New answers tagged r
1
vote
Accepted
Ordinary Kriging: "Warning message: In fit.variogram(data.var, vgm("Mat")) : No convergence after 200 iterations: try different initial values?"
The code is struggling to find well-defined parameter estimates for the model. This is often a sign that the model is maybe over-defined (too many parameters) for the data it is fitting. Variograms ...
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3
votes
Clipping dataframe (spatial data) to area of interest using R
I would recommend modernizing your workflow a bit. The depreciation schedule for sp and rgdal have been announced, being replaced by sf. The terra library is the replacement for raster, with much of ...
- 29.2k
1
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R Terra: Write multiple time series variables to NetCDF
A SpatRasterDataset does not have a time dimension. The SpatRasters it contains can have that dimension, and it may be different for each SpatRaster.
Here is a simplified script that suggests that all ...
- 8,681
2
votes
Clipping dataframe (spatial data) to area of interest using R
To clip a dataframe with spatial info to a desired study area:
(1) Convert the dataframe to a spatialpointdataframe by assigning spatial info.
# where your dataframe has the following columns:
# Lat, ...
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0
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Enlarging gBuffer width changes polygon shape
The gBuffer function needed a joinStyle = "MITRE" argument.
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0
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Accepted
Applying Moran's I across columns
As a possible alternative to the approach suggested by Spacedman I propose one based on {dplyr} and iterating via a for cycle over a vector of names of your variables of interest.
As I don't have ...
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2
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Applying Moran's I across columns
Make a vector of your variable names either by subsetting the column names or programmatically, eg:
vars = names(data_lisa)[2:5]
vars = paste0("var_",letters[1:4])
For an example, I'm using ...
- 51.2k
2
votes
Accepted
Creating regular sampling grid, with specific distance between points using R
I would create a SpatRaster using the SpatVector as template, and set the resolution to 10 meters. Then you got a Raster with the desired gap that you can transform to points if needed.
On this ...
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4
votes
QGIS reads blank cells as "nan" instead of "NULL"
I wouldn't be able to help with sorting this in R, however regarding the post-processing in QGIS, you current request in the field calculator is:
if("field" = "nan", NULL, "...
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0
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Downloading CHIRPS data sets using R
Here an example using the R package chirps. You can also change the data provider using the argument server. ClimateSERV takes the data from SERVIR Global, which I recommend when you have few data ...
0
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Spillover Binary variable based on neighboring cell in R
Since it seems that you started out with raster data let's go back to that:
library(terra)
r = rast(px[, c("xcoord", "ycoord", "gid")]) |> extend(2)
f = focal(r, 3, ...
- 8,681
3
votes
Accepted
Which point lies on which linestring?
Use st_intersects which returns a list for each point of which features the point is on.
EG the nc data cast to linear features:
> nc
Simple feature collection with 100 features and 14 fields
...
- 51.2k
0
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Soilgrids points outside of projection domain
Perhaps this is because the extent of your template raster is a bit off:
-180.0001, 179.9999, -90.00014, 83.99986 (xmin, xmax, ymin, ymax)
Now, -180.0001 is not wrong (it is the same as 179.9999) but ...
- 8,681
1
vote
Accepted
How to export result of point_metrics() in lidR?
There are plenty of options depending on what you really want to do.
You can keep only the points with min Z that way
library(lidR)
f = system.file("extdata", "Topography.laz", ...
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1
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'union' between spatial polygons and spatial points in R
I found out how to do it.
Two ways:
applying point.in.poly(grid, acled). So x= polygons, y=points.
applying point.in.poly(ACLED, grid) in the right way then merging with the initial grid.
grid....
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1
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Calculate sum/average of variable within each group of neighboring counties using R
I had this exact issue a few months ago working on a project and ended up developing a package to do just that.
I just now published the package on GitHub and can be installed in R by running devtools:...
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0
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Write layer style .qml as predefined within a gpkg using R
Thanks to @Spacedman I manage to do so by :
-in Qgis(3.2) save your style in database (Geopackage) and export as .gpkg
in R :
#I save my style layer as an object
mystyle <- sf::st_read("...
