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Anthony Darrouzet-Nardi

2004-May-29 20:24 UTC

[R] panel function in a conditioned lattice graphic

I'm trying to use plotting character to encode the variable
"block"
from my dataset in a conditioned lattice graphic (R 1.9.0 on Mac OS 
10.3.3). The data I'm using is the dataframe "dryoutcover" which
is
here (4k):

http://anthony.darrouzet-nardi.net/downloads/dryoutcover.Rdata

The code that generates my graphic almost correctly is as follows:

xyplot(coversage ~ dryout | year,
	data=dryoutcover,
	panel = function(x,y) {
		panel.lmline(x,y)
		one <- dryoutcover$block==1
		two <- dryoutcover$block==2
		thr <- dryoutcover$block==3
		fou <- dryoutcover$block==4
		fiv <- dryoutcover$block==5
		six <- dryoutcover$block==6
		grid.points(x[one], y[one], pch=49)
		grid.points(x[two], y[two], pch=50)
		grid.points(x[thr], y[thr], pch=51)
		grid.points(x[fou], y[fou], pch=52)
		grid.points(x[fiv], y[fiv], pch=53)
		grid.points(x[six], y[six], pch=54)
		}
	)

The only thing wrong is that this does not correctly encode blocks 5 
and 6, which only appear in the third year of the study, 2003 (the 
third panel of the graphic). It instead labels blocks 5 and 6 as 
blocks 1 and 2 as if another year had started over (but on the same 
panel). For example, the point farthest to the right in the third 
panel says "2" when I want it to say "6." When I do not
condition by
year, it correctly displays blocks 5 and 6.

How can I correct this in the conditioned graphic?

Anthony Darrouzet-Nardi

Deepayan Sarkar

2004-May-29 21:33 UTC

head link

[R] panel function in a conditioned lattice graphic

On Saturday 29 May 2004 15:24, Anthony Darrouzet-Nardi
wrote:> I'm trying to use plotting character to encode the variable
"block"
> from my dataset in a conditioned lattice graphic (R 1.9.0 on Mac OS
> 10.3.3). The data I'm using is the dataframe "dryoutcover"
which is
> here (4k):
>
> http://anthony.darrouzet-nardi.net/downloads/dryoutcover.Rdata
>
> The code that generates my graphic almost correctly is as follows:
>
> xyplot(coversage ~ dryout | year,
> 	data=dryoutcover,
> 	panel = function(x,y) {
> 		panel.lmline(x,y)
> 		one <- dryoutcover$block==1
> 		two <- dryoutcover$block==2
> 		thr <- dryoutcover$block==3
> 		fou <- dryoutcover$block==4
> 		fiv <- dryoutcover$block==5
> 		six <- dryoutcover$block==6
> 		grid.points(x[one], y[one], pch=49)
> 		grid.points(x[two], y[two], pch=50)
> 		grid.points(x[thr], y[thr], pch=51)
> 		grid.points(x[fou], y[fou], pch=52)
> 		grid.points(x[fiv], y[fiv], pch=53)
> 		grid.points(x[six], y[six], pch=54)
> 		}
> 	)
>
> The only thing wrong is that this does not correctly encode blocks 5
> and 6, which only appear in the third year of the study, 2003 (the
> third panel of the graphic). It instead labels blocks 5 and 6 as
> blocks 1 and 2 as if another year had started over (but on the same
> panel). For example, the point farthest to the right in the third
> panel says "2" when I want it to say "6." When I do not
condition by
> year, it correctly displays blocks 5 and 6.
>
> How can I correct this in the conditioned graphic?
This probably happens because things like `one <- dryoutcover$block==1` 
are logical vectors as long as the total number of rows in the data 
frame, whereas x and y (which you subset using x[one], y[one]) are 
shorter (only those rows for a particular year). Consequently, the 
vector you are indexing and the indexing vector are not comparable.

I would suggest you use the feature meant for this sort of display, 
namely as:

xyplot(coversage ~ dryout | year, 
       data=dryoutcover, groups = block, pch = c(49:54))

