Re: [R] custom graphing of box and whisker plots

2012-06-29 Thread Mark Difford
ve provided in your example.) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/custom-graphing-of-box-and-whisker-plots-tp4634826p463484

Re: [R] Fwd: How to best analyze dataset with zero-inflated loglinear dependent variable?

2012-06-09 Thread Mark Difford
is > loglinear. I believe this is called a zero-inflated loglinear > continuous dependent variable. Look at package gamlss, where you might find something. It has a number of zero-inflated and zero-adjusted distributions. Package VGAM might also fit this. Regards, Mark. - Mark Difford (

Re: [R] meaning of sigma from LM, is it the same as RMSE

2012-04-05 Thread Mark Difford
9.8652 0.54807 > sum(resid(T.lm)^2) [1] 9.865225 > sqrt(sum(resid(T.lm)^2)/18) [1] 0.7403162 > sqrt(sum(resid(T.lm)^2)/20) ## RMSE (y = 20) [1] 0.7023256 ## OR > sqrt(mean((y-fitted(T.lm))^2)) [1] 0.7023256 Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Depar

Re: [R] Principal Components for matrices with NA

2012-02-28 Thread Mark Difford
l find a full range of options for carrying out principal component analysis using matrices with missing values. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: ht

Re: [R] error in fitdistr

2012-02-23 Thread Mark Difford
uot;, start=list(df=1), method="Brent")$estimate) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/error-in-fitdistr-tp44

Re: [R] Why does the order of terms in a formula translate into different models/ model matrices?

2012-01-27 Thread Mark Difford
en there is no problem reversing terms: > logLik(m2 <- lm(Y ~ A*B + x*A, dat)) 'log Lik.' -13.22186 (df=11) > logLik(m3 <- lm(Y ~ x*A + A*B, dat)) 'log Lik.' -13.22186 (df=11) Regards, Mark Difford - Mark Difford (Ph.D.) Research Associate Botany Department Nelso

Re: [R] a question about taylor.diagram in plotrix package

2012-01-21 Thread Mark Difford
lcome to it, but I don't have access to it until tomorrow or the day after. I will send it to you off list. Note: It would be nice to have a real name and affiliation. Regards Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port El

Re: [R] 4th corner analysis ade4 - what do the colors mean

2012-01-20 Thread Mark Difford
king at the summary statistics: "The function plot produces a graphical representation of the results (white for non siginficant, light grey for negative sgnificant and dark grey for positive suignficant relationships)." Regards, Mark. - Mark Difford (Ph.D.) Research Associate Bot

Re: [R] Unexpected results using the oneway_test in the coin package

2012-01-10 Thread Mark Difford
lue(NDWD, method = "single-step")) ## use nparcomp library(nparcomp) npar <- nparcomp(breeding ~ habitat, data = mydata, type = "Tukey") npar Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth,

Re: [R] Lavaan and Average Variance Extracted

2011-12-28 Thread Mark Difford
On Dec 28, 2011 at 3:47am T.M. Rajkumar wrote: > I need a way to get at the Variance Extracted information. Is there a > simple way to do the calculation. Lavaan > does not seem to output this. It does. See: library(lavaan) ?inspect inspect( fit, "rsquare" ) Regards, Mark.

Re: [R] PCA on high dimentional data

2011-12-10 Thread Mark Difford
mponent (PC). Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/PCA-on-high-dimentional-data-tp4180467p4180890.html Sent from the R help m

Re: [R] How to scale arrows to approximately fill a plot region?

