Extract coordinates from spatialpolygonsdataframe. The maptools function takes the same data from maps, and converts them into a SpatialPolygons object. Improve this answer. Then, you subtract them from the original data frame and create a new object. The points are stored as a window ( owin) in x. This nested structure, representing each polygon, has to be accounted for using something like sapply to operate on each list object (polygon). selected, 'polygons') > sub. 4. Adjust centroids spatial polygons using sf. dput: Sep 17, 2018 · I want to find out the coordinates (latitude and longitude) of Texas precincts. When you create a SpatialPointsDataFrame, you need to assign proj4string. If character: indicates the column in data with Polygons IDs to match. a sf object with st_transform() Mar 2, 2020 · How to extract xy-coordinates from raster where its highest value is located within a polygon? 4 How to compute the greatest distance between a centroid and the edge of the polygon using the SF package? Jun 8, 2015 · I am trying to extract the coordinates from Sr1 and Sr2 from the SpP object. They cannot be recovered from a saved R session either or directly passed to nodes on a computer cluster. shp <- sf:st_read('example. No, I don't have the study window/owin and am trying to create that - hence my question on how to do that. Below is my R code attempting to do that. frame, which is not very helpful. shp" shp <- readOGR(dsn=dsn. raster (version 1 Jan 9, 2018 · Extract raster values of particular polygons of a SpatialPolygonsDataFrame (indexation) 14. We’ll use use some randomly generated XY coordinates. Extracting points with polygon in R. Extract feature coordinates from SpatialPolygons and other sp classes. You can supply a list of SpatVectors to append them into a single Jul 21, 2023 · Both ggplot2 and plotly support sf objects, those can be used as regular dataframes / tibbles when working with geometry attributes and there's no need to fortify(). Then I wish to convert the polygon for Kruger National Park into a SpatialPolygonsDataFrame. To compute the centre point of a raster, take the centre point of the X and Y extents. Even if you have some specific requirements and you'd need to stick with sp ( SpatialPolygonsDataFrame) for now, you can convert your Spatial* objects to sf for plotting. Feb 4, 2008 · Takatsugu Kobayashi <tkobayas <at> indiana. From the sp::over help:. Dec 29, 2017 · given is a raster as well as a SpatialPolygonsDataframe. However, when using extract (), it returns only NAs, so I guess I made a mistake with the projection. Here is an example taken from this. Choose an appropriate one for you. 7. tif') extract <- raster::extract(r, shp, df=TRUE) This gives me a data frame of two columns: the numeric ID for each polygon and the associated extracted raster value. Using what I have in the below code as an example, I want to clip the rectangular spatial polygon so that only oceanic portions of the polygon remain. There are 64 in total, all stored in shp. It gets slow with large Oct 2, 2013 · What I get when I run is what I am looking for, but I want to change the islands in the south west (Islas Canarias) to be closer to Spain country. I also have a shape file of North America. Oct 13, 2023 · Methods to create a SpatVector from a filename or other R object. frame form pretty routinely to get these kinds of answers, but it's all doable. Raster resolution varies from 1 to 30 meters and the plot size is r = 6 meters. Package sp provides a number of classes for different spatial concepts (points, lines, polygons). Elements may be NA valued; if all elements are NA the CRS is missing valued, and object of class data. It works fine. The raster way is quicker for less complex SpatialPolygonsDataFrames and returns a SpatialPolygonsDataFrame as in the example. For this first accomplished task, the objective was to associate to each GPS coordinates the information about City and Region which they belong to Convert set of coordinates in specyfic format into sf object (polygon) in R. Jun 28, 2017 · Extract raster values of particular polygons of a SpatialPolygonsDataFrame (indexation) Crop for SpatialPolygonsDataFrame. Nov 13, 2017 · I am trying to extract median values from rasters for 1043 different polygons (plots). Description. load the sp package if you haven’t already done so. Jun 2, 2017 · It works well for the majority of polygons but there are those with no point inside and others with more than one point. How can I preserve it, or is there another way to get the lat&long values into separate columns from