spatial - R: How can I count how many points are in each cell of my grid?

Question

I have made a reference grid, cells 50x50m, based on GPS locations of a collared animal. I want to do the equivalent to a spatial join in ArcGIS, and count the number of points in each cell.

I have made a reference grid, using a SpatialPointsDataFrame object (the data frame is already projected, using UTM coordinate system)

RESO <- 50 # grid resolution (m)
BUFF <- 500 # grid extent (m) (buffer around location extremes) 
XMIN <- RESO*(round(((min(dat.spdf$Longitude)-BUFF)/RESO),0))
YMIN <- RESO*(round(((min(dat.spdf$Latitude)-BUFF)/RESO),0))
XMAX <- XMIN+RESO*(round(((max(dat.spdf$Longitude)+BUFF-XMIN)/RESO),0))
YMAX <- YMIN+RESO*(round(((max(dat.spdf$Latitude)+BUFF-YMIN)/RESO),0))
NRW <- ((YMAX-YMIN)/RESO)
NCL <- ((XMAX-XMIN)/RESO)
refgrid<-raster(nrows=NRW, ncols=NCL, xmn=XMIN, xmx=XMAX, ymn=YMIN, ymx=YMAX) 
refgrid<-as(refgrid,"SpatialPixels")

To make sure my grid was in the same projection as the SpatialPoints:

proj4string(refgrid)=proj4string(dat.sp.utm) #makes the grid the same CRS as point

count.point function in adehabitatMA seems like the function that will do the trick

cp<- count.points(dat.spdf, refgrid)

But I get this error:

Error in w[[1]] : no [[ method for object without attributes

Is this not the right route to take to achieve my goal? Or how can I resolve this error? Or would the over function (sp package) be more suitable?

output from SpatialPointsDataFrame (dat.spdf)

dput(head(dat.spdf, 20))
structure(list(Latitude = c(5.4118432, 5.4118815, 5.4115713, 
5.4111541, 5.4087853, 5.4083702, 5.4082527, 5.4078161, 5.4075528, 
5.407321, 5.4070598, 5.4064237, 5.4070621, 5.4070555, 5.4065127, 
5.4065134, 5.4064872, 5.4056724, 5.4038751, 5.4024223), Longitude = c(118.0225467, 
118.0222841, 118.0211875, 118.0208637, 118.0205413, 118.0206064, 
118.0204101, 118.0209272, 118.0213827, 118.0214189, 118.0217748, 
118.0223343, 118.0227079, 118.0226916, 118.0220733, 118.02218, 
118.0221843, 118.0223316, 118.0198153, 118.0196021), DayNo = c(1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L)), .Names = c("Latitude", "Longitude", "DayNo"), row.names = c(1L, 
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 15L, 16L, 
17L, 18L, 19L, 20L, 21L), class = "data.frame")

And summary:

summary(dat.spdf)
Object of class SpatialPointsDataFrame
Coordinates:
           min      max
Longitude 610361.0 613575.5
Latitude  596583.5 599385.2
Is projected: TRUE 
proj4string : [+proj=utm +zone=50 +ellps=WGS84]
Number of points: 5078
Data attributes:
Latitude       Longitude       DayNo      
Min.   :5.396   Min.   :118   Min.   :  1.0  
1st Qu.:5.404   1st Qu.:118   1st Qu.: 92.0  
Median :5.406   Median :118   Median :183.0  
Mean   :5.407   Mean   :118   Mean   :182.6  
3rd Qu.:5.408   3rd Qu.:118   3rd Qu.:273.0  
Max.   :5.422   Max.   :118   Max.   :364.0  

Answer 1

The rasterize function can do that for you:

library(raster)
r <- raster(xmn=0, ymn=0, xmx=10, ymx=10, res=1)
xy <- spsample(as(extent(r), 'SpatialPolygons'), 100, 'random')

x <- rasterize(xy, r, fun='count')