[R] GarchOxFit Interface
Hello, I am having problems with the GarchOxFit. I have my Ox Console instaled in c:\Program Files\ox, and when I execute the GarchOxFit the result is C:\Ox\bin\oxl.exe not found. I there any posiblility to execute the command without installing again Ox in c:\? My OS is windows XP. Thankyou for your help. Pilar Grau __ R-help@stat.math.ethz.ch 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] format of summary.lm for 2-way ANOVA
Hi, I am performing a two-way ANOVA (2 factors with 4 and 5 levels, respectively). If I'm interpreting the output of summary correctly, then the interaction between both factors is significant: , | ## Two-way ANOVA with possible interaction: | model1 - aov(log(y) ~ xForce*xVel, data=mydataset) | | summary(model1) | Df Sum Sq Mean Sq F valuePr(F) | xForce3 16.640 5.547 19.0191 1.708e-11 *** | xVel 4 96.391 24.098 82.6312 2.2e-16 *** | xForce:xVel 12 10.037 0.836 2.8681 0.0008528 *** | Residuals 371 108.194 0.292 | --- | Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 | 3 observations deleted due to missingness ` To see the interactions in detail I call summary.lm: , | summary.lm(model1) | | Call: | aov(formula = log(y) ~ xForce * xVel, data = mydataset) | | Residuals: | Min 1Q Median 3Q Max | -2.04830 -0.32420 -0.04653 0.34928 1.46755 | | Coefficients: | Estimate Std. Error t value Pr(|t|) | (Intercept) -1.663406 0.027335 -60.853 2e-16 *** | xForce.L 0.408977 0.054726 7.473 5.68e-13 *** | xForce.Q 0.101240 0.054670 1.852 0.0648 . | xForce.C-0.068068 0.054613 -1.246 0.2134 | xVel.L 1.079042 0.061859 17.444 2e-16 *** | xVel.Q 0.339802 0.061439 5.531 6.03e-08 *** | xVel.C 0.015422 0.060751 0.254 0.7997 | xVel^4 -0.044399 0.060430 -0.735 0.4630 | xForce.L:xVel.L 0.622060 0.123966 5.018 8.12e-07 *** | xForce.Q:xVel.L 0.034298 0.123718 0.277 0.7818 | xForce.C:xVel.L -0.114776 0.123470 -0.930 0.3532 | xForce.L:xVel.Q 0.309293 0.123057 2.513 0.0124 * | xForce.Q:xVel.Q 0.054798 0.122879 0.446 0.6559 | xForce.C:xVel.Q -0.144219 0.122700 -1.175 0.2406 | xForce.L:xVel.C 0.110588 0.121565 0.910 0.3636 | xForce.Q:xVel.C -0.001929 0.121502 -0.016 0.9873 | xForce.C:xVel.C -0.039477 0.121438 -0.325 0.7453 | xForce.L:xVel^4 0.090491 0.120870 0.749 0.4545 | xForce.Q:xVel^4 -0.002762 0.120861 -0.023 0.9818 | xForce.C:xVel^4 -0.028836 0.120852 -0.239 0.8115 | --- | Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 | | Residual standard error: 0.54 on 371 degrees of freedom | (3 observations deleted due to missingness) | Multiple R-Squared: 0.5322, Adjusted R-squared: 0.5082 | F-statistic: 22.21 on 19 and 371 DF, p-value: 2.2e-16 ` I am wondering what the logic is behind the formatting of rownames. What do the strings L, Q, C and ^4 mean? Apologies in case I missed something obvious in the relevant documentations/archives. Thanks for any pointers, Patrick PS: Here are some details about the dataset: , | summary(mydataset) |yxForce xVel | Min. :0.03662 0.01:97 10 :79 | 1st Qu.:0.10376 0.1 :98 50 :80 | Median :0.16314 1 :98 100 :80 | Mean :0.26592 2 :98 500 :80 | 3rd Qu.:0.28077 NA's: 3 5000:72 | Max. :2.39490 NA's: 3 | NA's :3.0 | | str(mydataset) | 'data.frame': 394 obs. of 3 variables: | $ y : num 0.167 0.158 0.152 0.158 0.131 ... | $ xForce: Ord.factor w/ 4 levels 0.010.11..: 1 2 3 4 1 2 3 4 1 2 ... | $ xVel : Ord.factor w/ 5 levels 1050100..: 3 3 3 3 1 1 1 1 2 2 ... ` I am using platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) __ R-help@stat.math.ethz.ch 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.