the geometry column whilst keeping the ID in the same df? dput for the dataframe is: 2. The attributes of each polygon are then attached to this data frame as variables that vary by polygon id (the rownames of the object). May 16, 2015 · Simple question: how to extract the number of vertices in each polygon in R? I've found one way that works, but this is very slow (when x is a SpatialPolygonsDataFrame): y &lt;- fortify(x) n. Accessing the coordinates should look something like . agr. Sep 3, 2019 · datum=WGS84: the datum WGS84 (the datum refers to the 0,0 reference for the coordinate system used in the projection) units=m: the units for the coordinates are in METERS; ellps=WGS84: the ellipsoid (how the Earth’s roundness is calculated) for the data is WGS84; Note that the zone is unique to the UTM projection. coords. I want to plot all individual indexes on 1 map. 62. But the output does not match the coordinates which I specified in Sr1 or Sr2. Jan 8, 2018 · The task I'm trying to do is very simple with the sp package in R but I'm trying to learn sf hence my question. frame with exactly two columns. Nov 20, 2022 · I have a data. You'll need to load ggplot2, and then run fortify (yoursp). The output is a list, so that you can count the number of objects in the list. data. Each row contains the x and y coordinates of a pixel, and a logical value indicating whether the pixel lies inside the window. Details. Feb 8, 2020 · which is a coordinate system in metres. However, the powerful new spatial package sf is May 18, 2024 · sf_project: directly transform a set of coordinates; sgbp: Methods for dealing with sparse geometry binary predicate st: Create simple feature from a numeric vector, matrix or list; st_agr: get or set relation_to_geometry attribute of an 'sf' object; stars: functions only exported to be used internally by stars May 23, 2017 · Look into maptools::map2SpatialPolygons, an try its examples. sf). Functions to transform, or reproject spatial objects typically take the following two arguments: the spatial object to reproject; a CRS object with the new projection definition; You can reproject. x@coords contains the coordinates of an object of class or extending SpatialPoints , we strongly encourage users to access the data by using func-tions and methods, in this case coordinates(x) to retrieve the coordinates. But for consistency it makes a lot of sense. frame; the number of rows in data should equal the number of Polygons-class objects in Sr. But, when I want to insert the data already rounded back into the SpatialPolygonsDataFrame, I see that it keeps the data as it was originally, without being rounded. This comes from Roger Bivand on R-sig-Geo mailing list. data <- over(A, B[,"code"]) Instead of a point spatial object, this simply gives you a data frame, with the same no. sp@data = data. wkt. Jul 26, 2023 · Details. This cannot be used to subset your SpatialPoints*. SpatialPolygonsDataFrame <- function (shape, region = NULL) { attr <- as. I have lots of points so it has to be I would like to clip a spatial polygon (specified by a series of lat/long coordinates) according to a world map, such that any part of the polygon which overlaps with a map polygon is removed. table. cents <- SpatialPointsDataFrame(coords=cents, data=sids@data, proj4string=CRS("+proj=longlat +ellps=clrk66")) Jan 22, 2018 · It contains observations associated with coordinate points (lat/lon). I cannot understand the mismatch of the indexes in the square brackets, nevertheless it runs. I am a beginner in using R for spatial data analysis and want to simply extract some values for certain locations (with lon/lat positions) from a raster stack. map_data reads the data from maps and puts them in a data. finding points with polygon in sf package. Apr 3, 2015 · EDIT After more research and still no solution, I am adding a substantial edit as well as a link to the . Search all packages and functions. Once we create a SpatialPolygons object in R - we’ll take a closer look at its metadata and structure. Description Usage Arguments Details Value Note Author(s) References See Also Examples. This attribute is of class crs , and is a list consisting of input (user input, e. In order to retrieve the highest value of the raster within the area of a polygon, raster::extract can be used. . Not all CRS will have a zone. Let df = data frame, sp = spatial polygon object and by = name or column number of common column. How to get additionally the coordinates of the extracted highest value of the raster within the area of a polygon? Feb 17, 2015 · 1. May 31, 2021 · I wish to extract just the polygon for Kruger National Park, not any of the neighboring nature or game reserves. The *crs functions create, get, set or replace the crs attribute of a simple feature geometry list-column. Unfortunately map2SpatialPolygons is buggy @EdzerPebesma. If x is numeric, return crs object for EPSG: x ; if x is character, return crs object for x ; if x is of class sf or sfc, return its crs object. Roger is one of the authors of the sp package. 