All Questions
Tagged with euclidean-distance r
186
questions
10
votes
4
answers
56k
views
How to calculate Euclidian distance between two points defined by matrix containing x, y?
I am very lost in Euclidean distance calculation. I have found functions dist2{SpatialTools} or rdist{fields} to do this, but they doesn´t work as expected.
I suppose that one point has two ...
- 3,980
8
votes
2
answers
8k
views
calculating the euclidean dist between each row of a dataframe with all other rows in another dataframe
I need to generate a dataframe with minimum euclidean distance between each row of a dataframe and all other rows of another dataframe.Both my dataframes are large (approx 40,000 rows).This is what I ...
- 105
6
votes
2
answers
9k
views
Creating a distance matrix from a list of coordinates in R
I have a csv file with a list of co-ordinate positions for over 2000 farms, with the following structure;
FarmID | Latidue | Longitude |
------ |---------|-----------|
1 | y1 | x1 ...
- 83
6
votes
2
answers
5k
views
R - How to get row & column subscripts of matched elements from a distance matrix
I have an integer vector vec1 and I am generating a distant matrix using dist function. I want to get the coordinates (row and column) of element of certain value in the distance matrix. Essentially I ...
- 533
6
votes
1
answer
966
views
trying to draw circles based on distance between points
I'm trying to draw some circles and I was sort of hoping they would intersect with some points, alas...
library(maptools)
library(plotrix)
xy <- matrix(runif(20, min = -100, max = 100), ncol = 2)
...
- 70.1k
6
votes
1
answer
6k
views
Weighted Euclidean Distance in R
I'd like to create a distance-matrix with weighted euclidean distances from a data frame. The weights will be defined in a vector. Here's an example:
library("cluster")
a <- c(1,2,3,4,5)
b <- ...
- 355
6
votes
2
answers
95
views
Efficiently accessing pairwise distances
I have a distance matrix:
> mat
hydrogen helium lithium beryllium boron
hydrogen 0.000000 2.065564 3.940308 2.647510 2.671674
helium 2.065564 0.000000 2.365661 1.697749 1....
- 63
5
votes
2
answers
4k
views
Distance matrix from two separate data frames
I'd like to create a matrix which contains the euclidean distances of the rows from one data frame versus the rows from another. For example, say I have the following data frames:
a <- c(1,2,3,4,5)...
- 355
5
votes
1
answer
3k
views
Finding euclidean distance in R{spatstat} between points, confined by an irregular polygon window
I'm trying to find the euclidean distance between two points, confined by an irregular polygon. (ie. the distance would have to be calculated as a route through the window given)
Here is an ...
- 1,012
5
votes
1
answer
2k
views
What is the complexity of dist()?
I used the dist function in R and I am wondering the time complexity of it.
I know that the hierarchical clustering has a N^2*logN time complexity. And hierarchical clustering is composed of two ...
- 1,217
5
votes
2
answers
3k
views
r distance between rows
I apologize this is my attempt at redeeming myself after a disastrous earlier attempt . Now I have a bit more clarity. So here I go again.
My goal is to find rows that are similar. So first I am ...
- 413
4
votes
4
answers
1k
views
(Speed Challenge) Any faster method to calculate distance matrix between rows of two matrices, in terms of Euclidean distance?
First of all, this is NOT the problem of calculating Euclidean distance between two matrices.
Assuming I have two matrices x and y, e.g.,
set.seed(1)
x <- matrix(rnorm(15), ncol=5)
y <- matrix(...
- 89.5k
4
votes
1
answer
131
views
Wrong Euclidean distance H2O calculations R
I am using H2O with R to calculate the euclidean distance between 2 data.frames:
set.seed(121)
#create the data
df1<-data.frame(matrix(rnorm(1000),ncol=10))
df2<-data.frame(matrix(rnorm(300),...
- 462
3
votes
4
answers
881
views
Pairwise weighted distance vectorization
The following efficient and vectorized Matlab code computes the Weighted Euclidean Distance between 2 sets of points A and B using a weight vector WTS (1 weight for each dimension; same weights for ...
- 4,213
3
votes
2
answers
956
views
Computing Euclidean distances between subsequent positions
I have large data frames consisting of pairs of X and Y coordinates, and wish to calculate the Euclidean distances between consecutive coordinates (minimal size is around 2000 pairs of coordinates).
...
- 300
3
votes
1
answer
6k
views
Distance between two sets of points [duplicate]
So after looking at various Questions asked here on stackoverflow I'm still not able to wrap my head around the dist function in R or maybe even a distance matrix in general.
So I have two dataframes ...
- 433
3
votes
2
answers
430
views
R: calculate Euclidean distance between two raster layers pixels
I have two raster layers for same area. I need to find the Euclidean distance between cell of coarse resolution raster and cell of fine resolution raster that fall within each cell of the pixels from ...
