I am extremely new to working with spatial data and so most of what I'm about to say is me trying to speak a foreign language. Right now I am trying to learn how to do this all in R (I am slightly more capable with this data in QGIS but for this solution, I am looking for R only).
My research involves ecological data in Pennsylvania (PA) and so I am playing around with cropping the US NLCD dataset to PA. I have a raster layer for the NLCD and a shapefile for the boundary of Pennsylvania. I am able to successfully crop the larger US raster down to PA as follows:
library(raster)
library(rgdal)
pabound <- readOGR(dsn="...",
layer="PAbound")
nlcdRast <- raster(".../NLCD_2016_Land_Cover_L48_20190424.img")
pabound <- spTransform(pabound,CRS(proj4string(nlcdRast)))
PAnlcd <- raster::crop(nlcdRast,pabound)
If I run the simple plot command for both nlcdRast and PAnlcd (i.e. plot(nlcdRast) they maintain the same color scheme. But when I run it through tmap it seems to look at the cropped data differently and I am not exactly sure how to figure this out. Please see the plots below:
library(tmap)
tm_shape(nlcdRast) +
tm_raster()
And then when I plot the cropped version in tmap:
tm_shape(PAnlcd) +
tm_raster()
As you can see, it is not simply the color palette that is changing (I am confident I could figure that out) but the real problem is I'm losing the important information as seen in the legend. Whereas the full plot actually shows the categorical values for the raster NLCD, the cropped version now seems to show just some unknown numerical range. Even though it looks bad at the moment, I'd like to have the same legend/information as seen in the full US map.
I apologize for not having a more reproducible example but I am completely lost on what is happening here so I can't quite replicate it. I suppose right now I'm just looking for where to look to try and figure out what changed. Thank you in advance.
Cropping is changing the way the pixels are represented. To maintain your values use the stars package (also note I'm using the sf package for the shapefile):
library(stars)
library(sf)
# load in NLCD
nlcdRast <- read_stars(".../NLCD_2016_Land_Cover_L48_20190424.img")
# read in study area
pabound <- st_read(dsn="...", layer="PAbound")
# reproject pabound to match NLCD
pabound <- st_transform(pabound, CRSobj = crs(nlcdRast))
# now crop
panlcd <- st_crop(nlcdRast, pabound)
I downloaded level-0 US map (National border) in R(sf) format from https://gadm.org/download_country_v3.html. I plotted US border (level 0) as follows:
library(tidyverse)
us0 <- readRDS("<file.path>\\gadm36_USA_0_sf.rds")
ggplot() +
geom_sf(data = us0, size = 1, color = "steelblue", fill = NA)
Resultant image shown below
I would like to remove outlying islands A and B, and move Alaska from C to C'.
I tried but failed to extract longitude and latitude data from us0. I searched online but did not find adequate answers on how to do this in R. I would like to know how longitude and latitude data could be extracted from us0 with R so that I can freely delete A and B and remove C. Thank you.
using the raster package and the geom() function you can extract the raw coordinates from the RDS object, as well as which island/state the coordinate is part of and whether it is solid or a hole.
In your case:
geom(us0)
Then it's just a matter of finding out which vertices belong to which islands. A quick way of deleting B would be to delete everything with a positive x coordinate. You'll need to find out which objects correspond to Alaska if you're to move and scale it. The top of Hawaii is (i.i.r.c) lower down than the bottom of the Florida Keys so you can also get away with removing everything with a latitude less than 23.
Also, I suspect many Hawaiians would object to Hawaii being referred to as an outlying island....
I have a raster r, one polygon shapefile regions and a point shapefile cities. I need to plot all three into one map layout. In addition to this I need to label point file with names of cities (cities$city$Town.Name) and their temperature and precipitation value (assigned as cities$labels). So I have used the following code with packages 'raster' and 'rasterVis'.
p1<-levelplot(regions.r,par.settings=mytheme,scales=list(draw=FALSE),xlab="",ylab="",margin=F)+
layer(sp.polygons(regions))+
layer(sp.points(cities,pch=20,cex=1.5,col="black"))
p1+
layer(sp.text(coordinates(cities), txt = cities$city$Town.Name, pos = 3,col="black",font=list(face="bold"),cex=0.8))+
layer(sp.text(coordinates(cities),txt = cities$label,
pos = 1,cex=0.6,col="black"))#Add shapefile labels
This works fine when area has scattered cities distribution (see figure below).
However, if the cities are concentrated in one part I experience overlap of labels (see figure below). Is there a way to avoid the label overlap?
