gmane.comp.lang.r.general

How to assign height value on bar plot?

Manish Gupta — 2012-05-26T16:07:14

Hi,

How to assign height value on bar plot for each bar?

http://r.789695.n4.nabble.com/file/n4631457/Barplot.png 

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Plotting interactions from lme with ggplot

dadrivr — 2012-05-26T16:00:23

I'm fitting a lme growth curve model with two predictors and their
interaction as predictors. The multilevel model is nested so that level 1 is
time within the individual, and level 2 is the individual.  I would like to
plot the mean group-level trajectories at plus and minus 1 SD from the mean
of the main effects composing the interaction term.  Thus, the plot should
have 4 lines (mean trajectories) representing all combinations of the two
predictors (where LO = -1sd from its mean, and HI = +1sd from its mean):
-LO predictor, LO moderator
-LO predictor, HI moderator
-HI predictor, LO moderator
-HI predictor, HI moderator

They are growth curves, so the plot should have 'time' on the x-axis and
'outcome' on the y-axis.  Here's a sample model:

library(nlme)

set.seed(123)

dataset <- NULL
dataset$id <- rep(1:100, each=10)
dataset$time <- rep(1:10,100)
dataset$outcome <- rnorm(1000, mean=100, sd=15)
dataset$predictor <- rnorm(1000, mean=10, sd=3)
dataset$moderator <- rnorm(1000, mean=5, sd=2)

dataset <- as.d

Problem with readHTMLTable

Sven D — 2012-05-26T14:17:19

Hello All,

i was trying to simply run the readHTMLTable on the example published in the
package. And on a page I was working on. So running:

u = "http://en.wikipedia.org/wiki/List_of_countries_by_population"
tables = readHTMLTable(u)

returns the following error:

Error in tb[["thead"]] : subscript out of bounds


looking up this error on the web, didnt give me any hint. Is something wrong
with this function?


this is my sessioninfo:

R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United
Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] XML_3.9-4.1                  RCurl_1.91-1.1              
bitops_1.0-4.1               PerformanceAnalytics_1.0.3.2
 [5] quantstrat_0.6.4             blotter_0.8.4

avoid error within for loop, try, trycatch, while,move to next iteration, unlist

Λεωνίδας Μπαντής — 2012-05-26T13:14:37



Hi there,

I would like to ask something about how to avoid a possible error message within a for loop. I am running a simulation and in some repetitions there may be an error that will cause a crash and stop the whole procedure, what I want is to simply move on to the next iteration automatically and discard the "bad" repetitions from my results. I used the "try" function to do this and it partially works.

Here is the thing:

logitsboots <- function(x,y,Jbh) {
logitseb=0;logitspb=0;
for (j in 1:1) {


#some code here that has to do with random numbers that may or may not produce an error and calculates the values of two scalar quantities: spboots  and seboots,    


  logitspb=log(spboots/(1-spboots))
  logitseb=log(seboots/(1-seboots))
 
#assume that I only care about logitseb for the moment
}
list(lse=logitseb)

}



# Now the following works just fine:


res=0
for(bb in 1:100) {
res[bb] <- try(logitsboots(x,y,Jbh), TRUE)
    }
az=unlist(res[sapply(res, function(x) !inherits(x, "try-error"))]

Kolmogorov-Smirnov test and the plot of max distance between two ecdf curves

maxbre — 2012-05-26T13:33:49

Hi all, 

given this example 

#start 

a<-c(0,70,50,100,70,650,1300,6900,1780,4930,1120,700,190,940, 
   
760,100,300,36270,5610,249680,1760,4040,164890,17230,75140,1870,22380,5890,2430) 
length(a)

b<-c(0,0,10,30,50,440,1000,140,70,90,60,60,20,90,180,30,90, 
     3220,490,20790,290,740,5350,940,3910,0,640,850,260) 
length(b)

out<-ks.test(log10(a+1),log10(b+1)) 