- 440
3
votes
1
answer
108
views
How can I generate n points with euclidan distance less than d from X
Let's say I have a point:
point <- c(1, 2)
How can I generate 10 points with euclidan distance from point lower than some choosen value, e.g. 3.
In other words: how can I generate set of points in ...
- 826
3
votes
3
answers
2k
views
euclidean distance between vectors grouped by other variable in SPSS, R or Excel
I have a dataset containing something like this:
case,group,val1,val2,val3,val4
1,1,3,5,6,8
2,1,2,7,5,4
3,2,1,3,6,8
4,2,5,4,3,7
5,1,8,6,5,3
I'm trying to compute programmatically the Euclidean ...
- 91
3
votes
2
answers
978
views
R, compute the smallest Euclidean Distance for two dataset, and label it automatically
I'm working with Euclidean Distance with a pair of dataset.
First of all, my data.
centers <- data.frame(x_ce = c(300,180,450,500),
y_ce = c(23,15,10,20),
...
- 9,395
3
votes
2
answers
3k
views
5 nearest neighbors based on given distance in r
I have the following dataset:
id x y age
1 1745353 930284.1 30
2 1745317 930343.4 23
3 1745201 930433.9 10
4 1745351 930309.4 5
5 1745342 930335.2 2
6 ...
- 167
3
votes
1
answer
3k
views
Calculate euclidean distance in a faster way
I want to calculate the euclidean distances between rows of a dataframe with 30.000 observations. A simple way to do this is the dist function (e.g., dist(data)). However, since my dataframe is large, ...
- 2,077
3
votes
1
answer
947
views
How to use apply function to calculate the distance between two matrices
I'm trying to calculate the euclidean distance between two matrices. I have already achieved that using 2 for loops but trying to vectorize the calculation to speed up. I'm using pdist as a benchmark ...
- 59
3
votes
2
answers
522
views
How to pull points that are within a certain distance away in R?
I have a parameter space given by (x,y) with x values from 1:5 and y values from 1:8. Let's say my current point p is located at (2,5) (it is colored in red). My goal is to try to pull all the points ...
- 1,341
3
votes
1
answer
2k
views
Euclidean distance in R using two variables in a matrix
I am quite new to R and I am trying to compute the gross distance (or the sum of the Euclidean distance on all data points) from two variables in my matrix and net distance (Euclidean distance between ...
- 359
2
votes
3
answers
2k
views
How to calculate Euclidean distance in R for n-dimensions?
I'm trying to write a function which calculates Euclidean distance between two points across n-dimensions.
I have the following code:
euc_dist <- function(x1, x2) sqrt(sum((x1 - x2) ^ 2))
This ...
- 91
2
votes
1
answer
4k
views
Distance between two 3D points in R
I have two 2 points A(x,y,z) e B(x1,y1,z1).
I want to calculate the euclidean distance between these point at time1, time2, time3.
So, I have a matrix like this:
x y z x1 y1 ...
- 109
2
votes
5
answers
3k
views
Calculate Euclidean distances between all rows in matrices A and B
I have two matrices, A and B, with N_a and N_b rows, respectively. I need to calculate the Euclidean distance between all pairwise combinations of an element in A (a) and another in B (b), such that ...
2
votes
2
answers
1k
views
R User-defined function works alone but returns incorrect values when used with apply
The user defined function (dist.func) runs and provides the correct output when I use it on a single line of data but does not provide the correct output (still executes) when I embed it into the ...
- 617
2
votes
2
answers
344
views
How to improve processing time for euclidean distance calculation
I'm trying to calculate the weighted euclidean distance (squared) between twoo data frames that have the same number of columns (variables) and different number of rows (observations).
The ...
- 43
2
votes
2
answers
214
views
Automating (loops) Euclidean distance measurements in R
AIM: I want to automate (loop) the code below, without having to manually run it for each sample. I have a terrible habit of writing long-hand in base, and need to start using loops, which I find ...
- 23
2
votes
2
answers
95
views
Loop on a data frame with considering the types of the values
I have a large data set of coordinates and I want to calculate the Euclidean distance among them. The sample of that would be like this:
df <- data.frame("name" = c("a","b","c","a","e"), "type" = ...
- 565
2
votes
1
answer
1k
views
R: results differ when calculating Euclidean distance between two vectors with different methods
Suppose that I have two vectors.
x1 = c(-1, 2, 3)
x2 = c(4, 0, -3)
To calculate the Euclidean distance, I used three different ways
1- The built function norm
s = cbind(x1, x2)
norm(s, "2")
#[1] 5....