0), methods utils, stats, graphics, grDevices, lattice, grid RColorBrewer, gstat, deldir, knitr, rmarkdown, sf, terra, raster Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. 99045 -44. shp') r <- raster::raster('example. tx, stringsAsFactor = F) coords <- coordinates(shp) But the resulting coordinates are in an unusual format: Nov 12, 2020 · Is there a way to use ggplot2 in R to plot multiple spatialpolygonsdataframe that are stored as objects in a list? Each index has a spatialpolygonsdataframe. A filename can be for a shapefile or any spatial file format. 1 Standard methods Selecting, retrieving or replacing certain attributes in spatial objects with at- Sep 23, 2020 · Is there a straightforward way to convert polygonal SpatVector class objects (from the terra library) to either simple features or SpatialPolygonsDataFrames? Mar 3, 2019 · library(sf) centres<- as. We would like to show you a description here but the site won’t allow us. 3. Nov 27, 2014 · x <- clickpoly(add = TRUE, col = 2, lwd = 2) # Start locator overlayed on region. Learn R. Sep 7, 2015 · At this point, the object states is a SpatialPolygonsDataFrame. character vector; see details section of st_sf. Any help would be greatly appreciated. For some classes, accessing feature coordinates is straightforward, e. csv data file with postal codes, latitude and longitude. 5 degree raster grid cell locations, that would be excellent. How can I convert it to a SpatialPolygonsDataFrame object? Here's my data frame: >; buildings_df lon lat May 27, 2020 · It seems as if the precipitation values are given for specific coordinates, not areas. If you do overlay(pts, polys) where pts is a SpatialPointsDataFrame object and polys is a SpatialPolygonsDataFrame object then you get back a vector the same length as the points giving the row of the polygons data frame. Apr 4, 2015 · Have you tried readOGR in rgdal? If you are reading a polygon shapefile, readOGR will result in a SpatialPolygonsDataFrame object. Then, I round the data. 1-4 Classes and Methods for Spatial Data R (>= 3. First we need to create a set of XY coordinates that represent the vertices of a polygon. I would like to rescale the coordinates to kilometers (divide the coordinates by 1000). I saw this code elsewhere on stack exchange: Coords<-SpP@polygons[[2]]@Polygons[[1]]@coords. I just know they are here: gadm[14,] I try to make changes for example here: gadm[14,]@polygons[[1]]@Polygons[[1]]@coords May 28, 2018 · You can convert your raster to polygon then use to extract the centroid. If you in fact, do have a SpatialPolygons object and want to coerce into SpatialPolygonsDataFrame the specified dataframe will need to have its rownames match the polygon ID's in the polygons slot. All examples Mar 4, 2015 · I'm assuming you've already made "A" spatial with coordinates(A) <- ~longitude+latitude: # Overlay points and extract just the code column: a. You can do the following to convert the logical matrix to a vector that the subsetting operation can accommodate: d[complete. SpatialLines. So all you then need to do to combine the polygon data onto the points data frame is: o = overlay(pts, polys) Feb 19, 2012 · extract(raster, SpatialPolygons(SPdataframe@polygons)[i],fun="mean",na. If an (invalid) multipart polygon covers the Mar 25, 2018 · But if you are not familiar with sp class structures it is better to use the sf package, which uses simple geometries. fortify. I would like to extract the name of the polygons from the KML file to map to the . This function is mainly used for plotting SpatialPolygonsDataFrame objects with ggplot rather than spplot. logical: (default TRUE): match SpatialPolygons member Polygons ID slot values with data frame row names, and re-order the data frame rows if necessary. By clicking “Post Your Answer”, you agree to our terms of Jun 10, 2015 · Extract feature coordinates from SpatialPolygons and other sp classes. The match function inside aligns the columns so that order is Aug 9, 2018 · villages has a coordinate system, take it to the booths: st_crs(booths) = st_crs(villages) At this point you should plot the villages and the booths to make sure nothing has gone wrong. 