[R] r function for calculating extreme spread in group
I'm trying to figure out how to write a r function that will calculate
the extreme spread of a group of points given their (x,y)
coordinates. Extreme Spread is the maximal Euclidean distance between
two points in a group
ex.spread = max{ sqrt [ (xi-xj)^2 - (yi-yj)^2 ] } for i not equal to j
I have 60 levels to apply this to.
There is the combination function in the dprep package but I wasn't
sure how to use this or apply an index the points in each group.
Any ideas?
Steve
Steven Matthew Anderson
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Re: [R] r function for calculating extreme spread in group
Thank you Jorge,
My talent in building functions is weak. I think I'm close but I'm
not doing something right.
res=dist(yourdata)
res[which.max(res)]
does provide me with the correct distance but how do I apply it across
data with level such as ...
>
yourdata
=as.data.frame(cbind(lvl=LETTERS[1:2],x=rpois(10,10),y=rnorm(10) ))
> yourdata
lvl x y
1A 10 0.14377148075807
2B 5 -0.117753598165951
3A 14 -0.912068366948338
4B 10 -1.43758624082998
5A 16 -0.797089525071965
6B 11 1.25408310644997
7A 7 0.77214218580453
8B 9 -0.219515626753440
9A 12 -0.424810283377287
10 B 13 -0.418980099421959
My attempt to use tapply blew up on me.
> Extreme.Spread<-matrix(nrow=60,ncol=2)
> ES<-function(Level) {
+temp<-
subset(x=ES.Data,Level==level,select=c(Horizontal,Vertical))
+e<-dist(rbind(temp$Horizontal,temp
$Vertical),method="euclidean")
+m<-e[which.max(e)]
+es<-cbind(level,m)
+Extreme.Spread<-rbind(Extreme.Spread,es)
+}
> tapply(X=ES.Data,INDEX=Level,FUN=ES)
Error in tapply(X = ES.Data, INDEX = Level, FUN = ES) :
arguments must have same length
On Aug 27, 2008, at 2:30 PM, Jorge Ivan Velez wrote:
> R-help@r-project.org
Steven Matthew Anderson
[EMAIL PROTECTED]
Ad Astra per Aspera
[[alternative HTML version deleted]]
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[R] predicted values after fitting gamma2 function
Question: after fitting a gamma function to some data, how do I get
predicted values? I'm a SAS programmer, I new R, and am having
problems getting my brain to function with the concept of "object as
class ...". The following is specifics of what I am doing:
I'm trying to determine the pdf from data I have created in a
simulation.
I have generated frequency counts using the following:
Max.brks <- pretty(range(Max.Spread$Distance), 100)
Max.f<-hist(x=Max.Spread$Distance,
breaks=Max.brks,plot=FALSE )
Max.cnt<-as.data.frame(cbind(sim,Max.f$mids,Max.f$counts))
colnames(Max.cnt)<-c("Simulation","MidPoint","Count")
then I fit this to a gamma distribution function:
modl<-
vglm
(Count
~
MidPoint
,gamma2
,data
=subset(Max.cnt,select=(simulation,MidPoint,Count),trace=TRUE,crit="c")
print(coef(modl2,matrix=TRUE))
print(summary(modl2))
This produces the output:
VGLMlinear loop 1 : coefficients =
3.231473495, 0.597085743, -0.195591168
...