Re: [R] GarchOxFit Interface
[EMAIL PROTECTED] wrote: Hello, I am having problems with the GarchOxFit. I have my Ox Console instaled in c:\Program Files\ox, and when I execute the GarchOxFit the result is C:\Ox\bin\oxl.exe not found. I there any posiblility to execute the command without installing again Ox in c:\? I suppose you are speaking of GarchOxFit in package fSeries, but you didn't mention which version of fSeries you are using. I think, in current versions (240.10068), you may set OXPATH in the global environment to your installation of OX, maybe it is even necessary to do so. Apart from that I think there is still a buglet in the Ox-Interface functions, which I mentioned some time ago on R-sig-finance, see https://stat.ethz.ch/pipermail/r-sig-finance/2005q4/000498.html. I think you still find this buglet in the current version source (line 217 of 4D-GarchOxInterface.R), but since I don't use the Ox interface any more, I am not sure. I think the quick workaround is to always store the time series to be fitted in the variable x in the global environment. hth, Martin My OS is windows XP. Thankyou for your help. Pilar Grau __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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.
Re: [R] format of summary.lm for 2-way ANOVA
Patrick Drechsler wrote: Hi, I am performing a two-way ANOVA (2 factors with 4 and 5 levels, respectively). If I'm interpreting the output of summary correctly, then the interaction between both factors is significant: , | ## Two-way ANOVA with possible interaction: | model1 - aov(log(y) ~ xForce*xVel, data=mydataset) | | summary(model1) | Df Sum Sq Mean Sq F valuePr(F) | xForce3 16.640 5.547 19.0191 1.708e-11 *** | xVel 4 96.391 24.098 82.6312 2.2e-16 *** | xForce:xVel 12 10.037 0.836 2.8681 0.0008528 *** | Residuals 371 108.194 0.292 | --- | Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 | 3 observations deleted due to missingness ` To see the interactions in detail I call summary.lm: , | summary.lm(model1) | | Call: | aov(formula = log(y) ~ xForce * xVel, data = mydataset) | | Residuals: | Min 1Q Median 3Q Max | -2.04830 -0.32420 -0.04653 0.34928 1.46755 | | Coefficients: | Estimate Std. Error t value Pr(|t|) | (Intercept) -1.663406 0.027335 -60.853 2e-16 *** | xForce.L 0.408977 0.054726 7.473 5.68e-13 *** | xForce.Q 0.101240 0.054670 1.852 0.0648 . | xForce.C-0.068068 0.054613 -1.246 0.2134 | xVel.L 1.079042 0.061859 17.444 2e-16 *** | xVel.Q 0.339802 0.061439 5.531 6.03e-08 *** | xVel.C 0.015422 0.060751 0.254 0.7997 | xVel^4 -0.044399 0.060430 -0.735 0.4630 | xForce.L:xVel.L 0.622060 0.123966 5.018 8.12e-07 *** | xForce.Q:xVel.L 0.034298 0.123718 0.277 0.7818 | xForce.C:xVel.L -0.114776 0.123470 -0.930 0.3532 | xForce.L:xVel.Q 0.309293 0.123057 2.513 0.0124 * | xForce.Q:xVel.Q 0.054798 0.122879 0.446 0.6559 | xForce.C:xVel.Q -0.144219 0.122700 -1.175 0.2406 | xForce.L:xVel.C 0.110588 0.121565 0.910 0.3636 | xForce.Q:xVel.C -0.001929 0.121502 -0.016 0.9873 | xForce.C:xVel.C -0.039477 0.121438 -0.325 0.7453 | xForce.L:xVel^4 0.090491 0.120870 0.749 0.4545 | xForce.Q:xVel^4 -0.002762 0.120861 -0.023 0.9818 | xForce.C:xVel^4 -0.028836 0.120852 -0.239 0.8115 | --- | Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 | | Residual standard error: 0.54 on 371 degrees of freedom | (3 observations deleted due to missingness) | Multiple R-Squared: 0.5322, Adjusted R-squared: 0.5082 | F-statistic: 22.21 on 19 and 371 DF, p-value: 2.2e-16 ` I am wondering what the logic is behind the formatting of rownames. What do the strings L, Q, C and ^4 mean? The default contrast for ordered factors is contr.poly(), and L, Q, C and ^4 refer to linear, quadratic, cubic, and quartic, respectively. You might look at some plots if you have not already. For example: with(mydataset, interaction.plot(xForce, xVel, log(y))) library(lattice) bwplot(log(y) ~ xForce | xVel, data = mydataset) Apologies in case I missed something obvious in the relevant documentations/archives. Thanks for any pointers, Patrick PS: Here are some details about the dataset: , | summary(mydataset) |yxForce xVel | Min. :0.03662 0.01:97 10 :79 | 1st Qu.:0.10376 0.1 :98 50 :80 | Median :0.16314 1 :98 100 :80 | Mean :0.26592 2 :98 500 :80 | 3rd Qu.:0.28077 NA's: 3 5000:72 | Max. :2.39490 NA's: 3 | NA's :3.0 | | str(mydataset) | 'data.frame': 394 obs. of 3 variables: | $ y : num 0.167 0.158 0.152 0.158 0.131 ... | $ xForce: Ord.factor w/ 4 levels 0.010.11..: 1 2 3 4 1 2 3 4 1 2 ... | $ xVel : Ord.factor w/ 5 levels 1050100..: 3 3 3 3 1 1 1 1 2 2 ... ` I am using platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894
Re: [R] Horvitz Thompson Variance
Gen wrote: I am performing linear regression R and would like to incorporate sampling weights. There is a survey package for the analysis of data from complex sample designs of which svyglm might fit your purposes. For the home page of the package (with lots of materials), see http://faculty.washington.edu/tlumley/survey/ HTH, Tobias Does any one know how to obtain Horvitz-Thompson variance estimates when performing linear regression? Thank you for your help. -- Tobias Verbeke - Consultant Business Decision Benelux Rue de la révolution 8 1000 Brussels - BELGIUM +32 499 36 33 15 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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.