# max distance D 
out$statistic 

f.a<-ecdf(log10(a+1)) 
f.b<-ecdf(log10(b+1)) 

plot(f.a, verticals=TRUE, do.points=FALSE, col="red") 
plot(f.b, verticals=TRUE, do.points=FALSE, col="green", add=TRUE) 

#inverse of ecdf a
x.a<-get("x", environment(f.a))
y.a<-get("y", environment(f.a))

# inverse of ecdf b
x.b<-get("x", environment(f.b))
y.b<-get("y", environment(f.b))


#end

I want to plot the max distance between the two ecdf curves as in the above
given chart

Is that possible and how? 


Thanks for your help

PS: this is an amended version of a previous thread (but no reply followed)
that I’ve deleted from Nabble repository because I realis

how to check given number seq. is time series or not?

sagarnikam123 — 2012-05-26T09:13:37

i have following numbers 

 0.889046409368551 
 1.22726162946495 
 1.22726162946495 
 1.35785109728356 
 1.35785109728356 
 1.10704609982913 
 1.4424189950435 
 1.2277843378837 
 1.35785109728356 
 0.970883941918588 
 0.822170913920467 
 1.35785109728356 
 0.358815782262543 
 0.774234247460432 
 0.822170913920467 
 0.822170913920467 
 0.72599976881814 
 0.671583894425946 
 0.813223271443211 
 0.774234247460432 
 1.00184802593319 
 1.4424189950435 
 1.22726162946495 
 0.970883941918588 
 0.358815782262543 
 1.31016840948316 
 0.970883941918588 
 1.4424189950435 
 0.889046409368551 
 4.91679981837699 
 1.2277843378837 
 1.21605333196293 
 0.369861996166875 
 0.774748148811057 
 0.369861996166875 
 1.4424189950435 
 1.22726162946495 
 1.4424189950435 
 1.22726162946495 
 1.16291100715022 
 2.33863311242767 
 0.774234247460432 
 4.91679981837699 
 0.9670580678417 
 0.970883941918588 
 0.9670580678417 
 1.10704609982913 
 4.91679981837699 
 1.4424189950435 
 1.054

Values in scatterplot??

Jhope — 2012-05-26T06:17:37

Hi R-listers, 

I am having trouble plotting the values for the R2 line, lowess smooth,
smothered conditional spread, outlier identification. 
I have tried the function text and legend but was unsuccessful. Please see
below.

Your help would be appreciated. Thanks in advance.

Jean



library(car)
+                        data = data.to.analyze,
+                        xlab = "Distance to high tide line (metres)",
+                        ylab = "Hatching success (%)")

+                                         
format(summary(SPHSHTL)$adj.r.squared, digits=4)))
Error in summary(SPHSHTL)$adj.r.squared : 
  $ operator is invalid for atomic vectors

Error in text.default(SPHSHTL) : zero length 'labels'

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How to transform OLS covariance matrix to White standard errors?

Dunken — 2012-05-26T07:09:17

Hi!

I am working with a regression of a log-log model that suffers from
heteroskedasticity. I have calculated the "White standard errors". I would
like to use these "White standard errors" in a RESET test instead of the
originally OLS standard errors calculated by the regression. How can I
transform the covariance matrix of a model?


labmodel2 <- lm(formula = log(L) ~ log(W) + log(K) + log(Y), data=labordat)
sumlabmodel2 <- summary(labmodel2)
sumlabmodel2

coeftest(labmodel2,vcov=vcovHC(labmodel2,type="HC0"

That is, I want to replace vcov with vcovHC in labmodel2 to perform a RESET
test with the robust White standard errors.

Can anyone help?

Thank you!