VGLMlinear loop 20 : coefficients =
3.663316903, 0.897355891, -0.620449146
log(mu) log(shape)
(Intercept) 3.6633169 0.8973559
MidPoint-0.6204491 0.000
Call:
vglm(formula = Count ~ MidPoint, family = gamma2, data = modl.subset,
trace = TRUE, crit = "c")
Pearson Residuals:
Min1Q Median 3Q Max
log(mu)-1.4846 -0.715285 -0.15436 0.61641 2.17298
log(shape) -5.8348 -0.099617 0.42094 0.61865 0.70901
Coefficients:
Value Std. Error t value
(Intercept):1 3.66332 0.131643 27.8277
(Intercept):2 0.89736 0.138591 6.4749
MidPoint -0.62045 0.047505 -13.0607
Number of linear predictors: 2
Names of linear predictors: log(mu), log(shape)
Dispersion Parameter for gamma2 family: 1
Log-likelihood: -276.0009 on 181 degrees of freedom
Number of Iterations: 20
Now - how do I get this information to give me predicted values given
the same x-values I used in the experimental model (i.e. from Max.brks
<- pretty(range(Max.Spread$Distance), 100)).
Steven Matthew Anderson
Anderson Research, LLC
Statistical Programming and Analysis
SAS (R) Certified Professional
adastr...@mac.com
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שָׁלוֹם
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[R] exporting data to csv file -problem with column names
I have a data.frame with three columns + the row number Sample MidPoint Count [1,] 10.025 1 [2,] 10.075 3 [3,] 10.12515 [4,] 10.17512 [5,] 10.225 5 [6,] 10.275 8 When I export the data to a csv the column names are shifted because the row numbers are being exported as well. Sample MidPointCount 1 1 0.025 1 2 1 0.075 3 3 1 0.125 15 Is there a way to exclude the row numbers from the exported csv file? Or add a column name for row number to keep this from happening? I obvisouly can go into each csv file and shift the column names over - but there are going to be a large number of csv files so I with to automate this. Thank you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] variable driven csv file names?
Is it possible to have variable driven csv file names? Such as:
ds.name<-"bob.csv"
write.table(
distribution.data,
file = "~//Documents/Research/Distribution Analysis/ds.name",
sep = ",",
col.names = FALSE,
qmethod = "double")
Steven Matthew Anderson
Anderson Research, LLC
Statistical Programming and Analysis
SAS (R) Certified Professional
adastr...@mac.com
Ad Astra per Aspera
שָׁלוֹם
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] turn off graphic plot in histogram()
Is there a way to just produce the data object in histogram() and not run the plot portion? All I want it the $mids and $counts. Thank you Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com Ad Astra per Aspera שָׁלוֹם __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] hist returning density larger than 1
The following code is giving me problems. I want to export densities
of a distribution to a csv file. At the bottom of the code I use the
hist function to generate the densities. But hist is returning values
greater than 1. I don't understand, why. Any help you can supply is
greatly appreciated.
# Set word path
dir<-"~/Research/MR Distribution Analysis/"
setwd(dir)
getwd()
# Define Objects
Max.Shots=3
Max.Groups=5000
hist.brks <- pretty(range(c(0,4)), 200)
for(sim in (2:Max.Shots)){
x.Data<-matrix(nrow=Max.Groups,ncol=sim,byrow=TRUE)
y.Data<-matrix(nrow=Max.Groups,ncol=sim,byrow=TRUE)
shot2mean.x<-matrix(nrow=Max.Groups,ncol=sim,byrow=TRUE)
shot2mean.y<-matrix(nrow=Max.Groups,ncol=sim,byrow=TRUE)
Euclid.Dist<-matrix(nrow=Max.Groups,ncol=sim,byrow=TRUE)
mean.radius<-vector(mode="numeric",length=Max.Groups)