Re: [R] format of summary.lm for 2-way ANOVA
Chuck Cleland [EMAIL PROTECTED] writes: Patrick Drechsler wrote: [...] To see the interactions in detail I call summary.lm: , | summary.lm(model1) [...] | xVel.L 1.079042 0.061859 17.444 2e-16 *** | xVel.Q 0.339802 0.061439 5.531 6.03e-08 *** | xVel.C 0.015422 0.060751 0.254 0.7997 | xVel^4 -0.044399 0.060430 -0.735 0.4630 [...] I am wondering what the logic is behind the formatting of rownames. What do the strings L, Q, C and ^4 mean? The default contrast for ordered factors is contr.poly(), and L, Q, C and ^4 refer to linear, quadratic, cubic, and quartic, respectively. Thank you very much this explanation! Could you point me in the right direction where this is documented? I have looked at ?summary, ?summary.lm and ?contr.poly etc. You might look at some plots if you have not already. For example: with(mydataset, interaction.plot(xForce, xVel, log(y))) library(lattice) bwplot(log(y) ~ xForce | xVel, data = mydataset) Nice, thanks also for this pointer. Cheers Patrick -- By working faithfully eight hours a day, you may eventually get to be boss and work twelve. -- Robert Frost __ R-help@stat.math.ethz.ch 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.
Re: [R] significant anova but no distinct groups ?
Frederic Jean wrote: I am studying a dataset using the aov() function. The independant variable 'cds' is a factor() with 8 levels and here is the result in studying the dependant variable 'rta' with aov() : summary(aov(rta ~ cds)) Df Sum Sq Mean Sq F value Pr(F) cds 7 0.34713 0.04959 2.3807 0.02777 Residuals 92 1.91635 0.02083 The dependant variable 'rta' is normally distributed and variances are homogeneous. But when studying the result with TukeyHSD, no differences in 'rta' are seen among groups of 'cds' : TukeyHSD(aov(rta ~ cds), which=cds) Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = rta ~ cds) $cds difflwrupr p adj 1-0 -0.1046092796 -0.4331100 0.22389141 0.9751178 2-0 0.0359991860 -0.1371359 0.20913425 0.9980970 3-0 0.0261665235 -0.1348524 0.18718540 0.9996165 4-0 0.0004502442 -0.1805448 0.18144531 1.000 5-0 -0.1438949939 -0.3104752 0.02268526 0.1422670 [...] 7-5 0.0621598639 -0.1027595 0.22707926 0.9386170 7-6 0.0256519274 -0.1757408 0.22704465 0.248 I tried a pairwise.t.test (holm correction) which also was not able to detect differences in 'rta' among groups of 'cds' I've never been confronted to such a situation before : is it just a problem of power of the /a posteriori/ tests used ? Do I miss something important in basic stats or in R ? How to highlight differences among 'cds' groups seen with aov() ? The apparent paradox is only apparent. This sort of thing can and does happen. One way of thinking about this situation is to envisage a circle (Anova) and a square (multiple comparisons), superimposed, with the corners of the square sticking outside of the circle, and the extremities of the circle protruding beyond the edges of the square. You get a ``significant'' result from the Anova if a point lands outside the circle; you get a ``significant'' result from the multiple comparisons if a point lands outside the square. So if a point lands in the corners of the square that stick out beyond the circle, you have a ``significant'' Anova result, but find no ``significant'' differences in the multiple comparisons. Conversely a point could land in the extremities of the circle that protrude beyond the edges of the square, in which case you would find ``significant'' differences in the multiple comparisons but your Anova test would not be ``significant''. These are rare but not unheard of phenomena. The essence of the situation is that the data are giving you an ambiguous message. There is no real way to resolve the ambiguity except by collecting more data. Note that if there is a significant Anova result there will be at least one ``contrast'' amongst the means that is significantly different from zero on an a posteriori basis. This contrast need not however be a pairwise difference between means. cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] How to convert List object to function arguments?