2011-12-07 Thread Mark Difford
3 <- min(coocol[, 2])/born[3] k4 <- max(coocol[, 2])/born[4] k <- c(k1, k2, k3, k4) coocol <- 0.9 * coocol/max(k) s.arrow(coocol, clab = clab.col, add.p = TRUE, sub = sub, possub = "bottomright") add.scatter.eig(x$eig, x$nf, xax, yax, posi = posieig,

Re: [R] glht for lme object with significant interaction term

2011-11-23 Thread Mark Difford
action(Tdf$treat, Tdf$day, drop=T) m.finalI<-lme(mean.on.active ~ IntFac,random=~1|id,na.action=na.omit, data=Tdf) summary(m.final) summary(m.finalI) glht(m.finalI, linfct=mcp(IntFac = "Tukey")) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metr

Re: [R] Has anyone used SIAR package add on?

2011-11-13 Thread Mark Difford
urse, if your data set has many rows then you want to adjust the "by" argument (increase it). Twenty to thirty rows should be sufficient. myPartData <- myData[seq(1, nrow(myDat), by=3), ] dput(myPartData) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department N

Re: [R] Errors in SIAR

2011-11-11 Thread Mark Difford
d indeed on R`s homepage. Regards, Mark. [1] R is case-sensitive: the package is called siar, not SIAR. Please respect the author's designation. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this messa

Re: [R] Estimate of intercept in loglinear model

2011-11-08 Thread Mark Difford
t; fitted(glm.D93N) 12345678 9 19.40460 16.52414 14.07126 19.40460 16.52414 14.07126 19.40460 16.52414 14.07126 Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University

Re: [R] Estimate of intercept in loglinear model

2011-11-07 Thread Mark Difford
would have said, "But it's elementary, my dear Watson. Oftentimes a corpse is not necessary, as here." Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context

Re: [R] Estimate of intercept in loglinear model

2011-11-07 Thread Mark Difford
"3" So here the intercept represents the estimated counts at the first level of "outcome" (i.e. outcome = 1) and the first level of "treatment" (i.e. treatment = 1). > predict(glm.D93, newdata=data.frame(outcome="1", treatment="1")) 1 3.044522

Re: [R] Estimate of intercept in loglinear model

2011-11-07 Thread Mark Difford
On Nov 07, 2011 at 9:04pm Mark Difford wrote: > So here the intercept represents the estimated counts... Perhaps I should have added (though surely unnecessary in your case) that exponentiation gives the predicted/estimated counts, viz 21 (compared to 18 for the saturated model). ## &g

Re: [R] testing significance of axis loadings from multivariate dudi.mix

2011-11-06 Thread Mark Difford
## scaling not accounted for: deug.princ <- princomp(deug$tab, cor=F) qqplot(predict(deug.princ)[,1], tt[,1]) rm(tt, deug.dudi, deug.princ) Note that in the code given above, "as.matrix(deug.dudi$tab) %*% as.matrix(deug.dudi$c1)" is based on how stats:::predict.princomp does it. Regards, Mark

Re: [R] Determining r2 values for a SEM

2011-11-04 Thread Mark Difford
On Nov 04, 2011 at 6:55pm Katherine Stewart wrote: > Is there a way to determine r2 values for an SEM in the SEM package or > another way to get > these values in R? Katherine, rsquare.sem() in package sem.additions will do it for you. Regards, Mark. ----- Mark Difford (Ph.D.)

Re: [R] Contrasts with an interaction. How does one specify the dummy variables for the interaction

2011-10-29 Thread Mark Difford
John, There is a good example of one way of doing this in "multcomp-examples.pdf" of package multcomp. See pages 8 to 10. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this

Re: [R] Levenshtein-Distance

2011-10-20 Thread Mark Difford
ackage vwr has a function to calculate Levenshtein distances. Regards, Mark. ----- Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/Levenshtein-Distance-tp3920

Re: [R] Ordered probit model -marginal effects and relative importance of each predictor-

2011-08-28 Thread Mark Difford
or a), and the Anova() function in his car package (for b). Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/Ordered-probit-model-margin

Re: [R] How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction

2011-08-19 Thread Mark Difford
riptive multivariate analysis}, journal = {Statistical Science}, year = {1998}, volume = {13}, pages = {307--336}, abstract = {} } Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this

