1.5 Import and Format Datasets

First we need to load the packages needed for the exercise
library(chron)
library(rgdal)
library(RAtmosphere)

4. Now open the script "TimeLagScript.R" and run code directly from the script

Determine the name of your file ("temp" in our case here)
We can then enter the path with this name to bring our dataset into R

Next we can add code below to include night and day into datasets and to also to
account for daylight savings. Package RAtmosphere will eliminate the need for the
chunk of code below if working on an earlier version of R (i.e., code not available for R
3.2.1 plus). Thanks to Duane Diefenbach, PA Coop Unit Leader, for compiling all this
from online sources.
###################################################################
#We first need to create a SPDF and transform to Lat Long then return to a
#Data Frame. You only need this section of code if you need to acquire Lat #Long coordinates for your dataset
###################################################################
#utm.crs <-CRS("+proj=utm +zone=12 +datum=WGS84")
#dataSPDF<-data.frame(x = temp$UTMe, y = temp$UTMn)
#utm.spdf <- SpatialPointsDataFrame(coords = dataSPDF, data = temp,
proj4string = utm.crs)
#ll.crs <- CRS("+proj=longlat +ellps=WGS84")
#datall <-spTransform(utm.spdf, CRS=ll.crs)
#str(datall)

#temp <- as.data.frame(datall)
#str(temp)

Separate times into categories "Day" and "Night" based on sunrise-sunset table by running function below or simply using the RAtmosphere package if available

First run line of code below with d being the day of year, Lat is latitude in decimal
degrees, and Long is longitude in decimal degrees (negative == West) available at
suncalc
suncalc <- function(d,Lat=39.14133,Long=-106.7722){
##This method is copied from:
##Teets, D.A. 2003. Predicting sunrise and sunset times.
## The College Mathematics Journal 34(4):317-321.
## At the default location the estimates of sunrise and sunset are within
## seven minutes of the correct times
##(http://aa.usno.navy.mil/data/docs/RS_OneYear.php)
## with a mean of 2.4 minutes error.
## Function to convert degrees to radians
rad <- function(x)pi*x/180
##Radius of the earth (km)
R=6378
##Radians between the xy-plane and the ecliptic plane
epsilon=rad(23.45)
##Convert observer's latitude to radians
L=rad(Lat)
## Calculate offset of sunrise based on longitude (min)
## If Long is negative, then the mod represents degrees West of
## a standard time meridian, so timing of sunrise and sunset should
## be made later.
##NOTE: If working with UTC times use timezone = -4*(abs(Long)%%15)*sign(Long)
timezone = -6*(abs(Long)%%15)*sign(Long)
## The earth's mean distance from the sun (km)
r = 149598000
theta = 2*pi/365.25*(d-80)
z.s = r*sin(theta)*sin(epsilon)
r.p = sqrt(r^2-z.s^2)
t0 = 1440/(2*pi)*acos((R-z.s*sin(L))/(r.p*cos(L)))
##a kludge adjustment for the radius of the sun
that = t0+5

## Adjust "noon" for the fact that the earth's orbit is not circular:
n = 720-10*sin(4*pi*(d-80)/365.25)+8*sin(2*pi*d/365.25)
## now sunrise and after sunset are:
sunrise = (n-that+timezone)/60
sunset = (n+that+timezone)/60
suntime <- cbind(sunrise,sunset)
return(suntime)
}

Read in location data and retain lat, lon, and date
temp$Date <- paste((temp$Year),substr(temp$date_time, 2,3),
substr(temp$date_time, 5,6),sep="-")
str(temp)
#calculate calendar day and center of locations
calday <- as.numeric(as.Date(temp$Date)-as.Date("2005-01-01"), units="days")
dat1 <- cbind(temp,calday)
moda <- format(as.Date(temp$Date),"%d-%b")
str(dat1)
dat1 <- cbind(dat1, suncalc(dat1$calday, Lat=dat1$LATITUDE, Long=dat1$LONGITUDE),
moda)
hrchar <- as.character(substr(dat1$time,1,2))
hr <- as.numeric(as.character(substr(dat1$time,1,2)))
minchar <- as.character(substr(dat1$time,4,5))
min <- as.numeric(minchar)
localhr <- hr+min/60
dat1 <- cbind(dat1,hr,hrchar,minchar,localhr)
Diel <- ifelse(localhr<dat1$sunrise | localhr>dat1$sunset, 'Night', 'Day')
dat1 <- cbind(dat1,Diel)
str(dat1)
dat1[1:50,]