5783 value<-extract(raster, SpatialPoints(cbind(x,y))) Without it, you may just receive NA values. Now I create a new directory ("tempdir") and save the shapefiles there: dir. Value. You finally use SpatialPointsDataFrame() to create a SpatialPointsDataFrame. 2. rm=TRUE,method="simple") Can anyone explain the difference between the use of the same indexation in this two cases? What is the official way to choose particular polygons of a SpatialPolygonsDataFrame with indices? Obsolete functions. cases(over(d, plgn)), ] name, e. Assigning to proj4string in sp doesn't transform coordinates, so now you have data in UTM 21 metres. csv to give 4 columns: postal_code latitude longitude Name Where Name is the name the polygon if the postal_code fall within the polygon. tmp <- slot(tmp[[1]],'Polygons') > sub. It seems that the coordinates of centroids are not corrected for all polygons. ID. – Jan 6, 2022 · I have done this many times before (with other shapefiles) using the extract command in R, i. Now I would like to add the x, y coordinates for each extracted raster value. The following code chunk can be used to extract addition coordinate information from the data. Finally, if this is actually what you are after it won't take any time at all, as long as your virtual memory resources are a match for the data set you have, to read it all in Feb 4, 2021 · So I do that in the following code. 5. Object of class crs, which is a list with elements input (length-1 character) and wkt (length-1 character). "EPSG:4326" or "WGS84" or a proj4string), and wkt, an automatically generated wkt2 representation of the crs. Pixels covered by all parts of the polygon are considered. May 6, 2021 · @EgeRubak Thanks for the reply. . I am using R to read the file and extract the coordinates: dsn. I loaded the lon/lat-locations into a SpatialPointsDataFrame, changed the lon/lat Oct 23, 2020 · I have a separate . Exactextract is SO much faster than raster::extract (even if I run the latter in parallel and therefore a fantastic addition to my GIS toolset), so I definitively favor it over raster::extract. How do I do this using R? Here is a sample data Nov 27, 2023 · coordinates: set spatial coordinates to create a Spatial object, or coordinates-methods: retrieve (or set) spatial coordinates; coordnames-methods: retrieve or assign coordinate names for classes in sp; CRS-class: Class "CRS" of coordinate reference system arguments; degaxis: axis with degrees; dimensions: retrieve spatial dimensions from name, e. Oct 14, 2023 · coords: Coordinates of the Extent of a Raster object; corLocal: Local correlation coefficient; cover: Replace NA values with values of other layers; crop: Crop; crosstab: Cross-tabulate; cut: Convert values to classes; cv: Coefficient of variation; datasource: Are values in memory and/or on disk? dataType: Data type; density: Density plot I have a data frame with a bunch of polygons, several points per polygon. A data. e. The shape file is included here. Extracting values from soilGrids for xy coordinates in R 0 How to extract point data (latitude, longitude) of different soil variables from SoilGrids without actually downloading the TIFF files longitude/latitude lines and labels to a map with another coordinate reference system. (This was found in the class description of the SpatialPolygonsDataFrame R data class for the overarching spatial package in R, sp) This seems to do exactly the same thing as . I download the shapefile from here. ps <- gadm@polygons[1] then something like Jun 12, 2020 · Extract coordinates of polygon centroids and label them by polygon number. Then you just left click the points you need and middle/right click when you are done. Jul 11, 2017 · Based on your comment: Ok so the object you load is an object of type SpatialPolygonsDataFrame, and that has a Slot/property called Polygons, with objects of type Polygon. example list: Compared to other data science topics, analysis of spatial data using the tidyverse is relatively underdeveloped. By default, this extracts the cell info for each polygon of the SpatialPolygonDataFrame. id and NAME_2 from the SpatialPolygonsDataframe countryPolygons? Perhaps there is an easier way to achieve this goal (a dataframe with the individual IDs as one column and the region that they are from based on their coordinates as another column). match. frame (shape) # If not specified, split into regions based on first variable in attributes Feb 5, 2014 · Your plgn is a SpatialPolygonsDataFrame, and as such, is. frame to make a SpatVector of points; or a "geom" matrix to make a SpatVector of any supported geometry (see examples and geom ). 