I am working with shapefiles in R that I need to convert from polygon to raster. While the vectors look perfect when plotted, when converted to raster using 'rasterize' they produce erroneous horizontal lines. Here is an example of the problem:
Here is a generic example of the code that I am using (sorry that I cannot upload the data itself as it is proprietary):
spdf.dat <- readOGR("directory here", "layer here")
# Plot polygon
plot(spdf.dat, col = 'dimgrey', border = 'black')
# Extract boundaries
ext <- extent(spdf.dat)
# Set resolution for rasterization
res <- 1
# determine no. of columns from extents and resolution
yrow <- round((ext#ymax - ext#ymin) / res)
xcol <- round((ext#xmax - ext#xmin) / res)
# Rasterize base
rast.base <- raster(ext, yrow, xcol, crs = projection(spdf.dat))
# Rasterize substrate polygons
rast <- rasterize(spdf.dat, rast.base, field = 1, fun = 'min', progress='text')
plot(rast, col = 'dimgrey')
Does this seem to be a problem with the source data or the rasterize function? Has anyone seen this sort of error before? Thank you for any advice that you can provide.
To make it official so the question is considered answered, I'll copy my commented responses here. You can therefor accept it.
When I look at your figure, it seems to me that the problematic appearing lines in the raster are situated at the same latitude of some islands. Try to removes these islands from your dataset. If the problem disappear, you'll know that your data is the problem and where in your data the problem lies.
An other option is to try the gdalUtils package which has a function: gdal_rasterize. Maybe gdal is less exigent in the input data.
I had a similar problem rasterizing the TIGER areal water data for the San Juan Islands in Washington State , as well as for Maui - both of these spatial polygon data frames at the default resolution returned by package Tigris using a raster defined by points 1 arc-second of lat/lon apart. There were several horizontal stripes starting at what appeared to be sharp bends of the coastline. Various simplification algorithms helped, but not predictably, and not perfectly.
Try package Velox, which takes some getting used to as it uses Reference Classes. It probably has size limits, as it uses the Boost geometry libraries and works in memory. You don't need to understand it all, I don't. It is fast compared to raster::rasterize (especially for large and complicated spatial lines dataframes), although I didn't experience the hundred-fold speedups claimed, I am not gonna complain about a mere factor of 10 or 20 speedup. Most importantly, velox$rasterize() doesn't leave streaks for the locations I found where raster::rasterize did!
I found that it leaves a lot of memory garbage, and when converting large rasterLayers derived from velox$rasterize, running gc() was helpful before writing the raster in native R .grd format (in INT1S format to save disk space).
Just as a follow up to this question based on my experiences.
The horizontal lines are as a result of these 'islands' as described above. However, it only occurs if the polygon is 'multi-part'. If 'islands' are distinct polygons rather than a separate part of one polygon, then raster:rasterize() works fine.
Sorry for the wall of text, but I explain the question, include the data, and provide some code :)
QUESTION:
I have some climate data that I want to plot using R. I am working with data that is on an irregular, 277x349 grid, where (x=longitude, y=latitude, z=observation). Say z is a measure of pressure (500 hPa height (m)). I tried to plot contours (or isobars) on top of a map using the package ggplot2, but I am having some trouble due to the structure of the data.
The data comes from a regular, evenly spaced out 277x349 grid on a Lambert conformal projection, and for each grid point we have the actual longitude, latitude, and pressure measurement. It is a regular grid on the projection, but if I plot the data as points on a map using the actual longitude and latitude where the observations were recorded, I get the following:
I can make it look a little nicer by translating the rightmost piece to the left (maybe this can be done with some function, but I did this manually) or by ignoring the rightmost piece. Here is the plot with the right piece translated to the left:
(An aside) Just for fun, I tried my best to re-apply the original projection. I have some of the parameters for applying the projection from the data source, but I do not know what these parameters mean. Also, I do not know how R handles projections (I did read the help files...), so this plot was produced through some trial and error:
I tried to add the contour lines using the geom_contour function in ggplot2, but it froze my R. After trying it on a very small subset of the data, I found that out after some googling that ggplot was complaining because the data was on an irregular grid. I also found out that that is the reason geom_tile was not working. I am guessing that I have to make my grid of points evenly spaced out - probably by projecting it back into the original projection (?), or by evenly spacing out my data by either sampling a regular grid (?) or by extrapolating between points (?).
My questions are:
How can I draw contours on top of the map (preferably using ggplot2) for my data?
Bonus questions:
How do I transform my data back to a regular grid on the Lambert conformal projection? The parameters of the projection according to the data file include (mpLambertParallel1F=50, mpLambertParallel2F=50, mpLambertMeridianF=253, corners, La1=1, Lo1=214.5, Lov=253). I have no idea what these are.
How do I center my maps so that one side is not clipped (like in the first map)?
How do I make the projected plot of the map look nice (without the unnecessary parts of the map hanging around)? I tried adjusting the xlim and ylim, but it seems to apply the axes limits before projecting.
DATA:
I uploaded the data as rds files on Google drive. You can read in the files using the readRDS function in R.
lat2d: The actual latitude for the observations on the 2d grid
lon2d: The actual longitude for the observations on the 2d grid
z500: The observed height (m) where pressure is 500 millibars
dat: The data arranged in a nice data frame (for ggplot2)
I am told that the data is from the North American Regional Reanalysis data base.