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0
votes
Check for NAs in `RasterLayer` and plot them in different colour
Example data
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
Count the cells that are NA (1, TRUE) or not-NA (0, FALSE)
freq(is.na(r))
layer value count
[...
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0
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R - gdistance: setting to 0 the conductance values of cells corresponding to a polyline
Transform your first AtoB path into a 0/1 raster, invert the values and create a new raster with 0 values on that path.
> library(spatialEco)
> r2 <- rasterize(AtoB,r,background=0)
> r2 &...
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0
votes
Accepted
R stars read_ncdf returns "vector memory exhausted (limit reached?)" when proxy = TRUE
Answer thanks to comments from @Spacedman
The current version of stars on CRAN does not include the option to set proxy = TRUE for read_ncdf(). This was included in the latest update to 0.5.6
Update ...
1
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grid_canopy() fails when chunk has 1 veg return
A good work around is the one provided by JRR in the comments.
if (npoints(vegetation) < 3) return(NULL)
This is because it's not the single return that's causing the problem, but the fact that the ...
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0
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Converting points to latitude and longitude values in R
I've used the following code to make a test raster that prints like yours (but is about 1/100000000 of the size):
testlat = raster(matrix(1:100,10,10))
extent(testlat) = c(xmin=13000,xmax=278000,ymin=...
- 51.2k
4
votes
Accepted
How to treat NAs using a custom function in the lapp function of {terra} in R
As @Spacedman says, a vectorized solution should work this function should give you the expected result.
t <- lapp(c(r,s),
fun = function(a,b){
a[is.na(a)] <- 55
...
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2
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How to treat NAs using a custom function in the lapp function of {terra} in R
This from the docs:
Before you use the function, test it to make sure that it is
vectorized. That is, it should work for vectors longer than one,
not only for single numbers.
Let's test:
> fun(...
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3
votes
Accepted
Extracting mean of multiple SpatRasters using Terra?
The terra equivalent of raster::calc is terra::app so, to return the mean for a multi-band raster you would use:
rmean <- app(x, mean)
or to return the mean for an entire raster:
global(x, mean).
- 29.2k
0
votes
Accepted
Ripley's K function and toroidal shift with Splancs
Yup. The code takes the bounding box of your polygon window and uses that. Yup points will get shifted out of the window. Quite how that breaks things I'm not sure, but splancs never was much for ...
- 51.2k
1
vote
Accepted
Read geo-spatial data in R via Leaflet
Here's a sample sp-class points data frame in a projected coordinate system like your data is:
> ps
class : SpatialPointsDataFrame
features : 4
extent : 1, 4, 1, 4 (xmin, xmax, ...
- 51.2k
0
votes
Apply linear stretch to Landsat 8 images in the tmap R package
I figured out how to improve the contrast:
fcc_nir_s <- terra::stretch(fcc_nir, minv = 0, maxv = 255, minq = 0.2, maxq = 0.98)
tm_shape(fcc_nir_s) +
tm_rgb()
This rescales rasters to 8-bit and ...
- 103
0
votes
Accepted
Count multilinestring elements crossing a raster cell in R
Following @JeffreyEvans suggestion, I achieved it using an "extract" approach:
First, I assigned an unique ID to each raster pixel:
values(rast.w) <- 1:ncell(rast.w)
Then, I used the ...
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0
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Apply linear stretch to Landsat 8 images in the tmap R package
Linear stretch with stretch="lin" in plotRGB will stretch up to the max of your data, which is 23358. If you do:
tmap(fcc_nir) +
tm_rgb(max.value = max(values(fcc_nir)))
then you should ...
- 51.2k
1
vote
Convert rworldMap to UTM
This does not change the numbers in the data, it only sets the coordinate system metadata:
> projection(map.cp.utm) <- CRS(proj4string(CP.utm))
see how the extent is still in degrees:
> map....