- 299
2
votes
3
answers
82
views
Euclidean distant for NON-CONSECUTIVE classes of factors iterated by groups
This question is an extension of this question.
Euclidean distant for distinct classes of factors iterated by groups
The same explanations from the previous question apply here as well. I want to ...
- 521
2
votes
1
answer
448
views
Calculate Euclidean distance between points with rolling function in data.table
I have a data.table with transects in different areas, coordinates x and y are projected as UTM 36S.
How can I calculate the (Euclidean) distance between consecutive points with data.table, per area, ...
- 3,656
2
votes
1
answer
83
views
Permutation of euclidean distances between 13 row indexes in R
I have 13 Area of Interests (AOIs) with x and y values for each test image. How can I get all possible combination of euclidian distance between pairs of AOIs, ((x-xi)+(y-yi))^(1/2)? Ultimately I am ...
- 33
2
votes
1
answer
403
views
How to select n objects from a set of N objects, maximizing the sum of pairwise distances between them
You have a set of N=400 objects, each having its own coordinates in a, say, 19-dimensional space.
You calculate the (Euclidean) distance matrix (all pairwise distances).
Now you want to select n=50 ...
- 595
2
votes
1
answer
46
views
Distance matrix to reshaped vector of distances sorted by positions
I have a data frame of 5 items, as follows:
df = structure(list(item1 = c(1, 1, 1, 1, 2, 2, 2, 3, 3, 4), item2 = c(0,
2, 3, 4, 0, 3, 4, 0, 4, 0)), row.names = c(NA, -10L), class = c("tbl_df",
"tbl",...
- 2,443
2
votes
1
answer
898
views
Compute the Euclidean distances between corresponding rows of 2 matrices
I have 2 matrices A and B, and I want to compute the Euclidean distances between 1st row of A and 1st row of B, 2nd row of A and 2nd row of B, etc. I know I can use rdist function to compute the ...
- 1,076
2
votes
4
answers
5k
views
Find shortest distance between multiple points
Imagine a small dataset of xy coordinates. These points are grouped by a variable called indexR, there are 3 groups in total. All xy coordinates are in the same units. The data looks approximately ...
- 419
2
votes
1
answer
2k
views
Calculate Rao's quadratic entropy
Rao QE is a weighted Euclidian distance matrix. I have the vectors for the elements of the d_ijs in a data table dt, one column per element (say there are x of them). p is the final column. nrow = S. ...
- 2,456
2
votes
2
answers
1k
views
Find which points are within a given distance of each point
I have a dataframe that has a list of places and their geographical locations in UTM (Universal Transverse Mercator) coordinates.
It looks something like this:
Place X_UTM Y_UTM
1 574262.0 ...
2
votes
1
answer
50
views
Calculate distance with multiple starting coordinates
I calculated the travelled distance called distance_m per date with the function points_in_circle for two ID's called HEX_Tag_ID. The coordinates that I put in the function are based on the Datum &...
- 321
2
votes
1
answer
438
views
Calculating two dimensions Euclidean distance and adding it as a column in the data
I need to create a variable that measures distance from APP.
The center of APP is at the coordinates 1440000 east, 12160000 north.
I need to make a new column calculating the euclidean distance ...
- 95
2
votes
1
answer
148
views
Euclidean distant for distinct classes of factors iterated by groups
*Update: The answer suggested by Rui is great and works as it should. However, when I run it on about 7 million observations (my actual dataset), R gets stuck in a computational block (I'm using a ...
- 521
2
votes
1
answer
172
views
Calculate distances between a line and all points on an intersecting plane in r
I have a regular, rectangular grid of x, y, z values (an image).
I also have an x, y, z line that intersects the grid.
For each plane (z-level) in the grid, I want to compute the Euclidean distance ...
- 2,650
2
votes
1
answer
205
views
What is dist() actually computing?
I have a data frame, tmp:
class x y
1 A -2.8959969 -0.3192259
2 B -0.2401775 0.5801373
I compute dist(tmp, method="euclidean", diag=TRUE, upper=FALSE, p=2) which yields :
...
- 4,871
2
votes
1
answer
2k
views
Get maximum distance between points in a vector (R)
I have two vectors of latitudes and longitudes. I would like to find the maximum distance between the points. The way I see it, I should get a matrix of distances between all points and get the max of ...
- 2,280
2
votes
1
answer
192
views
Unique combinations by group
I have the following data frame structured in terms of 3 variables, i.e Location, Latitude, and Longitude within every single group. I would like to calculate the euclidean distance between all unique ...
- 21
2
votes
0
answers
154
views
Interactive visualization of Euclidean distance with R
I would like to know if there is any way to visualize in an interactive way the process of euclidean distance with R. In a few words to recreate the plot below with a package that permits interactive ...
- 8,034