[R] subsetting to exclude different values for each subject in study

arun smartpink111 at yahoo.com
Tue May 27 15:43:19 CEST 2014


Hi Monaly,

According to the description of ?tri2nb
The function uses the ‘deldir’ package to convert a matrix of
     two-dimensional coordinates into a neighbours list of class ‘nb’
     with a list of integer vectors containing neighbour region number
     ids.


So, col.tri.nb is a list of length 76. 

 str(col.tri.nb)
List of 76
 $ : int [1:6] 11 26 33 46 57 75
 $ : int [1:6] 27 31 36 42 70 75
---------------------------

 lst1 <- lapply(col.tri.nb,function(x) ind[x]) 
 lst1[1:5] #returns 1st five elements
##Regarding the last piece of code:
#Check the output of

res <- sapply(seq_along(col.tri.nb), function(i) {
    ind1 <- as.character(ind[i])
    ind2 <- as.character(ind[col.tri.nb[[i]]])
    XOind1 <- XO[1, ind1]
    XOind2 <- XO[1, ind2]
    cat(" list element=", i, "\n", " NestkastNummer=", ind1, "\n", " Neighbouring NestkastNummer=", 
        ind2, "\n", " EBScore=", XOind1, "\n", " EBScore Neighbour element=", XOind2, 
        "\n", " avg=", mean(abs(XOind1 - XOind2)), sep = " ", "\n")
    mean(abs(XOind1 - XOind2))
})



A.K.




On Tuesday, May 27, 2014 7:20 AM, Monaly Mistry <monaly.mistry at gmail.com> wrote:



Hi Arun,

Thank you for your help,  I have a few questions though if you don't mind. I'm a bit confused about the following 2 lines of code:
col.tri.nb <- tri2nb(coords, row.names=ind)
 lapply(col.tri.nb,function(x) ind[x])[1:5]

## from what I understand in the first line determines the neighbouring individuals, while in the second line it calls for the output of neighbours for the first 5 individuals.
Also for the last line of code that you resent I don't really understand what it is running?

Best,

Monaly.



On Sat, May 24, 2014 at 2:41 AM, arun <smartpink111 at yahoo.com> wrote:

Hi,
>Sorry, there is a mistake. XO[2,] should be:
>XO[2,] <-  sapply(seq_along(col.tri.nb), function(i){ind1 <- as.character(ind[i]); ind2 <- as.character(ind[col.tri.nb[[i]]]); mean(abs(XO[1,ind1]-XO[1,ind2]))} )
>A.K.
>
>
>
>
>
>
>
>On Friday, May 23, 2014 12:56 PM, arun <smartpink111 at yahoo.com> wrote:
>
>Hi Monaly,
>May be this helps:
>b<- 77:99
>ao1 <- ao[-b,]
>##Your code:
>
>XO<- matrix( 0,6, 76, byrow=TRUE);XO
>abo<-ao$NestkastNummer[-b];abo  #removed values that were NA
>rownames(XO) = c("EB_score","avg","pop_size","pop_avg_score",
>"adj_pop_avg", "ind_pop_dif")
>colnames(XO) = abo
>t <- ao$COR_LOC;t
>i <- c(77:99)
>ti <- t[-i];ti
>XO[1,] = c(ti);XO
> 
>
>library(deldir)
>library(spdep)
>mat <- cbind(lat=ao1$lat_xm, long=ao1$long_ym)
>library(spdep)
> coords <- coordinates(mat)
>ind <- ao1$NestkastNummer
>
>col.tri.nb <- tri2nb(coords, row.names=ind)
> lapply(col.tri.nb,function(x) ind[x])[1:5] ###
>[[1]]
>[1] 713 715 162 148 140 117
>
>[[2]]
>[1] 130 128 172  64 113 117
>
>[[3]]
>[1] 54 19 16 73 74
>
>[[4]]
>[1]   2  31 704  34 707
>
>[[5]]
>[1] 51 94 57 73 62
>
>XO[2,] <- sapply(seq_along(col.tri.nb),function(i) mean(abs(ind[i]-ind[col.tri.nb[[i]]])))
>
>A.K.
>
>
>
>On Friday, May 23, 2014 7:17 AM, Monaly Mistry <monaly.mistry at gmail.com> wrote:
>
>
>
>Hi Arun and Frede,
>
>So the dput() is below (it's the same data file as before), but below that is the code I used to make the tessellation.  Thanks for your help.
>
>> dput(ao)
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>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
>23.57103359, 23.57103359)), .Names = c("num", "FORM_CHK", "RingNummerMan", 
>"year_score_taken", "COR_LOC", "IndividuID", "BroedJaar", "ManipulatieOuders", 
>"LegBeginDag", "LegBeginMaand", "broodinfo", "BroedselID", "NestkastNummer", 
>"lat_xm", "long_ym", "avg_pop_eb"), class = "data.frame", row.names = c(NA, 
>-99L))
>
>
>#Code for  tessellation
>library(deldir)
>
>ao= read.table("C:/Users/Monaly/Desktop/2012_malenest.txt", header=TRUE)
>
>a29= deldir(ao$lat_xm, ao$long_ym)
>
>a30=tile.list(a29)
>
>plot(a30, close=TRUE, main="2012 Male Nest", xlab="latitude (m)", ylab="longitude (m)", wpoints="real", verbose=FALSE,num=TRUE, rw=c(0, 1200, 0, 2000))
>
>text(ao$lat_xm, ao$long_ym,col=c(2,1,4),labels=round(ao$NestkastNummer, 3), pos=2, offset=0.2, cex=0.7)  #this was to identify the points
>



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