NA are ignored

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
testBivalve<-GeoRange_MultiTaxa(OccMatrix=BivalveMatrix,TaxaStart=3)
GeoCor(testBivalve,Start=1,method="kendall")

## End(Not run)

Function to calculate the skewness and coefficient of variance for a set of geographic range calculations

Description

Function to calculate the skewness and coefficient of variance for a set of geographic range calculations

Usage

GeoPerformance_SkewCV(GeoRange)

Arguments

Value

Returns a list of the skewness and coefficient of variance for each geographic range measure

Note

The coefficient of variance returned is standard deviation/mean

See Also

See the raster and moments packages for more details on the calculation of skewness and coefficient of variance

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
BivalveGeo<-GeoRange_MultiTaxa(OccMatrix=BivalveMatrix,TaxaStart=3)
GeoPerformance_SkewCV(BivalveGeo)

## End(Not run)

Function to tabulate number of occurrences/locations, six geographic range measures, minimum and maximum latitude and longitude for each taxon in a dataset

Description

Function to tabulate number of occurrences/locations, six geographic range measures, minimum and maximum latitude and longitude for each taxon in a dataset

Usage

GeoRange_MultiTaxa(OccMatrix, TaxaStart, LongPos = 1, LatPos = 2,
  CellSize = 5, longBounds = c(-180, 180), latBounds = c(-90, 90))

Arguments

Value

Returns a matrix of taxa by geographic range measures, including number of observations, number of unique locations observed at, minimum spanning tree distance, minimum convex hull area, maximum pairwise great circle distance, latitudinal range, longitudinal range, and number of degree X degree cells occupied

Note

Calculates the number of observations, localities, minimum spanning tree distance, convex hull area, longitudinal range, latitudinal range, and cell count

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
GeoRange_MultiTaxa(OccMatrix=BivalveMatrix,TaxaStart=3)

## End(Not run)

Calculates six geographic range measures at resampled a number of time from specified sample sizes

Description

Calculates six geographic range measures at resampled a number of time from specified sample sizes

Usage

GeoRarefaction_MultiTaxa(nLocCut = 3, OccMatrix, TaxaStart, LongPos = 1,
  LatPos = 2, iter = 10, CellSize = 5, longBounds = c(-180, 180),
  latBounds = c(-90, 90), steps = c(1, 50, 40, 30, 20, 10, 5),
  replacePts = FALSE)

Arguments

Details

The nLocCut parameter is the minimum number of distinct geographic locations a taxon must be observed at to have geographic range measures calcualted, if below retruns NA. The steps parameter typically begins with a 1 representing that all points should be used in calculations but this is not required. The replacePts parameter must be set to TRUE if any of the steps require a greater number of points to be sampled than there are actual locations for a taxon, otherwise the function will fail.

Value

Returns a vector where each element is a taxon with a list of each geographic range measure as a separate matrix of values. Measures include minimum spanning tree distance, minimum convex hull area, maxmimum pairwise great circle distance, latitudinal range, longitudinal range, and number of degree X degree cells occupied.

Note

If PEE values are to be calculated as a next step the steps parameter needs to have a value of 1 as its first value

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
GeoRarefaction_MultiTaxa(nLocCut=20,OccMatrix=BivalveMatrix,TaxaStart=3,replacePts=TRUE)

## End(Not run)

Calculates six geographic range measures at specified sample sizes for a single taxon

Description

Calculates six geographic range measures at specified sample sizes for a single taxon

Usage

GeoRarefaction_SingleTaxon(TName = "Bird1", OccMatrix, LongPos = 1,
  LatPos = 2, iter = 10, CellSize = 5, longBounds = c(-180, 180),
  latBounds = c(-90, 90), steps = c(1, 50, 40, 30, 20, 10, 5),
  replacePts = FALSE)

Arguments

Details

The nLocCut parameter is the minimum number of distinct geographic locations a taxon must be observed at to have geographic range measures calcualted, if below retruns NA. The steps parameter typically begins with a 1 representing that all points should be used in calculations but this is not required. The replacePts parameter must be set to TRUE if any of the steps require a greater number of points be locations be sampled than are available for a taxon, otherwise the function will fail.

