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R for Macroecology Spatial models. Next week  Any topics that we haven’t talked about?  Group projects.

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Presentation on theme: "R for Macroecology Spatial models. Next week  Any topics that we haven’t talked about?  Group projects."— Presentation transcript:

1 R for Macroecology Spatial models

2 Next week  Any topics that we haven’t talked about?  Group projects

3 SAR Models  Augment standard OLS with an additional term to model the spatial autocorrelation  We’ll focus on error SAR models, which focuses on spatial pattern in the error part of the model OLSY = β X + ε SAR lag Y = ρ WY + β X + ε SAR error Y = β X + λ Wu+ ε Defining the spatial weights matrix, W, is crucial

4 Neighborhoods in R  spdep  dnearneigh()  knearneigh() dnearneigh(x, d1, d2, row.names = NULL, longlat = NULL) Coordinates (matrix or SpatialPoints) Minimum and maximum distances (in km if longlat = T) Returns a list of vectors giving the neighbors for each point

5 Neighborhoods in R  spdep  dnearneigh()  knearneigh() > x = c(1,3,2,5) > y = c(3,2,4,4) > n = dnearneigh(cbind(x,y),d1 = 0,d2 = 3) > n Neighbour list object: Number of regions: 4 Number of nonzero links: 10 Percentage nonzero weights: 62.5 Average number of links: 2.5 > str(n) List of 4 $ : int [1:2] 2 3 $ : int [1:3] $ : int [1:3] $ : int [1:2] attr(*, "class")= chr "nb" - attr(*, "nbtype")= chr "distance”...

6 Converting a neighborhood to weights nb2listw(neighbours, style="W", zero.policy=NULL) neighbors listwhat to do with neighborless points W = row standardized (rows sum to 1) B = binary (0/1) C = global standardized (all links sum to n) U = C/n S = variance stabilization (Tiefelsdorf et al. 1999)

7 Converting a neighborhood to weights > nb2listw(n,style = "W")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1] > nb2listw(n,style = "B")$weights [[1]] [1] 1 1 [[2]] [1] [[3]] [1] [[4]] [1] 1 1 > nb2listw(n,style = "C")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1] > > nb2listw(n,style = "S")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1]

8 Converting a neighborhood to weights > nb2listw(n,style = "W")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1] > nb2listw(n,style = "B")$weights [[1]] [1] 1 1 [[2]] [1] [[3]] [1] [[4]] [1] 1 1 > nb2listw(n,style = "C")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1] > nb2listw(n,style = "S")$weights [[1]] [1] [[2]] [1] [[3]] [1] [[4]] [1] Emphasizes weakly connected points Emphasizes strongly connected points Tries to balance

9 Lots of options – how to choose?  Define the neighborhood  Define the spatial weights matrix  Try things out!  Look for stability in model estimates  Look for residual autocorrelation

10 Defining the neighborhood - d #1. Small distance n = dnearneigh(cbind(x,y),d1 = 0, d2 = 0.1) w1 = nb2listw(n,zero.policy = T) #2. Medium distance n = dnearneigh(cbind(x,y),d1 = 0, d2 = 0.3) w2 = nb2listw(n,zero.policy = T) #2. Large distance n = dnearneigh(cbind(x,y),d1 = 0, d2 = 0.5) w3 = nb2listw(n,zero.policy = T) par(mfrow = c(1,4)) plot(x,y,axes = F,xlab = "",ylab = "") plot(w1,cbind(x,y)) plot(w2,cbind(x,y)) plot(w3,cbind(x,y))

11 Defining the neighborhood - K #4. 2 neighbors n = knn2nb(knearneigh(cbind(x,y),k=2,RANN = F)) w4 = nb2listw(n,zero.policy = T) #5. 4 neighbors n = knn2nb(knearneigh(cbind(x,y),k=4,RANN = F)) w5 = nb2listw(n,zero.policy = T) #6. 8 neighbors n = knn2nb(knearneigh(cbind(x,y),k=8,RANN = F)) w6 = nb2listw(n,zero.policy = T) par(mfrow = c(1,4)) plot(x,y,axes = F,xlab = "",ylab = "") plot(w4,cbind(x,y)) plot(w5,cbind(x,y)) plot(w6,cbind(x,y))

12 Neighborhoods on grids x = rep(1:20,20) y = rep(1:20,each = 20) plot(x,y) n = dnearneigh(cbind(x,y),d1=0,d2 = 1) w = nb2listw(n) plot(w,cbind(x,y)) n = dnearneigh(cbind(x,y),d1=0,d2 = sqrt(2)) w = nb2listw(n) plot(w,cbind(x,y)) Rook’s caseQueen’s case

13 Data size  SAR models can take a very long time to fit  2000 points is the maximum I have used  sample() is useful again

14 Fitting the SAR model  errorsarlm() errorsarlm(formula, listw, zero.policy=NULL) just like lm()what to do with neighborless points The neighborhood weights

15 Try it out  Build several SAR models with different W  Which one works best?

16 Spatial eigenvector maps  Generate new predictors that represent the spatial structure of the data  Three steps  Calculate a pairwise distance matrix  Do a principal components analysis on this matrix  Select some of these PCA axes to add to an OLS model

17 Spatial eigenvector maps Diniz-Filho and Bini 2005

18 Filter 1Filter 2 Filter 3Filter 4

19 Filter 10 Filter 20 Filter 30Filter 40


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