Hope that helps,

Deepayan

Anthony Darrouzet-Nardi

2004-May-30 01:18 UTC

head link

[R] panel function in a conditioned lattice graphic

>On Saturday 29 May 2004 15:24, Anthony Darrouzet-Nardi wrote:
>  > I'm trying to use plotting character to encode the variable
"block"
>  > from my dataset in a conditioned lattice graphic (R 1.9.0 on Mac OS
>  > 10.3.3). The data I'm using is the dataframe
"dryoutcover" which is
>  > here (4k):
>  >
>  > http://anthony.darrouzet-nardi.net/downloads/dryoutcover.Rdata
>  >
>  > The code that generates my graphic almost correctly is as follows:
>  >
>  > xyplot(coversage ~ dryout | year,
>  >         data=dryoutcover,
>  >         panel = function(x,y) {
>  >                 panel.lmline(x,y)
>  >                 one <- dryoutcover$block==1
>  >                 two <- dryoutcover$block==2
>  >                 thr <- dryoutcover$block==3
>  >                 fou <- dryoutcover$block==4
>  >                 fiv <- dryoutcover$block==5
>  >                 six <- dryoutcover$block==6
>  >                 grid.points(x[one], y[one], pch=49)
>  >                 grid.points(x[two], y[two], pch=50)
>  >                 grid.points(x[thr], y[thr], pch=51)
>  >                 grid.points(x[fou], y[fou], pch=52)
>  >                 grid.points(x[fiv], y[fiv], pch=53)
>  >                 grid.points(x[six], y[six], pch=54)
>  >                 }
>  >         )
>  >
>  > The only thing wrong is that this does not correctly encode blocks 5
>  > and 6, which only appear in the third year of the study, 2003 (the
>  > third panel of the graphic). It instead labels blocks 5 and 6 as
>  > blocks 1 and 2 as if another year had started over (but on the same
>  > panel). For example, the point farthest to the right in the third
>  > panel says "2" when I want it to say "6." When I
do not condition by
>  > year, it correctly displays blocks 5 and 6.
>  >
>  > How can I correct this in the conditioned graphic?
>
>This probably happens because things like `one <- dryoutcover$block==1`
>are logical vectors as long as the total number of rows in the data
>frame, whereas x and y (which you subset using x[one], y[one]) are
>shorter (only those rows for a particular year). Consequently, the
>vector you are indexing and the indexing vector are not comparable.
>
>I would suggest you use the feature meant for this sort of display,
>namely as:
>
>xyplot(coversage ~ dryout | year,
>        data=dryoutcover, groups = block, pch = c(49:54))
>
>Hope that helps,
>
>Deepayan

Oh yes, that does indeed help. I should have thought of using 
"groups". And more importantly, thanks for explaining why the 
indexing method was not working.

I have a followup question. Suppose I want to encode two different 
variables within a panel: one variable encoded by plotting character 
and one variable encoded by symbol color (as if I could use two 
"groups" variables). The dataframe I discussed above also includes a 
variable called treatment. If I start with the existing code modified 
with your suggestions:

xyplot(coversage ~ dryout | year,
	data = dryoutcover,
	groups = block,
	panel = function(x,y, ...) {
		panel.lmline(x,y)
		panel.superpose(x,y,
			pch = 49:54,
			cex = rep(2,6),
			col = rep("black", 6), ...)
		}
	)

how could I make all of the symbols of one treatment red and all of 
the symbols of the other black while maintaining the encodings of 
block by plotting character? This would be a superbly useful 
technique as it would allow 4 dimensional data on a single panel 
(maybe even 5 using a point cloud!).

Anthony

Gabor Grothendieck

2004-May-31 16:44 UTC

head link

[R] Calculating distances between points in a data frame?

Try using running from the gregmisc package with pad = TRUE:


require(gregmisc)
XY <- data.frame(num = seq(0,10), X = seq(0,30,3), Y = seq(0, 40, 4) )
DistXY <- function(idx) {
   i <- idx[2]
   with(XY, sqrt( (X[i]-X[i-1])^2 + (Y[i]-Y[i-1])^2 ) )
}
XY$Dist <- running( 1:nrow(XY), width=2, fun = DistXY, pad = TRUE )


Sander Oom <slist <at> oomvanlieshout.net> writes:

: 
: Dear list,
: 
: I would like to calculate the distance between consecutive points in a data 
: frame. Of course the first point in the data frame does not have a point of 
: origin, and should get a value NA. I have tried two different loops, which 
: both result in error:
: 
:  > num <- seq(0,10,1)
:  > X <- seq(0,30,3)
:  > Y <- seq(0,40,4)
:  > XY <- data.frame(num, X, Y)
:  > attach(XY)
:  > summary(XY)
:        num             X              Y
:   Min.   : 0.0   Min.   : 0.0   Min.   : 0
:   1st Qu.: 2.5   1st Qu.: 7.5   1st Qu.:10
:   Median : 5.0   Median :15.0   Median :20
:   Mean   : 5.0   Mean   :15.0   Mean   :20
:   3rd Qu.: 7.5   3rd Qu.:22.5   3rd Qu.:30
:   Max.   :10.0   Max.   :30.0   Max.   :40
:  > plot(X,Y)
:  > rngNum <- range(num)
:  > for (i in rngNum){
: +     XY$DistXY[i] <- sqrt( ((X[i]-X[i-1])^2) + ((Y[i]-Y[i-1])^2) )
: + }
: Error in "$<-.data.frame"(`*tmp*`, "DistXY", value =
sqrt(((X[i] - X[i -  :
:          replacement has 10 rows, data has 11
:  > for (i in rngNum){
: +     XY$DistXY2[i] <- ifelse(i=min(rngNum), NA, sqrt(((X[i]-X[i-1])^2) + 
: ((Y[i]-Y[i-1])^2)) )
: + }
: Error in ifelse(i = min(rngNum), NA, sqrt(((X[i] - X[i - 1])^2) + ((Y[i] -  :
:          unused argument(s) (i ...)
:  > detach(XY)
:  >
: 
: Any suggestions much appreciated,
: 
: Sander Oom.
: 
: --------------------------------------------------------------
: Dr. Sander P. Oom
: Animal, Plant and Environmental Sciences
: University of the Witwatersrand
: Private Bag 3
: Wits 2050
: South Africa
: 
: Tel (work)      +27 (0)11 717 64 04
: Tel (home)      +27 (0)18 297 44 51
: Fax             +27 (0)18 299 24 64
: 
: Email   sander <at> oomvanlieshout.net
: Web     www.oomvanlieshout.net/sander
: 
: ______________________________________________
: R-help <at> stat.math.ethz.ch mailing list
: https://www.stat.math.ethz.ch/mailman/listinfo/r-help
: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
: 
:

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