Creating an interactive map of our sample sites

Here, I have created an interactive map of our sample collection sites using the mapping file. First I’m going to install some packages and access its library.

install.packages("leaflet", repos = "http://cran.us.r-project.org")

## Installing package into 'C:/Users/tropa/Documents/R/win-library/3.4'
## (as 'lib' is unspecified)

## package 'leaflet' successfully unpacked and MD5 sums checked
##
## The downloaded binary packages are in
##  C:\Users\tropa\AppData\Local\Temp\Rtmp8yPcpv\downloaded_packages

library(leaflet)
library(sp)

Next I’m going to retrieve the mapping file, and store it in the variable ‘data’.

data <- read.csv("allyears_map_corrected.csv")

Just so the code makes sense in context, I’ll display the mapping file here:

data

Now I’m going to make sure the contents of the longitude/latitude columns are numeric.

data$SampleLongitude <- as.numeric(data$SampleLongitude)
data$SampleLatitude <- as.numeric(data$SampleLatitude)

I’ve created a new SpatialPoints dataframe, and inside of this function I am telling R which columns to find the lattitude (first number) and longitude (second number) from the mapping file (which I have represented as ‘data’).

data.SP <- SpatialPointsDataFrame(data[,c(8,9)], data[,-c(8,9)])

Now I’m going to add the markers.

m <- leaflet() %>% addTiles() %>%
  addCircleMarkers(data = data, lng = ~SampleLongitude, lat = ~SampleLatitude, popup = ~X.SampleID)

Now for the part you’ve all been waiting for. Running m generates an interactive mapping file. You can click on the points to see which SAMPLEID they belong to.

m %>% addProviderTiles(providers$CartoDB.Positron)