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Assessing interaction effects in GLMMs

Luke Duncan — 2012-05-26T10:19:52

Dear R gurus

I am running a GLMM that looks at whether chimpanzees spend time in shade
more than sun (response variable 'y': used cbind() on counts in the sun and
shade) based on the time of day (Time) and the availability of shade
(Tertile). I've included some random factors too which are the chimpanzee
in question (Individual) and where they are in a given area (Zone). There
are also two continuous predictors (Minimum daily temperature: Min; Maximum
daily temperature: Max). I have run my GLMM and I know that Time and Min
are significant predictors of the patterns of shade use while Tertile and
Max are not. In addition, a Time*Tertile interaction effect is a good
predictor as well.

I now need to assess how the specific interaction effect conditions differ
to one another. So, for example, how does shade use differ between 10h00 at
low shade and 10h00 at high shade? I tried using the package multcomp, but
that will only allow me to work out the contrasts for the first-order
effects (Time, Tertile) but won't

How to draw y axis in horizontal bar plot?

Manish Gupta — 2012-05-26T02:53:43

http://r.789695.n4.nabble.com/file/n4631428/Image2.png 

How can i draw y axis in bar plot at x = 0?

After plotting axis it will look like.



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"shift" + "arrow" in getGraphicsEvent

cgenolin — 2012-05-25T22:33:40

Hi the list,

Do you know if getGraphicsEvent can detect the use of keys combinaison like
"shift+arrow" or "Crlt+arrow" ?

Best
Christophe

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evaluate whether function returns error

mdvaan — 2012-05-25T20:52:35

Hi,

The following returns an error message. How do I evaluate (TRUE or FALSE)
the function?

require(XML)
readHTMLTable("http://www.sec.gov/Archives/edgar/data/2969/000095012399010952/0000950123-99-010952.txt")

Thanks in advance!

Math

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change colors/ symbols of lda plots

2012-05-25T19:50:11

Greetings R experts,

I am running a simple lda on some simulation data of mine to show an illustration of my multivariate response data, since it is a simulation I have a very large amount of data and the default on plot seems to plot the category names. This is very difficult to interpret even changing the abbreviations. At the expense of sounding naive, my question(s) are:

How can I color code my four categories?

and how can I change the unit display to something simple like a dot, and not the names or abbreviated names of the categories?


Cheers,
-Dan

[[alternative HTML version deleted]]

Selecting with mouse the lines drawn by matplot()

servet cizmeli — 2012-05-25T20:52:43

Dear all,

I have a dataset of spectral measurements of sunlight. One row for each 
different observation, one column for each spectral channel.

I would like to select the spectral curves drawn with matplot() (I only 
know matplot() as a way of easily drawing them) with the help of the 
mouse and extract their row indexes  :

a=url("http://ekumen.homelinux.net/spectra.RData")
load(a)
matplot(lbd2, t(mySpectra), type="l",xlab="Wavelength [nm]",ylab="Radiance")

I was hoping that identify() would work on such a graphic but 
unfortunately it does not. I tried to the "identify" function of the 
package playwith(), but still the same problem.

I think I will have to write a function that does the job. But before 
that, I would like to have your opinions. What would be the easiest way 
of accomplishing this task?

Thank you very much
Best regards
servet

knitr customization

Giovanni Petris — 2012-05-25T19:30:04

I am trying to transition from Sweave to knitr, but there are a few
things about customization of the appearence of R input and output that
I did not get yet. Maybe somebody on the list can help me.

In my Sweave presentations I used a slanted font for the R input and a
normal font for the output, both in a small font. I also indented
everything by an extra 2em. All this was achieved by the following
instructions in the .Rnw file:

\DefineVerbatimEnvironment{Sinput}{Verbatim}{xleftmargin=2em, 
  fontsize=\footnotesize, fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em, 
  fontsize=\footnotesize}

In order to get a similar result (with a tiny size instead of a footnote
size, but that is not the point) with knitr I included in the .Rnw file
the lines

\ifdefined\knitrout
  \renewenvironment{knitrout}{\begin{tiny}\slshape}{\end{tiny}}
\else
\fi
  