Dear R gurus,
I have a function goftests that receives the following arguments:
* a vector x of data values;
* a distribution name dist;
* the dots list (...) containing a list a parameters to pass to CDF
function;
and calls several goodness-of-fit tests on the given data values against
the given distribution.
That is:
# BEGIN CODE SNIP #
# Covert a distribution name to the related CDF function name
distname2cdfname - function( dist )
{
if ( dist == beta ) { return( pbeta ); }
if ( dist == cauchy ) { return( pcauchy ); }
# many other and personalized (e.g. pareto, ...) distributions ...
return( ); # fall-back case
}
# Performs some GoF tests (KS, Chi-Square, Anderson-Darling,...)
# (the ... list contains parameters for CDF function)
goftests - function( x, dist, ... )
{
cdfname - distname2cdfname( dist );
res$ks - ks.test( x, cdfname, ... );
# res$chisq - ...
# res$anddarl - ...
return( res )
};
# END CODE SNIP #
So the problem is passing ... to CDF function (for instance, see
ks.test above) in the right form. The ... is passed (to goftests)
as a list object and it should be converted to an argument list.
For instance:
# BEGIN CODE SNIP #
parms - list( shape1 = 2, shape2 = 5 );
goftests( x, beta, parms[[shape1]], parms[[shape2]] ); # Works!
goftests( x, beta, parms ) # Don't Works!
parms - list( aNum = 5, aVector = c(1,2,3), aMatrix =
matrix(c(4,5,6,7,8,9),nrow=2,byrow=T) );
goftests( x, my-special-distr, parms[[aVector]], parms[[aMatrix]],
parms[[aNumber]] ); # Works!
goftests( x, my-special-distr, parms ) # Don't Works!
# END CODE SNIP #
Obviously I have to use the don't work form.
How can I do this in R (if possible)?
Thank you very much in advance!
Best regards,
-- Marco
__
R-help@stat.math.ethz.ch 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.
Re: [R] How to convert List object to function arguments?
Have a look at do.call
Hadley
On 3/3/07, Shiazy [EMAIL PROTECTED] wrote:
Dear R gurus,
I have a function goftests that receives the following arguments:
* a vector x of data values;
* a distribution name dist;
* the dots list (...) containing a list a parameters to pass to CDF
function;
and calls several goodness-of-fit tests on the given data values against
the given distribution.
That is:
# BEGIN CODE SNIP #
# Covert a distribution name to the related CDF function name
distname2cdfname - function( dist )
{
if ( dist == beta ) { return( pbeta ); }
if ( dist == cauchy ) { return( pcauchy ); }
# many other and personalized (e.g. pareto, ...) distributions ...
return( ); # fall-back case
}
# Performs some GoF tests (KS, Chi-Square, Anderson-Darling,...)
# (the ... list contains parameters for CDF function)
goftests - function( x, dist, ... )
{
cdfname - distname2cdfname( dist );
res$ks - ks.test( x, cdfname, ... );
# res$chisq - ...
# res$anddarl - ...
return( res )
};
# END CODE SNIP #
So the problem is passing ... to CDF function (for instance, see
ks.test above) in the right form. The ... is passed (to goftests)
as a list object and it should be converted to an argument list.
For instance:
# BEGIN CODE SNIP #
parms - list( shape1 = 2, shape2 = 5 );
goftests( x, beta, parms[[shape1]], parms[[shape2]] ); # Works!
goftests( x, beta, parms ) # Don't Works!
parms - list( aNum = 5, aVector = c(1,2,3), aMatrix =
matrix(c(4,5,6,7,8,9),nrow=2,byrow=T) );
goftests( x, my-special-distr, parms[[aVector]], parms[[aMatrix]],
parms[[aNumber]] ); # Works!
goftests( x, my-special-distr, parms ) # Don't Works!
# END CODE SNIP #
Obviously I have to use the don't work form.
How can I do this in R (if possible)?
Thank you very much in advance!
Best regards,
-- Marco
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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.
Re: [R] How to convert List object to function arguments?
do.call createa a function call and evaluates it. I think this isn't
for me. Same thing for call; it wants the function name as first argument.
However, I have to pass to ks.test the CDF function name and,
separately, the related arguments.
ks.test( x, cdfname, ... );
The problem is ... comes as a list object and I didn't find a way to
coerce this object to a arguments list, preserving names a values
(note each list item can be a complex object such as a vector, matrix,
... so I cannot use unlist o as.array)
-- Marco
hadley wickham wrote:
Have a look at do.call
Hadley
On 3/3/07, Shiazy [EMAIL PROTECTED] wrote:
Dear R gurus,
I have a function goftests that receives the following arguments:
* a vector x of data values;
* a distribution name dist;
* the dots list (...) containing a list a parameters to pass to CDF
function;
and calls several goodness-of-fit tests on the given data values against
the given distribution.