Value

Returns a list of each geographic range measure as a separate matrix of values. Measures include minimum spanning tree distance, minimum convex hull area, maximum pairwise great circle distance, latitudinal range, longitudinal range, and number of degree X degree cells occupied.

Note

If PEE values are to be calculated as a next step the steps parameter needs to have a value of 1 as its first value

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
GeoRarefaction_SingleTaxon(TName=names(BivalveMatrix)[3],OccMatrix=BivalveMatrix,replacePts=TRUE)

## End(Not run)

Function to calcuate the area of a given horseshoe shape

Description

Function to calcuate the area of a given horseshoe shape

Usage

HorseShoeArea(HorseShoeShape)

Arguments

Value

Returns the area of the horseshoe shape with the circular and rectangular portions separated

Note

Currently forces use of a height 5/4 width and r2=2*r1 of origin (center)

References

[1] From http://mathforum.org/library/drmath/view/51816.html

Examples

HorseShoeTest<-PtsAlgHorseShoe(z=2000,spacing=1,endAngles=c(-90,90))
HorseShoeArea(HorseShoeTest)

Calculates the latitudinal range in degrees and kilometers

Description

Calculates the latitudinal range in degrees and kilometers

Usage

LatRg(lats)

Arguments

Value

Returns the outermost coordinates of the set, the latitudinal span in degrees and in kilometers

Examples

lats<-c(-23,56,-2,45,66)
LatRg(lats)

Calculates the longitudinal range in degrees and kilometers, assuming a latitude of 45 degrees for all points by default. Accounts for the possibility of wrapping around the globe.

Description

Calculates the longitudinal range in degrees and kilometers, assuming a latitude of 45 degrees for all points by default. Accounts for the possibility of wrapping around the globe.

Usage

LongRg(longs, lats = 45)

Arguments

Details

Calculates the longitudinal range as 360-largest longitudinal gap and accounts for the possbility that a taxon's range wraps around the prime meridian

Value

Returns the outermost coordinates of the set, the longitudinal span in degrees and in kilometers

Examples

longs<-c(133,76,-77,7,-80)
lats<-c(45)
LongRg(longs)

Calculates the minimum spanning tree distance, in kilometers, using Prim's Algorithm [1]

Description

Calculates the minimum spanning tree distance, in kilometers, using Prim's Algorithm [1]

Usage

MSTDist(longs, lats)

Arguments

Details

Uses Prim's algorithm for finding the minimum spanning tree, time-consuming calculation as the number of locations increases past 1000

Value

Returns the minimum spanning tree distance in kilometers, the pairwise distance matrix of occurrences, the order points were connected in, and a 2-column array of coordinates

References

[1] Prim, R.C. 1957. Shortest Connection Networks and Some Generalizations. The Bell System Technical Journal 36:1389-1401.

Examples

longs<-c(12,34,-55)
lats<-c(-41,3,56)
MSTDist(longs,lats)

Calculates the minimum spanning tree distance, in kilometers, using Prim's Algorithm [1] and a previously calculated pairwsie distance matrix

Description

Calculates the minimum spanning tree distance, in kilometers, using Prim's Algorithm [1] and a previously calculated pairwsie distance matrix

Usage

MSTDist_FromMat(longs, lats, DistMat)

Arguments

Details

Uses Prim's algorithm for finding the minimum spanning tree

Value

Returns the minimum spanning tree distance in kilometers, the pairwise distance matrix of occurrences, the order points were connected in, and a 2-column array of coordinates

References

[1] Prim, R.C. 1957. Shortest Connection Networks and Some Generalizations. The Bell System Technical Journal 36:1389-1401.

Examples

MSTCalc<-MSTDist(longs=c(22,44,-12,67),lats=c(-77,56,22,56))
MSTDist_FromMat(MSTCalc$Longitude,MSTCalc$Latitude,MSTCalc$MST_DistMat)

Function to compile the PBDB_PEE_SingleTaxon output for a list of taxa

Description

Function to compile the PBDB_PEE_SingleTaxon output for a list of taxa

Usage

PEE_MultiTaxa(GeoRare_Multi)

Arguments

Value

Returns a vector list of six geographic range measures matrix with percent error of estimates [1] for each value

References

[1] Russell, M.P. & D.R. Lindberg. 1988. Real and Random Patterns Associated with Molluscan Spatial and Temporal Distributions. Paleobiology 14:322-330.

