convert multiple .csv files to .shp files in R

Question

I should preface that I am terrible at loops in R and I recognize this question is similar to this post Batch convert .csv files to .shp files in R. However, I was not able to leave a comment to see if this user found a solution on this thread because I do not have enough reputation points and the suggested solutions did not help me.

I have multiple .csv files that contain GPS points of animals. I would like to create multiple shapefiles for spatial analysis. I have tried creating a loop to read in the .csv file, make spatial data from csv file with latitudes and longitudes, transform the spatial data frame to a UTM projection so that I can calculate distances and then write the file as a shapefile. Here is the loop I have tried, but I think my indexing in the out and utm_out is incorrect.

Here is some test data; remember to set your working directory before writing the .csv:

#write sample .csv for animal 1
ID1<-rep(1, 3)
Latitude1<-c(25.48146, 25.49211, 25.47954)
Longitude1<-c(-84.66530, -84.64892, -84.69765)

df1<-data.frame(ID1, Latitude1, Longitude1)
colnames(df1)<-c("ID", "Latitude", "Longitude")
write.csv(df1, "df1.csv", row.names = FALSE)


#write sample .csv for animal 2
ID2<-rep(2, 2)
Latitude2<-c(28.48146, 28.49211)
Longitude2<-c(-88.66530, -88.64892)

df2<-data.frame(ID2, Latitude2, Longitude2)
colnames(df2)<-c("ID", "Latitude", "Longitude")
write.csv(df2, "df2.csv", row.names = FALSE)


#create a list of file names in my working directory where .csv files are located
all.files<-list.files(pattern="\\.csv")

#set the points geographic coordinate system
points_crs <- crs("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")

#write a loop to read in each file, specify the file as a spatial points data frame & project then write as .shp file
for(i in 1:length(all.files)) {
 file<-read.csv(all.files[i], header=TRUE, sep = ",", stringsAsFactors = FALSE) #read files
 coords<-file[c("Longitude", "Latitude")] #select coordinates from the file
 out<-SpatialPointsDataFrame(
      coords = coords,
      file,
      proj4string = points_crs) #create Spatial Points Data Frame and specify geographic coordinate system = points_crs
 utm_out<-spTransform(out, crs("+init=epsg:32616")) #transform to UTM
 writeOGR(utm_out[[i]],dsn="C:/Users/Desktop/Shapefile_test", 
 "*", driver="ESRI Shapefile")
}

This gives me the following: Error: inherits(obj, "Spatial") is not TRUE

I've also tried:

for(i in 1:length(all.files)) {
file<-read.csv(all.files[i], header=TRUE, sep = ",", stringsAsFactors = FALSE)
coords<-file[c("Longitude", "Latitude")]
out<-SpatialPointsDataFrame(
     coords = coords,
     file,
     proj4string = points_crs)
utm_out<-spTransform(out[[i]], crs("+init=epsg:32616"))
writeOGR(utm_out[[i]],dsn="C:/Users/Desktop/Shapefile_test", "*", driver="ESRI Shapefile")
}

This produces: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘spTransform’ for signature ‘"integer", "CRS"’

Ideally, the output file will be something like "animal1.shp" "animal2.shp"...etc.

Alternatively, I do have animal 1 and 2 in one file. I could bring in this file, set the projection and then create multiple subsets for each unique animal ID and write the subset to a .shp file, but I am having issues with subsetting the spatial data and I think that is a topic for another thread.

Thanks in advance for your assistance.

Answer 1

Here is a minor variation on the solution by Mako212

library(raster)

all.files <- list.files(pattern="\\.csv$")
out.files <- gsub("\\.csv$", ".shp")
crs <- CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")

for(i in 1:length(all.files)) {
    d <- read.csv(all.files[i], stringsAsFactors = FALSE)
    sp <- SpatialPointsDataFrame(coords = d[c("Longitude", "Latitude")], d, proj4string = crs) 
    utm <- spTransform(sp, CRS("+proj=utm +zone=16 +datum=WGS84"))
    shapefile(utm, out.files[i])
}

Answer 2

Expanding on my comment, it's important to test batch processing operations like this on a single file first, and then adapt your solution as necessary to process the batch. My first step in troubleshooting your issue was to strip away the for loop, and try running the code with the first file,all.files[1], and it still failed, indicating there was at least one issue not related to the loop.

Try this out. I've changed crs to CRS because the function in sp is capitalized. Your loop range can be simplified to for(i in all.files), and I removed the attempts to access non-existent lists with out and utm_out

require(sp)
require(rgdal)   

points_crs <- CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")

#write a loop to read in each file, specify the file as a spatial points data frame & project then write as .shp file
for(i in all.files) {
 file <- read.csv(i, header=TRUE, sep = ",", stringsAsFactors = FALSE) #read files
 coords <- file[c("Longitude", "Latitude")] #select coordinates from the file
 out <- SpatialPointsDataFrame(
      coords = coords,
      file,
      proj4string = points_crs) #create Spatial Points Data Frame and specify geographic coordinate system = points_crs
 names<-substr(i, 1, nchar(all.files)-4)
 utm_out <- spTransform(out, CRS("+init=epsg:32616")) #transform to UTM
 writeOGR(utm_out,dsn="/path/Shapefile_test", layer=names, driver="ESRI Shapefile")
}

Edit:

I had to modify the writeOGR line by specifying a layer name:

writeOGR(utm_out,dsn="/path/Shapefile_test", layer="test", driver="ESRI Shapefile")