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0
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Error message with Krige function: Error in as.character.default(X[[i]], ...) : no method for coercing this S4 class to a vector
I figured it out. It looks like I had duplicate coordinate points in my data. Once I removed the duplicates it worked for me.
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0
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Reprojecting a raster from long/lat to UTM take 2
Use projectRaster function with crs argument. You can also use terra since it's faster and projection takes a lot of time. But with raster library:
r3utm <- projectRaster(from = r3, crs = "+...
- 11.8k
0
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projectRaster on a list of rasters
You are reprojecting to the last raster's CRS. It's a bit confusing, I recommend you to:
Project to a known CRS (it could be stored in an object as well)
Use a raster as template
Also, since this ...
- 11.8k
1
vote
using function inside raster::calc with loop
I would use lag function from dplyr package:
Your data:
library(raster)
r1 <- raster(nrows = 1, ncols = 1, res = 0.5, xmn = -1.5, xmx = 1.5, ymn = -1.5, ymx = 1.5, vals = 0.3)
rr <- lapply(1:12, ...
- 11.8k
1
vote
Accepted
Create sf polygon from sf linestring and bounding box
I suggest using lwgeom::st_split() to split your counties object according to the coast linestring. It will return a geometry collection, so it needs to be piped to a sf::st_collection_extract("...
- 630
2
votes
How can I make a raster layer where each pixel is a value representing the minimum distance between that pixel and a value from another layer?
Use "Proximity (raster distance)":
Black is short distance, white is longer
- 51.4k
2
votes
Accepted
Unexpected resolutions when aggregating rasters with raster package in R
aggregate function decreases resolution x times according to fact. Since it's x times, fact is a positive integer. This is stated in description:
fact postive integer. Aggregation factor expressed as ...
- 11.8k
2
votes
Accepted
How to compute partial correlation of pixels in R
Lets first make some test data:
sos = rast(array(runif(10*10*20),c(10,10,20)))
tem = rast(array(runif(10*10*20),c(10,10,20)))
pre = rast(array(runif(10*10*20),c(10,10,20)))
NDVI = rast(array(runif(...
- 51.2k
0
votes
R lm.LMtests error in lag.listw(listw, y, zero.policy) : y not numeric
Changing the dependent variable's class from character to numeric resolved the problem.
fires_OGR$FIRE = as.numeric(fires_OGR$FIRE)
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1
vote
Accepted
Coloring polygons (made with concaveman) in ggplot by column
I recommend you to use fortify function getting a data.frame. Then you can easily add any other kind of variable adding a new column:
concave.spdf2 <- fortify(concave.spdf)
concave.spdf2 <- ...
- 11.8k
1
vote
R Distance from Point to Line: Negative if within shape
Outine solution:
Cast the polygons to lines using st_cast and compute distances of pounts to lines (otherwise you get zero for the distance of points inside polygons).
Use st_intersects on the ...
- 51.2k
0
votes
R Markdown Knitting Produces Garbage
You need to set up the chunk. You can deactivate the code call with echo, warning messages and any other kind of message (Use also fig.cap, fig.height, fig.width and fig.align for plot customization):
...
- 11.8k
0
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How can I get the correct mean from focal() with a circular window?
A somewhat simpler function (but perhaps no faster, though I haven't checked) using raster is to first convert the focal weights matrix to 1s and NAs, then (using focal) multiply the window (x) by ...
1
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How to iterate erasing multiple vectors from another vector using R?
I would read your 10 shapefiles into a list object so that you can easily combine them using do.call.
s <- do.call("rbind", lapply(list.files(getwd(), "shp$")[-1], st_read))
...
- 29.2k
3
votes
Formatting decimal point for X,Y coordinates using R
The data is in latitude, longitude order, you are assigning them in the wrong order.
According to the metadata on the page you linked to:
Latitude = non-decimal latitude. Please use this formula to ...
- 51.8k
6
votes
Accepted
Anonymize site locations
There's a function in the maptools package called elide that is designed to shift and rotate spatial data. It can also flip, reflect, and rotate vector data, but it might be hard to do the equivalent ...
- 51.2k
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