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
BivalveGeo<-GeoRarefaction_MultiTaxa(nLocCut=20,OccMatrix=BivalveMatrix,TaxaStart=3,replacePts=TRUE)
PEE_MultiTaxa(BivalveGeo)

## End(Not run)

Function to calculate PEE [1] matrices for all the geographic range measures

Description

Function to calculate PEE [1] matrices for all the geographic range measures

Usage

PEE_SingleTaxon(GeoRare, TName = "Brach 1")

Arguments

Value

Returns a list of six geographic range measures matrix with percent error of estimates for each value

References

[1] Russell, M.P. & D.R. Lindberg. 1988. Real and Random Patterns Associated with Molluscan Spatial and Temporal Distributions. Paleobiology 14:322-330.

See Also

See the velociraptr package for details of the downloadPBDB() function

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
BivalveGeo<-GeoRarefaction_MultiTaxa(nLocCut=50,OccMatrix=BivalveMatrix,TaxaStart=3,iter=20)
PEE_SingleTaxon(GeoRare=BivalveGeo,TName=names(BivalveGeo)[3])

## End(Not run)

Creates a sparse pairwise distance matrix of a coordinate set

Description

Creates a sparse pairwise distance matrix of a coordinate set

Usage

PWMatrix(Coords)

Arguments

Value

Returns a sparse pairwise distance matrix of great circle distances between pairs of points

Examples

longs<-runif(10,-22,33)
lats<-runif(10,-22,33)
Coords<-CoordCollapse(longs,lats)
PWMatrix(Coords)

Plots the minimum convex hull of a set of coordinates

Description

Plots the minimum convex hull of a set of coordinates

Usage

PlotConvexHull(xcoord, ycoord, lcolor = "blue")

Arguments

Value

Plots a minimum convex hull

Note

This function does not account for the possibility of points crossing the prime meridian and in cases where this occurs the convex hull shown will be incorrect

Examples

longs<-c(20,20,40,40)
lats<-c(-5,5,-5,5)
PlotConvexHull(xcoord=longs,ycoord=lats)

Plots the minimum spanning tree of a set of coordinates

Description

Plots the minimum spanning tree of a set of coordinates

Usage

PlotMST(MSTCalc, color = "black", symbol = 16, xlimit = "NA",
  ylimit = "NA")

Arguments

Value

Plots a minimum spanning tree

Note

If the xlimit and ylimit parameters are left to their default values the axis ranges are based on the minimum and maximum values of the coordinates This function does not account for the possibility of points crossing the prime meridian and in cases where this occurs lines will cut across the entire plot

Examples

w<-MSTDist(longs=c(23,78,-23,56),lats=c(21,4,55,-3))
PlotMST(MSTCalc=w)

Plots the measured value versus rarefied samples or percent error of estimates (PEE) of a rarefied samples for a geographic range measure

Description

Plots the measured value versus rarefied samples or percent error of estimates (PEE) of a rarefied samples for a geographic range measure

Usage

Plot_Rarefaction(Mes1_AllTaxa, Mes2_AllTaxa, symbol = 20, measure = 2,
  SampSize = 1, color = "black")

Arguments

Details

For each taxon for a specific geographic range measure using 95 Measure paramter is the ordinal position of the measure of interest 2=MST,3=CH,4=GCD,5=LatRg,6=LongRg,7=CellCount SampSize parameter indicates the index column position of steps size, default is first column (all points)

Value

Returns a plot of measured geographic range values or PEE versus true value for a specific geographic range measure at varying sample sizes

Examples

## Not run: 
data(BivalvePBDB)
BivalveMatrix<-CoordList_PBDB(BivalvePBDB)
BivalveGeo<-GeoRarefaction_MultiTaxa(nLocCut=20,OccMatrix=BivalveMatrix,TaxaStart=3,replacePts=TRUE)
BivalvePEE<-PEE_MultiTaxa(BivalveGeo)
Plot_Rarefaction(BivalvePEE,BivalveGeo,symbol=20,measure=2,SampSize=2)