MY CODE (THUS FAR):
library(ggplot2)
library(ggmap)
library(maps)
library(mapdata)
library(maptools)
gpclibPermit()
library(mapproj)
lat2d <- readRDS('lat2d.rds')
lon2d <- readRDS('lon2d.rds')
z500 <- readRDS('z500.rds')
dat <- readRDS('dat.rds')
# Get the map outlines
outlines <- as.data.frame(map("world", plot = FALSE,
xlim = c(min(lon2d), max(lon2d)),
ylim = c(min(lat2d), max(lat2d)))[c("x","y")])
worldmap <-geom_path(aes(x, y), inherit.aes = FALSE,
data = outlines, alpha = 0.8, show_guide = FALSE)
# The layer for the observed variable
z500map <- geom_point(aes(x=lon, y=lat, colour=z500), data=dat)
# Plot the first map
ggplot() + z500map + worldmap
# Fix the wrapping issue
dat2 <- dat
dat2$lon <- ifelse(dat2$lon>0, dat2$lon-max(dat2$lon)+min(dat2$lon), dat2$lon)
# Remake the outlines
outlines2 <- as.data.frame(map("world", plot = FALSE,
xlim = c(max(min(dat2$lon)), max(dat2$lon)),
ylim = c(min(dat2$lat), max(dat2$lat)))[c("x","y")])
worldmap2 <- geom_path(aes(x, y), inherit.aes = FALSE,
data = outlines2, alpha = 0.8, show_guide = FALSE)
# Remake the variable layer
ggp <- ggplot(aes(x=lon, y=lat), data=dat2)
z500map2 <- geom_point(aes(colour=z500), shape=15)
# Try a projection
projection <- coord_map(projection="lambert", lat0=30, lat1=60,
orientation=c(87.5,0,255))
# Plot
# Without projection
ggp + z500map2 + worldmap2
# With projection
ggp + z500map + worldmap + projection
Thanks!
UPDATE 1
Thanks to Spacedman's suggestions, I think I have made some progress. Using the raster package, I can directly read from an netcdf file and plot the contours:
library(raster)
# Note: ncdf4 may be a pain to install on windows.
# Try installing package 'ncdf' if this doesn't work
library(ncdf4)
# band=13 corresponds to the layer of interest, the 500 millibar height (m)
r <- raster(filename, band=13)
plot(r)
contour(r, add=TRUE)
Now all I need to do is get the map outlines to show under the contours! It sounds easy, but I'm guessing that the parameters for the projection need to be inputted correctly to do things properly.
The file in netcdf format, for those that are interested.
UPDATE 2
After much sleuthing, I made some more progress. I think I have the proper PROJ4 parameters now. I also found the proper values for the bounding box (I think). At the very least, I am able to roughly plot the same area as I did in ggplot.
# From running proj +proj=lcc +lat_1=50.0 +lat_2=50.0 +units=km +lon_0=-107
# in the command line and inputting the lat/lon corners of the grid
x2 <- c(-5628.21, -5648.71, 5680.72, 5660.14)
y2 <- c( 1481.40, 10430.58,10430.62, 1481.52)
plot(x2,y2)
# Read in the data as a raster
p4 <- "+proj=lcc +lat_1=50.0 +lat_2=50.0 +units=km +lon_0=-107 +lat_0=1.0"
r <- raster(nc.file.list[1], band=13, crs=CRS(p4))
r
# For some reason the coordinate system is not set properly
projection(r) <- CRS(p4)
extent(r) <- c(range(x2), range(y2))
r
# The contour map on the original Lambert grid
plot(r)
# Project to the lon/lat
p <- projectRaster(r, crs=CRS("+proj=longlat"))
p
extent(p)
str(p)
plot(p)
contour(p, add=TRUE)
Thanks to Spacedman for his help. I will probably start a new question about overlaying shapefiles if I can't figure things out!
Ditch the maps and ggplot packages for now.
Use package:raster and package:sp. Work in the projected coordinate system where everything is nicely on a grid. Use the standard contouring functions.
For map background, get a shapefile and read into a SpatialPolygonsDataFrame.
The names of the parameters for the projection don't match up with any standard names, and I can only find them in NCL code such as this
whereas the standard projection library, PROJ.4, wants these
So I think:
p4 = "+proj=lcc +lat_1=50 +lat_2=50 +lat_0=0 +lon_0=253 +x_0=0 +y_0=0"
is a good stab at a PROJ4 string for your data.
Now if I use that string to reproject your coordinates back (using rgdal:spTransform) I get a pretty regular grid, but not quite regular enough to transform to a SpatialPixelsDataFrame. Without knowing the original regular grid or the exact parameters that NCL uses we're a bit stuck for absolute precision here. But we can blunder on a bit with a good guess - basically just take the transformed bounding box and assume a regular grid in that:
coordinates(dat)=~lon+lat
proj4string(dat)=CRS("+init=epsg:4326")
dat2=spTransform(dat,CRS(p4))
bb=bbox(dat2)
lonx=seq(bb[1,1], bb[1,2],len=277)
laty=seq(bb[2,1], bb[2,2],len=349)
r=raster(list(x=laty,y=lonx,z=md))
plot(r)
contour(r,add=TRUE)
Now if you get a shapefile of your area you can transform it to this CRS to do a country overlay... But I would definitely try and get the original coordinates first.