15. I need to overlay around 6000 points and that runs fine with raster::extract. 1 Standard methods Selecting, retrieving or replacing certain attributes in spatial objects with at- Dec 21, 2012 · Here is an example of how to do this with rgeos using the world map as an example. The example data I've used aren't ideal (for one thing they're in unprojected coordinates), but I think it gets the idea across. 241589 y Apr 7, 2020 · Alternatively, if anyone knows how to extract species names directly form the SpatialPolygonsDataFrame which contains a range polygon for each species, at 0. I want to use coordinates to build the convex hulls to represent the study region. However, since I’m not sure how to extract the polygons id when using gCentroid, I’m not sure how to do the merge (see 3rd line of code below). If you want to transform sp data, use spTransform. tmp[[1 Aug 6, 2021 · I have a SpatialPolygonsDataFrame object with polygon coordinates in meters (UTM). tx <- "~//Texas. How to assign coordinates to a data Nov 27, 2023 · coordinates: set spatial coordinates to create a Spatial object, or coordinates-methods: retrieve (or set) spatial coordinates; coordnames-methods: retrieve or assign coordinate names for classes in sp; CRS-class: Class "CRS" of coordinate reference system arguments; degaxis: axis with degrees; dimensions: retrieve spatial dimensions from Jan 14, 2016 · Unfortunately with sp you need to manually convert between arrays of coordinates and data. exact_extract extracts the values of cells in a raster that are covered by polygonal features in a simple feature collection ( sf or sfc) or SpatialPolygonDataFrame, as well as the fraction or area of each cell that is covered by the feature. When I try to import the data with raster(), R gives the following error: "Cannot create a RasterLayer object from this file". RDocumentation. I have a SpatialPolygonsDataFrame that contains 9 polygons, each of which also contains multiple nested polygons - the 'holes'. May 22, 2017 · Tour Start here for a quick overview of the site Help Center Detailed answers to any questions you might have Mar 27, 2015 · This method uses the intersect() function from the raster package. rows as A, and a single variable "code" from each intersecting polygon from B. 1. g. passed on to st_sf, might included named arguments crs or precision. , monthly_temperatures <- raster::extract(tmp_month, Italy_map) However, this time it doesn't work because the RasterStack and the SpatialPolygonsDataFrame use different coordinate systems. Then proceed: Transform to metric coordinate system: The next few lines of output give us the layer’s bounding extent in the layer’s native coordinate system units. I found an example on how to get a list of the polygons with an area above the threshold (where burned_poly is the large SpatialPolygonsDataFrame): May 2, 2019 · In GeoXp: Interactive Exploratory Spatial Data Analysis. x = "SpatialPoints", y = "SpatialPolygons" returns a numeric vector of length equal to the number of points; the number is the index (number) of the polygon of ‘y’ in which a point falls; NA denotes the point does not fall in a polygon; if a point falls in multiple polygons, the last polygon is recorded. frame with a column called geo. SpatialPointsDataFrame objects are the most basic, whereas SpatialPolygonsDataFrame objects have nesting (as seen above). Share. Because the common spatial packages ( sp, rgdal, and rgeos) use S4 objects to represent spatial data, they do not play nice with the tidyverse packages (which require data frames). object to be converted into an object class sf. You can use a data. Nov 12, 2018 · I am trying to extract summed raster cell values from a single big file for various SpatialPolygonsDataFrames (SPDF) objects in R stored in a list, then add the extracted values to the SPDF objects Aug 25, 2020 · I have a SpatialPolygonsDataFrame which I extract the data columns and transform it into a standard dataframe. ver Apr 13, 2020 · What is the quickest way of cropping (clipping) a complex SpatialPolygonsDataFrame with the @data preserved in R using another, possibly complex, SpatialPolygon? I know of two ways (shown under). Those polygons I assume are the lat lng coordinates around the country. st_union (sf) polygons with data. name or number of the character column that holds WKT encoded geometries. Jul 4, 2020 · I’d like to add the latitude and the longitude of all polygons’ centroids to the dataframe of a SpatialPolygonsDataFrame. Each row of the data frame contains the x and y coordinates of a pixel that lies inside the window. 