Add SpatialPointsDataFrame and SpatialLinesDataFrame to raster plot - r

Question

I need to convert a shape file into a raster and have absolutely no clue where to even start.
If anyone could help me out I'd really appreciate!
Update: I have found out about the 'readOGR'-function, but everytime I use it I get the following message:
Warning messages:
1: In readOGR(dsn = "C:/Users/Giaco/Dropbox/Random Walk/Waterbodies", :
Dropping null geometries: 308, 309
2: In readOGR(dsn = "C:/Users/Giaco/Dropbox/Random Walk/Waterbodies", :
Z-dimension discarded
Can somebody tell me what that means?
Edit:
altdata <- raster("altitude.tif")
plot(altdata)
Lotic <- readOGR(dsn="C:/Users/Giaco/Dropbox/Random Walk/Waterbodies",layer="Lotic")
Lentic <- readOGR(dsn="C:/Users/Giaco/Dropbox/Random Walk/Waterbodies",layer="Lentic")
How can I plot the raster "altdata", the SpatialPointsDataFrame "Lentic" and the SpatialLinesDataFrame "Lotic" all in one plot ?
Edit:
altdata
class : RasterLayer
dimensions : 1286, 963, 1238418 (nrow, ncol, ncell)
resolution : 15, 15 (x, y)
extent : 90938.29, 105383.3, 190000, 209290 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=tmerc +lat_0=39.66666666666666 +lon_0=1 +k=1 +x_0=200000 +y_0=300000 +ellps=intl +pm=-9.131906111111112 +units=m +no_defs
data source : C:\Users\Giaco\Dropbox\Random Walk\altitude.tif
names : altitude
values : -32768, 32767 (min, max)
> Lentic
class : SpatialPointsDataFrame
features : 182
extent : -108473.2, -95455.86, -107870.9, -91344.22 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=tmerc +lat_0=39.66825833333333 +lon_0=-8.133108333333334 +k=1 +x_0=0 +y_0=0 +ellps=GRS80 +units=m +no_defs
variables : 3
names : Presence, Type, Accessible
min values : 0, Fountain, 0
max values : 1, Well, 2
> Lotic
class : SpatialLinesDataFrame
features : 317
extent : -108956.5, -93832.44, -108979.5, -90747.34 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=tmerc +lat_0=39.66825833333333 +lon_0=-8.133108333333334 +k=1 +x_0=0 +y_0=0 +ellps=GRS80 +units=m +no_defs
variables : 1
names : Presence
min values : 0
max values : 1

Answer 1

Using base plot, there are two way to overlay vector data on a raster. First plot the raster, then you can either call plot for each feature class using the add=TRUE argument. Alternately, you can use the points and lines functions which will also add to the current plot.
Create some example data
library(raster)
library(sp)
r <- raster(nrows=180, ncols=360, xmn=571823.6, xmx=616763.6, ymn=4423540,
ymx=4453690, resolution=270, crs = CRS("+proj=utm +zone=12 +datum=NAD83
+units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"))
r[] <- runif(ncell(r))
pts <- sampleRandom(r, 10, na.rm = TRUE, sp = TRUE)
Plot the raster then call plot again, with add=TRUE, to add points.
plot(r)
plot(pts, pch=20, cex=2, col="red", add=TRUE)
Or, plot the raster and use points to add the point feature class.
plot(r)
points(pts, pch=20, cex=2, col="red")
Edit: Your extents between the raster and vector feature classes do not overlap.
We can create SpatialPolygons using the extent of your objects and an example raster (with a uniform value of 1).
library(raster)
proj <- sp::CRS("+proj=tmerc +lat_0=39.66666666666666 +lon_0=1 +k=1 +x_0=200000 +y_0=300000
+ellps=intl +pm=-9.131906111111112 +units=m +no_defs")
r.ext <- as(extent(90938.29, 105383.3, 190000, 209290), "SpatialPolygons")
proj4string(r.ext) <- proj
pt.ext <- as(extent(-108473.2, -95455.86, -107870.9, -91344.22), "SpatialPolygons")
proj4string(pt.ext) <- proj
line.ext <- as(extent(-108956.5, -93832.44, -108979.5, -90747.34), "SpatialPolygons")
proj4string(line.ext) <- proj
r <- raster(r.ext, resolution = c(15,15), crs = proj)
r[] <- rep(1, ncell(r))
Here we see that if we plot the raster and then the point and line extent polygons, you cannot see them.
plot(r)
plot(pt.ext, add=TRUE)
plot(line.ext, add=TRUE)
However, if we plot the line and point extent polygons they overlay just fine.
plot(line.ext)
plot(pt.ext,add=TRUE)
If we limit the raster extent to the extent of the line object, you should see the raster sub-region, but do not. And, if you try to crop the raster you will receive an "Error in .local(x, y, ...) : extents do not overlap" error.
plot(line.ext)
plot(r, add=TRUE)