That is:
# BEGIN CODE SNIP #
# Covert a distribution name to the related CDF function name
distname2cdfname - function( dist )
{
if ( dist == beta ) { return( pbeta ); }
if ( dist == cauchy ) { return( pcauchy ); }
# many other and personalized (e.g. pareto, ...) distributions ...
return( ); # fall-back case
}
# Performs some GoF tests (KS, Chi-Square, Anderson-Darling,...)
# (the ... list contains parameters for CDF function)
goftests - function( x, dist, ... )
{
cdfname - distname2cdfname( dist );
res$ks - ks.test( x, cdfname, ... );
# res$chisq - ...
# res$anddarl - ...
return( res )
};
# END CODE SNIP #
So the problem is passing ... to CDF function (for instance, see
ks.test above) in the right form. The ... is passed (to goftests)
as a list object and it should be converted to an argument list.
For instance:
# BEGIN CODE SNIP #
parms - list( shape1 = 2, shape2 = 5 );
goftests( x, beta, parms[[shape1]], parms[[shape2]] ); # Works!
goftests( x, beta, parms ) # Don't Works!
parms - list( aNum = 5, aVector = c(1,2,3), aMatrix =
matrix(c(4,5,6,7,8,9),nrow=2,byrow=T) );
goftests( x, my-special-distr, parms[[aVector]], parms[[aMatrix]],
parms[[aNumber]] ); # Works!
goftests( x, my-special-distr, parms ) # Don't Works!
# END CODE SNIP #
Obviously I have to use the don't work form.
How can I do this in R (if possible)?
Thank you very much in advance!
Best regards,
-- Marco
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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.
Re: [R] How to convert List object to function arguments?
With a little change it's seem to work: x - c(0, 1855, 72, 4830, 493, 424, 193, 2489, 156262, 4557, 958) params - list(shape2=5, shape1=2) do.call( ks.test, c(list(x), cdfname( beta ), params )) In fact if I do call(ks.test, list(x=x, cdfname=cdfname, ...)) I get: ks.test(list(x = c(0, 1855, 72, 4830, 493, 424, 193, 2489, 156262, 4557, 958), y = pbeta, list(shape2 = 5, shape1 = 2))) and the error: Error in y(sort(x), ...) : argument shape2 is missing, with no default Instead with the new form: call( ks.test, c(list(x), mg_dists_cdfName( beta ), parms )) I get: ks.test(list(c(0, 1855, 72, 4830, 493, 424, 193, 2489, 156262, 4557, 958), pbeta, shape2 = 5, shape1 = 2)) and no error. Thank you so much!!! -- Marco hadley wickham wrote: On 3/3/07, Shiazy [EMAIL PROTECTED] wrote: do.call createa a function call and evaluates it. I think this isn't for me. Same thing for call; it wants the function name as first argument. However, I have to pass to ks.test the CDF function name and, separately, the related arguments. ks.test( x, cdfname, ... ); The problem is ... comes as a list object and I didn't find a way to coerce this object to a arguments list, preserving names a values (note each list item can be a complex object such as a vector, matrix, ... so I cannot use unlist o as.array) I think do.call(ks.test, list(x=x, cdfname=cdfname, ...)) will do what you want. Hadley PS. You don't need ; at the end of every line. __ R-help@stat.math.ethz.ch 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.
Re: [R] Mitools and lmer
On 3/2/07, Beth Gifford [EMAIL PROTECTED] wrote: Hey there I am estimating a multilevel model using lmer. I have 5 imputed datasets so I am using mitools to pool the estimates from the 5 datasets. Everything seems to work until I try to use MIcombine to produced pooled estimates. Does anyone have any suggestions? The betas and the standard errors were extracted with no problem so everything seems to work smoothly up until that point. I'm not familiar with the mltools package and I didn't see it listed in the CRAN packages. Can you provide a reference or a link to the package? Program #Read data data.dir-system.file(dta,package=mitools) files.imp-imputationList(lapply(list.files(data.dir, pattern=imp.\\.dta, full=TRUE), read.dta)) #estimate model over each imputed dataset model0-with(files.imp,lmer( erq2tnc ~1+trt2+nash+wash+male+coh2+coh3+(1 | sitebeth))) #extract betas and standard errors betas-MIextract(model0,fun=coef) vars-MIextract(model0,fun=vcov) #Combine the results summary(MIcombine(betas,vars)) Error in cbar + results[[i]] : non-numeric argument to binary operator Error in summary(MIcombine(betas, vars)) : error in evaluating the argument 'object' in selecting a method for function 'summary' First use traceback() to discover where the (first) error occurred. My guess is that Mlcombine expects a particular type of object for the vars argument and it is not getting that type (and not checking for the correct type). Thanks Beth [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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.
Re: [R] How to convert List object to function arguments?
Patrick Burns wrote:
You might have found 'do.call' in S Poetry.