# Generate the Simulation Data
###
# Number of Groups
for(Groups in (1:Max.Groups)) {
# Number of Shots per Group
for(Shots in (1:sim)) {
# Populate the Simulation Data
x.Data[Groups,Shots]<-rnorm(n=1,mean=0,sd=1)
y.Data[Groups,Shots]<-rnorm(n=1,mean=0,sd=1)
}
}
# Calculate the Component Distances from the Shots to the Group Mean
# Calculate the Euclidean Distance from the Shots to the Group Mean
# Calculate the Group Mean Radius
###
# Number of Groups
for(Groups in (1:Max.Groups)){
# Number of Shots per Group
for(Shots in (1:sim)){
shot2mean.x[Groups,Shots]<-(x.Data[Groups,Shots]-
mean(x.Data[Groups,]))^2
shot2mean.y[Groups,Shots]<-(y.Data[Groups,Shots]-
mean(y.Data[Groups,]))^2
Euclid.Dist[Groups,Shots]<-sqrt(shot2mean.x[Groups,Shots]
+shot2mean.y[Groups,Shots])
}
mean.radius[Groups]<-mean(Euclid.Dist[Groups,])
}
f<-hist(mean.radius,breaks=hist.brks,plot=FALSE)
density.data<-cbind(sim,f$mids,f$density)
colnames(density.data)<-c("Simulation","MidPoint","Density")
if (sim==2) {Simulation.Data<-density.data} else {Simulation.Data<-
rbind(Simulation.Data,density.data)}
rm(x.Data)
rm(y.Data)
rm(shot2mean.x)
rm(shot2mean.y)
rm(Euclid.Dist)
rm(mean.radius)
}
write.table(
Simulation.Data,
file=paste(dir,"/DATA/Simulation_Data.csv",sep=''),
sep=",",
quote=FALSE,
row.names=FALSE,
qmethod="double")
Steven Matthew Anderson
Anderson Research, LLC
Statistical Programming and Analysis
SAS (R) Certified Professional
adastr...@mac.com
Ad Astra per Aspera
שָׁלוֹם
__
R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.
[R] p-values from VGAM function vglm
Anyone know how to get p-values for the t-values from the coefficients
produced in vglm?
Attached is the code and output — see comment added to output to show
where I need p-values
+ print(paste("** Using VGAM function gamma2 **"))
+ modl2<-
vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit="c")
+ print(coef(modl2,matrix=TRUE))
+ print(summary(modl2))
[1] "** Using VGAM function gamma2 **"
VGLMlinear loop 1 : coefficients =
0.408464609241, 3.255887520104, -0.000220585671
VGLMlinear loop 2 : coefficients =
2.34723239e-01, 1.28969691e+00, -4.52393778e-05
VGLMlinear loop 3 : coefficients =
2.19500481e-01, 1.92534895e+00, -3.02160949e-05
VGLMlinear loop 4 : coefficients =
2.19383151e-01, 2.26845910e+00, -3.00838664e-05
VGLMlinear loop 5 : coefficients =
2.19383045e-01, 2.34645688e+00, -3.00836087e-05
VGLMlinear loop 6 : coefficients =
2.19383045e-01, 2.34977070e+00, -3.00836082e-05
VGLMlinear loop 7 : coefficients =
2.19383045e-01, 2.34977637e+00, -3.00836082e-05
VGLMlinear loop 8 : coefficients =
2.19383045e-01, 2.34977637e+00, -3.00836082e-05
log(mu) log(shape)
(Intercept) 2.193830e-01 2.349776
Count -3.008361e-05 0.00
Call:
vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset,
trace = TRUE, crit = "c")
Pearson Residuals:
Min 1Q Median 3Q Max
log(mu)-1.7037 -0.82997 0.072275 0.78520 1.72834
log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678
# NEED P-VALUES HERE #
Coefficients:
Value Std. Error t value
(Intercept):1 2.1938e-01 5.2679e-02 4.16455
(Intercept):2 2.3498e+00 1.7541e-01 13.39574
Count -3.0084e-05 8.9484e-05 -0.33619
Number of linear predictors: 2
Names of linear predictors: log(mu), log(shape)
Dispersion Parameter for gamma2 family: 1
Log-likelihood: -26.39268 on 123 degrees of freedom
Number of Iterations: 8
Steven Matthew Anderson
Anderson Research, LLC
Statistical Programming and Analysis
SAS (R) Certified Professional
adastr...@mac.com
Ad Astra per Aspera
שָׁלוֹם
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