## End(Not run)

Function to find points along a horseshoe shape

Description

Function to find points along a horseshoe shape

Usage

PtsAlgHorseShoe(z, spacing = 1, endAngles = c(-90, 90))

Arguments

Details

Currently forces use 0,0 as the center, a height 5/4 width, and r2=2*r1 of origin (center)

Value

Returns a 2-dimensional array of decimal degree coordinates outlining a horseshoe shape

Note

Currently only works when endAngles are multiples of -90,90; otherwise rectangle point positions are off

References

[1] From http://mathforum.org/library/drmath/view/51816.html

Examples

PtsAlgHorseShoe(z=2000,spacing=1,endAngles=c(-90,90))

Function to randomly generate points within a horseshoe-shape

Description

Function to randomly generate points within a horseshoe-shape

Usage

RandHorseShoe(center = c(0, 0), npts = 100, HorseShoeShape, HRatio = 1.5,
  RadRatio = 0.5)

Arguments

Value

Returns a 2-dimensional array of decimal degree coordinates within the horseshoe shape and the total area of the shape

Note

HRatio Currently defaults to 3/2 per the PtsAlgHorseShoe() function RadRatio currently defaults to 1/2 per the PtsAlgHorseShoe() function Center currently defaults to c(0,0) as this is always the center of the PtsAlgHorseShoe() function currently Function currently does not take acount of the decreasing surface area moving toward the poles so points closer to the poles will be overrepresented relative to the actual surface area they represent

Examples

HorseShoeTest<-PtsAlgHorseShoe(z=2000,spacing=1,endAngles=c(-90,90))
RandHorseShoe(center=c(0,0),npts=100,HorseShoeShape=HorseShoeTest)

Function to randomly generate points within a given rectangular shaped distribution

Description

Function to randomly generate points within a given rectangular shaped distribution

Usage

RandRec(RecShape, npts = 100)

Arguments

Value

Returns a 2-dimensional array of decimal degree coordinates within a rectangular shape

Note

Function currently does not take acount of the decreasing surface area moving toward the poles so points closer to the poles will be overrepresented relative to the actual surface area they represent

Examples

HorseShoeTest<-PtsAlgHorseShoe(z=2000,spacing=1,endAngles=c(-90,90))
HorseShoePts<-RandHorseShoe(center=c(0,0),npts=100,HorseShoeShape=HorseShoeTest)
RecOutline<-EqualAreaRectangle(TargetArea=as.numeric(HorseShoePts$TotalArea_km2),error=0.001)
RandRec(RecShape=RecOutline,npts=100)

Converts degrees to radians

Description

Converts degrees to radians

Usage

deg2rad(deg)

Arguments

Value

Returns the degree in radians

References

[1]Originally from http://www.r-bloggers.com/great-circle-distance-calculations-in-r/

Examples

deg2rad(45)

Calculates the geodesic distance between two points specified by latitude and longitude using the Haversine formula

Description

Calculates the geodesic distance between two points specified by latitude and longitude using the Haversine formula

Usage

gcd_hf(long1, lat1, long2, lat2)

Arguments

Details

The Haversine formula can be inaccurate depending on coordinates

Value

Returns the distance between two points on the Earth in kilometers

Note

The haversine method is inaccuarate and should only be used when the vicenty formula fails or over very small distances

References

[1] Adapted from http://www.r-bloggers.com/great-circle-distance-calculations-in-r/

Examples

long1<-22
lat1<-44
long2<-52
lat2<-51
gcd_hf(long1,lat1,long2,lat2)

Calculates the geodesic distance between two points specified by latitude/longitude using Vincenty inverse formula for ellipsoids

Description

Calculates the geodesic distance between two points specified by latitude/longitude using Vincenty inverse formula for ellipsoids

Usage

gcd_vif(long1, lat1, long2, lat2)

Arguments

Value

Returns the distance between two points on the Earth in kilometers

References

[1] Adapted from http://www.r-bloggers.com/great-circle-distance-calculations-in-r/

Examples

long1<-22
lat1<-44
long2<-52
lat2<-51
gcd_vif(long1,lat1,long2,lat2)

Prints Hello, world!

Description

Prints Hello, world!

Usage

hello()

Value

Prints 'Hello, world!