I've taken a look just now.
Thank you so much!
-- Marco
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Shiazy wrote:
Dear R gurus,
I have a function goftests that receives the following arguments:
* a vector x of data values;
* a distribution name dist;
* the dots list (...) containing a list a parameters to pass to CDF
function;
and calls several goodness-of-fit tests on the given data values
against the given distribution.
That is:
# BEGIN CODE SNIP #
# Covert a distribution name to the related CDF function name
distname2cdfname - function( dist )
{
if ( dist == beta ) { return( pbeta ); }
if ( dist == cauchy ) { return( pcauchy ); }
# many other and personalized (e.g. pareto, ...) distributions ...
return( ); # fall-back case
}
# Performs some GoF tests (KS, Chi-Square, Anderson-Darling,...)
# (the ... list contains parameters for CDF function)
goftests - function( x, dist, ... )
{
cdfname - distname2cdfname( dist );
res$ks - ks.test( x, cdfname, ... );
# res$chisq - ...
# res$anddarl - ...
return( res )
};
# END CODE SNIP #
So the problem is passing ... to CDF function (for instance, see
ks.test above) in the right form. The ... is passed (to
goftests) as a list object and it should be converted to an
argument list.
For instance:
# BEGIN CODE SNIP #
parms - list( shape1 = 2, shape2 = 5 );
goftests( x, beta, parms[[shape1]], parms[[shape2]] ); # Works!
goftests( x, beta, parms ) # Don't Works!
parms - list( aNum = 5, aVector = c(1,2,3), aMatrix =
matrix(c(4,5,6,7,8,9),nrow=2,byrow=T) );
goftests( x, my-special-distr, parms[[aVector]],
parms[[aMatrix]], parms[[aNumber]] ); # Works!
goftests( x, my-special-distr, parms ) # Don't Works!
# END CODE SNIP #
Obviously I have to use the don't work form.
How can I do this in R (if possible)?
Thank you very much in advance!
Best regards,
-- Marco
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[R] Help with paste()
Dear r-helpers,
Could you please tell me what's missing:
rbind(paste('txt.est',1:24, sep = ''))
txt.est1, ... txt.est24 are vectors that I wish to rbind.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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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.
Re: [R] Help with paste()
What do you want to do with rbind?
paste produces a single vector of 24 character-valued elements.
If you want a column vector, you could do that by
x - paste('txt.est',1:24, sep = '')
matrix(x, ncol=1)
-Christos
Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830
www.nuverabio.com
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Michael Kubovy
Sent: Saturday, March 03, 2007 2:30 PM
To: r-help@stat.math.ethz.ch list
Subject: [R] Help with paste()
Dear r-helpers,
Could you please tell me what's missing:
rbind(paste('txt.est',1:24, sep = ''))
txt.est1, ... txt.est24 are vectors that I wish to rbind.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
__
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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.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Help with paste()
On Mar 3, 2007, at 2:29 PM, Michael Kubovy wrote:
Dear r-helpers,
Could you please tell me what's missing:
rbind(paste('txt.est',1:24, sep = ''))
txt.est1, ... txt.est24 are vectors that I wish to rbind.
the paste call just returns a vector of the strings txt.est1 and so
on. Then you tell it to rbind this vector with nothing else.
You might want to try something like this, though I hope someone else
comes with a better solution:
cmd - paste(rbind(,paste('txt.est',1:24, sep = '',collapse=, ),
), sep=)
eval(parse(text=cmd))
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
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[R] R software to place points on Yahoo maps
Is there any R software that create an image from Yahoo maps together with points of known UTM coordinates (or lat/long marked? Note that my region of interest is not covered in sufficient detail by Google maps. It actually does not have to be Yahoo maps as long as it has sufficient coverage of my region but that's the one I have found with coverage of my region. The scale I am interested in is a city block. Thanks. __ R-help@stat.math.ethz.ch 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] How to override ordering of panels in xyplot()
Dear r-helpers, I'm conditioning an xyplot on a variable whose levels are'low', 'med', 'high'. How do I override the alphabetical ordering for the panels of the plot? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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.
Re: [R] Help with paste()
On Sat, 2007-03-03 at 14:29 -0500, Michael Kubovy wrote:
Dear r-helpers,
Could you please tell me what's missing:
rbind(paste('txt.est',1:24, sep = ''))
txt.est1, ... txt.est24 are vectors that I wish to rbind.
