

In [11]:

    
#####################################################
##
## change multiple bird script to combined bird csv
##
####################################################

#fix MOCH
mountainchickadee <-read.table("C://Users/kate.reid709/Documents/Data/mountain_chick.csv", header = TRUE, sep = ",")

head(mountainchickadee)

mountainchickadee<-setNames(mountainchickadee, c("species", "lat", "long")) #hooray it's fixed

MOCH<-na.omit(mountainchickadee)

MOCH<- unique(MOCH)

#fix Mountain bluebird MOBL

mountainbluebird <-read.table("C://Users/kate.reid709/Documents/Data/mountain_bluebird.csv", header = TRUE, sep = ",")

head(mountainbluebird)
mountainbluebird<-setNames(mountainbluebird, c("species", "lat", "long")) #hooray it's fixed

MOBL<-na.omit(mountainbluebird)

MOBL<- unique(MOBL)

#fix the Lewis's woodpecker LEWO

lewiswoodpecker <-read.table("C://Users/kate.reid709/Documents/Data/lewis_wp.csv", header = TRUE, sep = ",")

head(lewiswoodpecker)

lewiswoodpecker<-setNames(lewiswoodpecker, c("species", "lat", "long")) #hooray it's fixed

LEWO<-na.omit(lewiswoodpecker)

LEWO<- unique(LEWO)

#fix housewren data

housewren <-read.table("C://Users/kate.reid709/Documents/Data/house_wren.csv", header = TRUE, sep = ",")

head(housewren)

housewren<-setNames(housewren, c("species", "lat", "long")) #hooray it's fixed
HOWR<-na.omit(housewren)

HOWR<- unique(HOWR)

#fix black-backed woodpecker BBWO


black <-read.table("C://Users/kate.reid709/Documents/Data/black_back_wp.csv", header = TRUE, sep = ",")

head(black)

black<-setNames(black, c("species", "lat", "long")) #hooray it's fixed
BBWO<-na.omit(black)

BBWO<- unique(BBWO)

allbird<- rbind(HOWR,BBWO,LEWO,MOCH,MOBL) #rbind all cleaned scripts together

plot(allbird$long, allbird$lat) #what's the lat long plot look like?

head(allbird)

write.csv(allbird,file = "C://Users/kate.reid709/Documents/Data/allbird_combined.csv", row.names = FALSE)









    





COMMON_NAME LATITUDE LONGITUDE

	Mountain_Chickadee 38.41718          -119.7492         
	Mountain_Chickadee 38.74602          -119.7780         
	Mountain_Chickadee 38.59111          -119.7846         
	Mountain_Chickadee 38.69454          -119.7800         
	Mountain_Chickadee 38.68812          -120.0670         
	Mountain_Chickadee 38.68812          -120.0670         









    





COMMON_NAME LATITUDE LONGITUDE

	Mountain_Bluebird 37.68668         -121.6401        
	Mountain_Bluebird 37.69095         -121.5934        
	Mountain_Bluebird 37.68668         -121.6401        
	Mountain_Bluebird 37.69401         -121.6765        
	Mountain_Bluebird 37.69095         -121.5934        
	Mountain_Bluebird 37.69095         -121.5934        









    





COMMON_NAME LATITUDE LONGITUDE

	Lewis_Woodpecker 37.55342        -121.5735       
	Lewis_Woodpecker 37.55342        -121.5735       
	Lewis_Woodpecker 37.55342        -121.5735       
	Lewis_Woodpecker 37.55342        -121.5735       
	Lewis_Woodpecker 37.55342        -121.5735       
	Lewis_Woodpecker 37.55342        -121.5735       









    





COMMON_NAME LATITUDE LONGITUDE

	House_Wren 37.87163  -122.2731 
	House_Wren 37.87163  -122.2731 
	House_Wren 37.55342  -121.5735 
	House_Wren 37.55342  -121.5735 
	House_Wren 37.51590  -121.8318 
	House_Wren 37.80043  -122.1547 









    





COMMON_NAME LATITUDE LONGITUDE

	Black_backed_Woodpecker 37.72492               -119.0192              
	Black_backed_Woodpecker 37.72492               -119.0192              
	Black_backed_Woodpecker 38.06060               -118.9246              
	Black_backed_Woodpecker 37.88705               -118.9596              
	Black_backed_Woodpecker 38.06060               -118.9246              
	Black_backed_Woodpecker 37.89799               -118.9816              









    





species lat long

	1 House_Wren 37.87163  -122.2731 
	3 House_Wren 37.55342  -121.5735 
	5 House_Wren 37.51590  -121.8318 
	6 House_Wren 37.80043  -122.1547 
	8 House_Wren 37.83252  -122.2355 
	9 House_Wren 37.87402  -122.2378

Joint species distribution modelling of birds in California

The Question: Do four different species in California compete?

The Data:

Information about the bird species was taken from the eBird database, opened in Open Refine, and cleaned. Here the data was cut down to just observations from California from 1996-2016.

In R, the seperate bird data were converted into the same format and combined into one csv file.

Climate data was taken from World Clim, cleaned in R and the precipitation and temperture were formed into raster layers.

A Raster layer for land use data was also created in R using a US gov tif image cropped for the Calfornia region.

To get the pseudoabsences

Script

COMMON_NAME	LATITUDE	LONGITUDE
Mountain_Chickadee	38.41718	-119.7492
Mountain_Chickadee	38.74602	-119.7780
Mountain_Chickadee	38.59111	-119.7846
Mountain_Chickadee	38.69454	-119.7800
Mountain_Chickadee	38.68812	-120.0670
Mountain_Chickadee	38.68812	-120.0670

COMMON_NAME	LATITUDE	LONGITUDE
Mountain_Bluebird	37.68668	-121.6401
Mountain_Bluebird	37.69095	-121.5934
Mountain_Bluebird	37.68668	-121.6401
Mountain_Bluebird	37.69401	-121.6765
Mountain_Bluebird	37.69095	-121.5934
Mountain_Bluebird	37.69095	-121.5934

COMMON_NAME	LATITUDE	LONGITUDE
Lewis_Woodpecker	37.55342	-121.5735
Lewis_Woodpecker	37.55342	-121.5735
Lewis_Woodpecker	37.55342	-121.5735
Lewis_Woodpecker	37.55342	-121.5735
Lewis_Woodpecker	37.55342	-121.5735
Lewis_Woodpecker	37.55342	-121.5735

COMMON_NAME	LATITUDE	LONGITUDE
House_Wren	37.87163	-122.2731
House_Wren	37.87163	-122.2731
House_Wren	37.55342	-121.5735
House_Wren	37.55342	-121.5735
House_Wren	37.51590	-121.8318
House_Wren	37.80043	-122.1547

COMMON_NAME	LATITUDE	LONGITUDE
Black_backed_Woodpecker	37.72492	-119.0192
Black_backed_Woodpecker	37.72492	-119.0192
Black_backed_Woodpecker	38.06060	-118.9246
Black_backed_Woodpecker	37.88705	-118.9596
Black_backed_Woodpecker	38.06060	-118.9246
Black_backed_Woodpecker	37.89799	-118.9816