haotu : an open lab notebook

2017/07/18

Make ggplot look like base plot in R

Filed under: ggplot, R, R graphics — Tags: , , , , , , — S @ 04:46
myplot + theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))
myplot + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))

here

 

 

 

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2017/06/22

Automatic MIT License for R Packages

Filed under: errors in R, R, R Stats — Tags: , — S @ 07:01
devtools::use_mit_license()

2016/10/28

The relationship between VIF and R2 (r squared)

Filed under: Math and Stats, R, R Stats — Tags: , , — S @ 09:08

Variance Inflation Factor (VIF) is a common simple stat used to quantify multicollinearity in least squares regressions. It is calculated for each covariate in a regression, with higher values meaning that the covariate is more colinear with the other covariates. It technically measures “how much the variance (the square of the estimate’s standard deviation) of an estimated regression coefficient is increased because of collinearity.” The equation is:

{\displaystyle \mathrm {VIF_{i}} ={\frac {1}{1-R_{i}^{2}}}}

where R2i is from the regression of the covariate i on all the other covariates. The problem is where to draw the cutoff? Is a VIF > 2.5 too high? >5? or how about VIF>10, all have been used as cutoffs. Here is a figure of R2 vs VIF. As you can see, a cuttoff of 2.5 is an R2 of 0.60 and 10 is 0.90! While statistically, you could perhaps get away with these high inflations, what does it mean for your particular question? If you are dealing with a relationship among covariates that is as strong as 0.90, can you really be sure that the model and your interpretations are valid?

rplot

 

 

#VIF function
r<-function(x){1-(1/x)} #r is R2 and x is VIF
x<-seq(1,15,.1) #seq of VIFs
y<-sapply(x,r) #seq of R2
#plot
par(las=1)
plot(x,y,type="l",xlab="VIF",ylab="R2 of regression of focal covariate on all other covariates")
# common VIF cutoffs = 2.5, 5, 10
ly<-c(y[x==2.5],y[x==5],y[x==10])
lx<-c(2.5,5,10)
segments(lx,0,lx,ly,col="red")
segments(lx,ly,0,ly,col="red")

2016/07/14

aggregate by removing NA

Filed under: Manipulate Data in R, R, R Stats, Uncategorized — Tags: — S @ 08:43
na.collapse<-function(x)
{
 x.<-unique(x[!is.na(x)])
   if(length(x.)==0)
 {
   return(NA)
   } else {
     if(length(x.)==1){
     return(x.)
   } else {
     return(paste(x.,collapse="|"))
   }
  }
}
na.collapse(x)

2016/06/24

save rda data file with compression

Filed under: errors in R, R, R, R Stats — Tags: , , , , — S @ 06:36
save(mydata,file="mydata.rda",compress="xz")

find non-ascii in R

Filed under: errors in R, R, R, R Stats, Uncategorized — Tags: , , , , — S @ 06:34
tools::showNonASCII(readLines("myfiles.R"))

2016/04/25

assign nearest point to a polygon

Filed under: R, R spatial, R Stats, Uncategorized — S @ 11:31

 

wer<-SpatialPointsDataFrame(data.frame(x.subset[,"longitude"],x.subset[,"latitude"]),data=data.frame(x.subset))
n <- length(wer)
nearest <- character(n)
for (i in seq_along(nearest)) {
 nearest[i] <- names(polys)[which.min(gDistance(wer[i,], polys, byid=TRUE))]
}

This may give you warnings if your code is not projected into a planar coordinate system

http://stackoverflow.com/questions/26308426/how-do-i-find-the-polygon-nearest-to-a-point-in-r

2016/04/22

add unique id to duplicated grouped rows

Filed under: Manipulate Data in R, R, R, Uncategorized — S @ 12:30
library(plyr)
id(x)

2016/04/19

get latitude longitude raster cells

Filed under: R, R graphics, R spatial, Uncategorized — S @ 07:46
rasterToPoints(stacked) #this also gives the cell values of the raster layer or layers

http://gis.stackexchange.com/questions/142156/r-how-to-get-latitudes-and-longitudes-from-a-rasterlayer

 

 

number of layers in raster stack

Filed under: R, R graphics, R spatial, R Stats, Uncategorized — S @ 07:08
dimension(stacked)[3]
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