Toni — Apr 25, 2013, 7:37 PM
library(knitr)
#ny <- (file.choose())
library(spdep)
Loading required package: sp
Warning: package 'sp' was built under R version 2.15.3
Loading required package: boot
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'lattice'
The following object(s) are masked from 'package:boot':
melanoma
Loading required package: MASS
Loading required package: nlme
Loading required package: maptools
Loading required package: foreign
Loading required package: grid
Checking rgeos availability: FALSE Note: when rgeos is not available,
polygon geometry computations in maptools depend on gpclib, which has a
restricted licence. It is disabled by default; to enable gpclib, type
gpclibPermit()
Loading required package: deldir
deldir 0.0-21
Loading required package: coda
Loading required package: splines
library(sp)
summary(ny)
Error: error in evaluating the argument 'object' in selecting a method for
function 'summary': Error: object 'ny' not found
plot(ny)
Error: error in evaluating the argument 'x' in selecting a method for
function 'plot': Error: object 'ny' not found
leuk <- lm(ny$CASES~ny$PEXPOSURE+ny$PCTAGE65P+ny$PCTOWNHOME)
Error: object 'ny' not found
plot(leuk)
#lm.LMtests(leuk) this needs weights. doesn't work here.
leuk2 <- lm(ny$CASES~ny$PCTAGE65P+ny$PCTOWNHOME)
Error: object 'ny' not found
summary(leuk) #pexosure is not significant!
wbc ag time
Min. : 750 absent :16 Min. : 1.0
1st Qu.: 5300 present:17 1st Qu.: 4.0
Median : 10500 Median : 22.0
Mean : 29165 Mean : 40.9
3rd Qu.: 32000 3rd Qu.: 65.0
Max. :100000 Max. :156.0
summary(leuk2)
Error: error in evaluating the argument 'object' in selecting a method for
function 'summary': Error: object 'leuk2' not found
anova(leuk, leuk2) #the difference is not significant
Error: no applicable method for 'anova' applied to an object of class
"data.frame"
expos<-lm(ny$CASES~ny$PEXPOSURE)
Error: object 'ny' not found
summary(expos) #this is significant
Error: error in evaluating the argument 'object' in selecting a method for
function 'summary': Error: object 'expos' not found
anova(leuk, expos)
Error: no applicable method for 'anova' applied to an object of class
"data.frame"
plot(ny$CASES, ny$PEXPOSURE, main="Scatterplot of Leukemia Cases and Exposure to TCE",
xlab="Proximity to Waste Site", ylab="Number of Cases")
Error: error in evaluating the argument 'x' in selecting a method for
function 'plot': Error: object 'ny' not found
abline(lm(ny$CASES~ny$PEXPOSURE))
Error: object 'ny' not found
plot(expos)
Error: error in evaluating the argument 'x' in selecting a method for
function 'plot': Error: object 'expos' not found
shapiro.test(ny$CASES)
Error: object 'ny' not found
ny$lmresid<-residuals(leuk)
Error: object 'ny' not found
shapiro.test(ny$CASES) #significant p=1.039e-10
Error: object 'ny' not found
coefficients(leuk)
NULL
step<-stepAIC(leuk, direction="both")
Error: no terms component nor attribute
#6.2.1 Running a Regression
#• using lm with a “formula,” y ∼ x1 + x2
#• assigning the regression results to an object
#• extracting the residuals as resid(regressionObject)
#6.2.2 Testing OLS Residuals for Spatial Autocorrelation
#• Moran test for residuals using lm.morantest
#• parameters: a regression object and a listw object
#• Lagrange Multiplier tests using lm.LMtests
#• parameters: a regression object, listw object and the type of test
#step 1
ny_nbq<-poly2nb(ny)
Error: object 'ny' not found
#step 2 assign weights
ny_nbqw<-nb2listw(ny_nbq) #row standardized weights matrix
Error: object 'ny_nbq' not found
ny_nbqwb<-nb2listw(ny_nbq, style="B") #binary weights
Error: object 'ny_nbq' not found
ny_nbqw
Error: object 'ny_nbqw' not found
#step 3 examine autocorrelation
#moran's I
leuk #the regression coefficient IS the Moran's I
wbc ag time
1 2300 present 65
2 750 present 156
3 4300 present 100
4 2600 present 134
5 6000 present 16
6 10500 present 108
7 10000 present 121
8 17000 present 4
9 5400 present 39
10 7000 present 143
11 9400 present 56
12 32000 present 26
13 35000 present 22
14 100000 present 1
15 100000 present 1
16 52000 present 5
17 100000 present 65
18 4400 absent 56
19 3000 absent 65
20 4000 absent 17
21 1500 absent 7
22 9000 absent 16
23 5300 absent 22
24 10000 absent 3
25 19000 absent 4
26 27000 absent 2
27 28000 absent 3
28 31000 absent 8
29 26000 absent 4
30 21000 absent 3
31 79000 absent 30
32 100000 absent 4
33 100000 absent 43
moran.test(leuk, ny_nbqw) #except that moran's I can't run on a MODEl, only on a variable
Error: object 'ny_nbqw' not found
coords <- coordinates(ny)
Error: error in evaluating the argument 'obj' in selecting a method for
function 'coordinates': Error: object 'ny' not found
FIPS <- row.names(as(ny, "data.frame")) # Define the fips code so that I can use K nearest neighbors
Error: object 'ny' not found
lk_kn1 <- knn2nb(knearneigh(coords, k = 1), row.names = FIPS)
Error: object 'coords' not found
lk_kn1_w <- nb2listw(lk_kn1, zero.policy = T)
Error: object 'lk_kn1' not found
#data$lmresid2 <- residuals(pov_lm) ny$lmresid
lm.morantest(leuk2, lk_kn1_w) # moran I=.9152 p=.18
Error: object 'lk_kn1_w' not found
moran.test(ny$CASES, listw = ny_nbqwb, zero.policy = T) #moran=5.9487 p=1.352e-09
Error: object 'ny_nbqwb' not found
#moran's I on the residuals
ny$resid <-resid(leuk)
Error: object 'ny' not found
plot(moran.mc(ny$resid, ny_nbqw, nsim=999))
Error: error in evaluating the argument 'x' in selecting a method for
function 'plot': Error in inherits(listw, "listw") : object 'ny_nbqw' not
found Calls: moran.mc -> inherits
lm.LMtests(leuk, listw=ny_nbqw, test="all")
Error: object 'ny_nbqw' not found
summary(lm.LMtests(leuk, listw=ny_nbqw, test="all"))
Error: error in evaluating the argument 'object' in selecting a method for
function 'summary': Error in inherits(listw, "listw") : object 'ny_nbqw'
not found Calls: lm.LMtests -> inherits
summary(lm.LMtests(expos, listw=ny_nbqw, test="all"))
Error: error in evaluating the argument 'object' in selecting a method for
function 'summary': Error in lm.LMtests(expos, listw = ny_nbqw, test =
"all") : object 'expos' not found
#lm.morantest(leuk, weights)