What I get is something like this: 

http://definetti.uark.edu/~gpetris/knitr-output.pdf 

The problem is that the prompt sign '>' did not

question about TryCatch and lapply

John Kerpel — 2012-05-25T18:51:23

Folks:

I've replaced an outer for-loop with lapply and it works great.  But, I
can't seem to do the following type of exception handling:

tryCatch(dlmMLE(x)$value==Inf,error = function(e) NULL)

which basically says if the likelihood is Inf, throw an error.  But what I
want it to do is just go to the next index in the list.  When I was using a
for-loop I used:

if(tryCatch(dlmMLE(x)$value==Inf,error = function(e) 1)==1) {next} else
.... which worked fine.

Is there a way to do the same thing in lapply?

Thanks for your time. (I've checked Gmane for this type of problem and I
wasn't sure if this problem was answered or not...)

John

[[alternative HTML version deleted]]

How to change width of bar when there are very few bars?

Manish Gupta — 2012-05-25T18:03:31

http://r.789695.n4.nabble.com/file/n4631371/Bar_Chart.png 


How to control width of bar chart when there are very few bars in plot? 


Regards

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Reading a bunch of csv files into R

HJ YAN — 2012-05-25T17:16:15

Dear R users


I am struggling from a data importing issue:

I have some hundreds of csv files needed to be read into R for futher
analysis. All those csv files are named in one of the three formats:

(1) strings: e.g. London_Oxford street
(2) Integer: e.g. 1234_5678
(3) combined: e.g. London_1234

I intend to use read.csv("xxxx_xxx.csv") but I only dealt with
sigle documents before and if there are only no more than 20 files, I do
not bother to search a more efficient way.


Is there any claver way that I do not have to type in all these hundreds
names by hand, maybe using a R package or write some code in some other
languages if it is not too difficult to learn.

Any thoughts/hints please??

Many thanks in advance!

HJ

[[alternative HTML version deleted]]

difference between qnorm and qqnorm

QAMAR MUHAMMAD UZAIR — 2012-05-25T16:41:54

dear all,
it will just take you a minute to tell me the difference 
between qnorm and qqnorm. are they same or is there any 
difference between them??
regards

subset columns from list with variable substitution

jween — 2012-05-25T18:09:34

Hi there, I would like to use a list variable to select columns in a subset
from a parent table:

I have a data frame "table" with column headers a,b,c,d,e,x,y,z

and list variables

list1=c("a","b","c","d")
list2=c("a","b","x",y","z")
namelist=c("peter","paul","mary","jane")
group1=c("peter","paul")
group2=c("mary","jane")

I would like to subset "table" based on the list variable in a for loop:

for (i %in% namelist){
     if (i %in% group1){table2<-subset(table, select=list1)}
     else {{table2<-subset(table, select=list2)}
}

the "select=list1" syntax does not work. What would be the correct way to do
this?

Many Thanks

Jon

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Query about creating time sequences

Shivam — 2012-05-25T17:14:02

Hi All,

I have a query about time based sequences. I know such questions have been
asked a lot on forums, but I couldnt find the exact thing that I was
looking for.

I want to create a time-based sequence which will mimic the trading window
AND would span multiple days. Something like below:

"2011-01-03 09:15:00 IST"
"2011-01-03 09:15:01 IST"
....
....
....
"2011-01-03 15:29:59 IST"
"2011-01-03 15:30:00 IST"
"2011-01-04 09:15:00 IST"
"2011-01-04 09:15:01 IST"
....
....
....
"2011-01-04 15:29:59 IST"
"2011-01-04 15:30:00 IST"

Kindly notice the change of date in the sequence.

The Indian Equity markets open at 09:15:00 and close at 15:30:00. I have
equity data that spans 124 days, and I need to create a corresponding
sequence which I will later use to regularize the irregular dataset to make
a regular time-series.

I was able to accomplish this task for a single day (i.e. creating a
sequence then merging my dataset with it and use na.locf to make my dataset
regular) but am unable to create a sequence for 'n