1) You can convert your sp object to an sf class: New<-st_as_sf (Old) 2) You can retrieve the coordinates with: CoordNew<-st_coordinates (New) CoordNew is a matrix of x,y coordinates. Here is my code. frame(sp@data, df[match(sp@data[,by], df[,by]),]) Here is how the code works. In the empty column (NA filled) in my data frame, labelled BCR, I want to insert the region name which each coordinate falls into according to the shapefile. I'm tring to extract pixels values from raster by intersct with SPDF (SPDF) Object of class SpatialPolygonsDataFrame Coordinates: min max x -73. Aug 21, 2019 · 1. First, you take the columns of lon and lat and create an object for coord. You can get a list with the x,y coordinates: vertices(x) edited Nov 27, 2014 at 23:16. Use extract or rasterize instead. As you can see, at coarser Jan 4, 2020 · Now I want to remove all the polygons with an area below a certain threshold value. The coordinates of each polygon are extracted and concatenated into one long data frame. However, I cannot find a way to subset the large SpatialPolygonsDataFrame. edu> writes: > > try > > tmp<- slot(ex_1. I want to split a single spatialPolygonsDataFrame row that consists of multiple polygon geometries, and I'm not sure about the most sensible way to achieve this. This R code is a little messy because I show the results of many steps and includes several dead ends: Just a short remark to the extract function from raster package when you work with lat and lon values - use SpatialPoints: x<- 44. You can extract the extent via the st_bbox() function as in st_bbox(s. There's no need to convert the raster to a polygon and then run a centroid algorithm. The SpatialPolygonsDataFrame was obtained through getData('GADM', country='ITA', level=3) of rgeos. How could I extract the data of a polygon shape Nov 18, 2017 · How do I extract a dataframe with the columns . For example if we want to remove Alaska from usa below here, we could filter out polygons with centroid over 50 degrees latitude. I'll eventually be refining the convex hull I create in the code above to better define the species distributions. 8386 y<- 0. na(over(d, plgn)) returns a logical matrix. Oct 20, 2023 · Each row of the data frame corresponds to one pixel. I would like to grab the coordinates that are inside each list and create two points. shp file. The function spdf2list() calculates the middle coordinates of boundary box and in the case where polygons are included into a SpatialPolygonsDataFrame object, it extracts the vertices of the polygons, seperating polygons from each other by Occasionally you may have to change the coordinates of your spatial object into a new Coordinate Reference System (CRS). frame(st_coordinates(df)) This new 'centres' dataframe has the lat&long values, but misses the ID column. in case of point data: names or numbers of the numeric columns holding coordinates. Dec 11, 2017 · The first step was joining my SpatialPoints with a SpatialPolygonsDataFrame using over() of rgeos. These classes hold a C++ pointer to the data "reference class" and that creates some limitations. 8. create("tempdir") writeOGR(obj=states, dsn="tempdir", layer="states", driver="ESRI Shapefile") The shapes are now saved to the directory ~/scratch/tempdir, as files states. answered Nov 27, 2014 at 6:49. Could I send you the shapefile of my polygons ? – Not in terms of speed I guess. In this column, there are lists with coordinates that used to represent bounding boxes. You can then merge the data frame into the sp object using the following line of code. I'm trying to create a shape of points in R. shp, etc. Jun 28, 2018 · library(sf) out <- st_intersection(p, li) I get the error Error in UseMethod("st_intersection") : no applicable method for 'st_intersection' applied to an object of class "c('SpatialPointsDataFrame', 'SpatialPoints', 'Spatial', 'SpatialVector')" Not all points intersect with the polygon shape. All the data have the same attributes, just different IDs and areas. 49. I don't know what to do to change the coordinates of the islands. I cannot find the problems. R_Extracting coordinates from Apr 22, 2017 · You can use function raster::extract. I have the following code in ggplot2 for turning a SpatialPolygon into a regular data frame of coordinates. You need to assign this data with its correct CRS string, which is probably something like lat-long in the WGS84 system, ie "+init=epsg:4326". hm vd lp ne vz wb pw jg av wm