Micheal,
Try this, presuming that each vector is the same length:
# Create three vectors
txt.est1 - letters
txt.est2 - letters
txt.est3 - letters
MAT - t(sapply(paste('txt.est',1:3, sep = ''), get))
MAT
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
txt.est1 a b c d e f g h i j k l
txt.est2 a b c d e f g h i j k l
txt.est3 a b c d e f g h i j k l
[,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
txt.est1 m n o p q r s t u v
txt.est2 m n o p q r s t u v
txt.est3 m n o p q r s t u v
[,23] [,24] [,25] [,26]
txt.est1 w x y z
txt.est2 w x y z
txt.est3 w x y z
So in your case:
MAT - t(sapply(paste('txt.est',1:24, sep = ''), get))
See ?get
You need to use get() in order to 'get' the actual vectors using the
vector names created in paste()
HTH,
Marc Schwartz
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to override ordering of panels in xyplot()
On 3/3/07, Michael Kubovy [EMAIL PROTECTED] wrote: Dear r-helpers, I'm conditioning an xyplot on a variable whose levels are'low', 'med', 'high'. How do I override the alphabetical ordering for the panels of the plot? This has less to do with xyplot and more to do with the default of the 'levels' argument in the factor() function. Just make sure the levels are in the right order in your data when xyplot is called. Deepayan __ R-help@stat.math.ethz.ch 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] function doesnt return/create object
hello,
i have written a function to extract certain lines from a matrix. the
result is a matrix with 6 cols, named dynamically according to the
functions arguments.
the problem is now, that i'm not able to return the resultmatrix for
further use. the object is not being created.
example from my console:
getans(27,27)
[...]
[189,] 3969 161 27101
[190,] 2142 87 27101
[191,] 1318 52 27101
[192,] 2881 120 27101
[193,] 3669 152 27101
[194,] 5653 229 27101
[195,] 2308 95 27102
[196,] 4942 200 27101
the matrix ansblock27 contains answers to block 27
ansblock27
error: object ansblock27 not found
the code of the function:
getans = function(x=qids,bnr=1,type=block)
{
#generate name of matrix
matnam=paste(ans,type,as.character(bnr),sep=)
#display result matrix
show(assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in
% x), , drop = FALSE])),ncol=dim(allans)[2])))
#create result matrix
assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in%
x), , drop = FALSE])),ncol=dim(allans)[2]))
#print info
cat(the matrix,matnam,contains answers to,type,as.character(bnr))
}
i have tried to use return, but had no success.
what else can i do?
thx in advance, and have a nice weekend
regards,
matthias
es schreibt Ihnen:
Matthias Bannert
---
mediabar (Off / Bannert GbR)
Brüelstr.21
78462 Konstanz
fon.: 0711 50 88 72 34
mobil.: 0179 29 85 630
web: http://www.mediabar.info
email: [EMAIL PROTECTED]
[[alternative HTML version deleted]]
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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] apply ? function doesnt create object
hello,
i have written a function to extract certain lines from a matrix. the
result is a matrix with 6 cols, named dynamically according to the
functions arguments.
the problem is now, that i'm not able to return the resultmatrix for
further use. the object is not being created.
example from my console:
getans(27,27)
[...]
[189,] 3969 161 27101
[190,] 2142 87 27101
[191,] 1318 52 27101
[192,] 2881 120 27101
[193,] 3669 152 27101
[194,] 5653 229 27101
[195,] 2308 95 27102
[196,] 4942 200 27101
the matrix ansblock27 contains answers to block 27
ansblock27
error: object ansblock27 not found
the code of the function:
getans = function(x=qids,bnr=1,type=block)
{
#generate name of matrix
matnam=paste(ans,type,as.character(bnr),sep=)
#display result matrix
show(assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in
% x), , drop = FALSE])),ncol=dim(allans)[2])))
#create result matrix
assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in%
x), , drop = FALSE])),ncol=dim(allans)[2]))
#print info
cat(the matrix,matnam,contains answers to,type,as.character(bnr))
}
i have tried to use return, but had no success.
what else can i do?
thx in advance, and have a nice weekend
regards,
[[alternative HTML version deleted]]
__
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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] Sigmoidal fitting
I am trying to write a function that fits a sigmoid given a X and Y vector guessing the start parameters. I use nls. What I did (enclosed) seems to work well with many data points but if I want to fit small vectors like : pressure - c(5,15,9,35,45) gas - c(1000,2000,3000,4000,5000) it do not work. The help page says that it do no not work on zero residual data. Massimo Cressoni __ R-help@stat.math.ethz.ch 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] Fitting a sigmoid
I am trying to write a function that fits a sigmoid given a X and Y vector
guessing the start parameters.
I use nls. What I did (enclosed) seems to work well with many data points but
if I want to fit small
vectors like :
pressure - c(5,15,9,35,45)
gas - c(1000,2000,3000,4000,5000)
it do not work. The help page says that it do no not work on zero residual data.
Massimo Cressoni
PS
The functions I wrote are the following :
x25 = function(y_range)
{
x25r = min(y_range) + (max(y_range) - min(y_range))/4
x25r
}
x75 = function(y_range)
{
x75r = min(y_range) + 3*(max(y_range) - min(y_range))/4
x75r
}Get
GetStartSigmoidValues = function(pointsY)
{
start_a = max(pointsY) - min(pointsY)
start_x0 = min(pointsY) + (max(pointsY) - min(pointsY))/2
start_b = (x75(pointsY) - x25(pointsY))/4
start_y0 = min(pointsY)
start_list = list(a=start_a,x0=start_x0,b=start_b,y0=start_y0)
start_list
}
FitSigmoid = function(pointsX,pointsY)
{
start_list = GetStartSigmoidValues(pointsY)
fitting = nls(pointsY ~ y0+a/(1+exp(-(pointsX - x0)/b)),start=start_list)
fitting
}
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Re: [R] apply ? function doesnt create object
On Mar 3, 2007, at 4:28 PM, bunny , lautloscrew.com wrote:
Please use - for assignments instead of = :
getans = function(x=qids,bnr=1,type=block)
{
#generate name of matrix
matnam=paste(ans,type,as.character(bnr),sep=)
#display result matrix
show(assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in
% x), , drop = FALSE])),ncol=dim(allans)[2])))
You are assigning things twice here.
#create result matrix
assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in%
x), , drop = FALSE])),ncol=dim(allans)[2]))
The documentation for assign makes it pretty clear that the
assignment happens by default in the current environment, so it will
be local to the function unless you alter the call. The description
there, along with the examples, and a study of environments, should
provide you with the answer.
#print info
cat(the matrix,matnam,contains answers to,type,as.character
(bnr))
}
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
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[R] tcl/tk printing to console is far too slow
Hello - I am finding that printing to the console from a function that
is invoked from tcl/tk (i.e. pushing a button) is really slow.
Consider the following example.
doStuff - function() {
source(file.path(system.file(package = base), demo,
is.things.R), echo=TRUE)
}
tt - tktoplevel()
button.widget - tkbutton(tt,text=Do Stuff, command=doStuff)
tkpack(button.widget)
I find that this is significantly slower than if I ran source(...)
directly from the console prompt. In the back of my mind, I am thinking
this might be some effect related to multi-threading and the
locking/unlocking of a mutex - am I right?
Any help to speed this up would be appreciated.
Thanks,
Alex Couture-Beil
PS: I am running this test with R 2.4.1 on WinXP
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] function doesnt return/create object
Instead of trying to create object back in the global environment (which is
not really recommended from a function), return the answer in a list that
you can then access it as you want. Here is an example:
getans - function(x){
+ # create the name that you want in the list
+ .name - paste(x, '.Ans', sep='')
+ .ans - list(runif(10)) # create some data to return
+ names(.ans) - .name
+ .ans# return the answer
+ }
my.ans - getans('newName')
my.ans # show what was returned
$newName.Ans
[1] 0.2059746 0.1765568 0.6870228 0.3841037 0.7698414 0.4976992 0.7176185
0.9919061 0.3800352 0.7774452
# access by the new name
my.ans$newName.Ans
[1] 0.2059746 0.1765568 0.6870228 0.3841037 0.7698414 0.4976992 0.7176185
0.9919061 0.3800352 0.7774452
On 3/3/07, Matthias Bannert [EMAIL PROTECTED] wrote:
hello,
i have written a function to extract certain lines from a matrix. the
result is a matrix with 6 cols, named dynamically according to the
functions arguments.
the problem is now, that i'm not able to return the resultmatrix for
further use. the object is not being created.
example from my console:
getans(27,27)
[...]
[189,] 3969 161 27101
[190,] 2142 87 27101
[191,] 1318 52 27101
[192,] 2881 120 27101
[193,] 3669 152 27101
[194,] 5653 229 27101
[195,] 2308 95 27102
[196,] 4942 200 27101
the matrix ansblock27 contains answers to block 27
ansblock27
error: object ansblock27 not found
the code of the function:
getans = function(x=qids,bnr=1,type=block)
{
#generate name of matrix
matnam=paste(ans,type,as.character(bnr),sep=)
#display result matrix
show(assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in
% x), , drop = FALSE])),ncol=dim(allans)[2])))
#create result matrix
assign(matnam,matrix(as.numeric(as.matrix(allans[(allans[, 3] %in%
x), , drop = FALSE])),ncol=dim(allans)[2]))
#print info
cat(the matrix,matnam,contains answers to,type,as.character(bnr))
}
i have tried to use return, but had no success.
what else can i do?
thx in advance, and have a nice weekend
regards,
matthias
es schreibt Ihnen:
Matthias Bannert
---
mediabar (Off / Bannert GbR)
Brüelstr.21
78462 Konstanz
fon.: 0711 50 88 72 34
mobil.: 0179 29 85 630
web: http://www.mediabar.info
email: [EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] lattice histogram
How to add mean,sd, number of observation in each panel for lattice histogram? Aimin __ R-help@stat.math.ethz.ch 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.