Re: [R] How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction

2011-08-18 Thread Mark Difford
i.mix$li, it doesn't matter: the former is a scaled version of the latter. Same for dudi.acm. To see this do the following: ## plot(x18.dudi.mix$li[, 1], x18.dudi.mix$l1[, 1]) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan Un

Re: [R] How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction

2011-08-18 Thread Mark Difford
ontinuous variables, viz dudi.mix and dudi.hillsmith in package ade4. De Leeuw's homals method takes this a step further, doing amongst other things, a non-linear version of PCA using any type of variable. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandel

Re: [R] How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction

2011-08-18 Thread Mark Difford
; the correct values as a predictor of > logistic regression model like PC1 of PCA? Hi Kohkichi, If you want to do this, i.e. PCA-type analysis with different variable-types, then look at dudi.mix() in package ade4 and homals() in package homals. Regards, Mark. - Mark Difford (Ph.D

Re: [R] Getting vastly different results when running GLMs

2011-08-17 Thread Mark Difford
t but are identical ## Type I SS anova(model1) anova(model2) ## Type II SS library(car) Anova(model1, type="II") Anova(model2, type="II") Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth,

Re: [R] Regression - how to deal with past values?

2011-08-16 Thread Mark Difford
odels) by Giovanni Petris Regards, Mark. ----- Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/Regression-how-to-deal-with-past-values-tp3745817p3747302.html

Re: [R] GLM different results with the same factors

2011-07-28 Thread Mark Difford
Type II analysis of variance test that I advised you to do is carried out. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/GLM-different-

Re: [R] a question about glht function

2011-07-26 Thread Mark Difford
otes ("f_GROUP"). Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/a-question-about-glht-function-tp3695038p3695067.html Sent fro

Re: [R] GLM different results with the same factors

2011-07-24 Thread Mark Difford
called Type II tests. To get them use drop1() on your glm object or install the car package and use its Anova function. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context

Re: [R] Latex Table Help on R

2011-07-21 Thread Mark Difford
\underset','{',data$SDs,'}','{',data$means,'}$', sep="") Hope this gets you going. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this

Re: [R] Package rrcov, functions PcaCov, PcaHubert, PcaGrid

2011-07-13 Thread Mark Difford
ou at least need to feed it something sensible. Look at your matrix: x<-matrix(0.5,30,30) x Try the following: x <- rmultinom(30, size = 30, prob=rep(c(0.1,0.2,0.8), 30)) PcaCov(x) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan Un

Re: [R] ordiellipse

2011-05-25 Thread Mark Difford
s here, > however I would like to plot one if I could, if only for the sake of > pictorial consistency. Ouch! for the rod that is likely to come. Advice? Collect more data, for the sake of pictorial consistency. And if you can't then you can't. What you have are the (available)

Re: [R] Multinomial Logistical Model

2011-05-25 Thread Mark Difford
to do this. Suggest you do some work in that area. Look especially at how model formulas are used/specified. This is at least one area where you have gone wrong, as the error message clearly tells you. Good luck. Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela M

Re: [R] combine lattice plot and standard R plot

2011-05-05 Thread Mark Difford
s, 3(2):7-12, October 2003 http://cran.r-project.org/doc/Rnews/Rnews_2003-2.pdf Hope this helps. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789

Re: [R] Panels order in lattice graphs

2011-05-05 Thread Mark Difford
dex.cond [[1]] [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 T.xyplot$index.cond[[1]] <- c(13, 1:12) print(T.xyplot) Hope this helps to solve your problem. Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, So

Re: [R] bwplot in ascending order

2011-05-02 Thread Mark Difford
On May 01 (2011) Harold Doran wrote: >> Can anyone point me to examples with R code where bwplot in lattice is >> used to order the boxes in >> ascending order? You don't give an example and what you want is not entirely clear. Presumably you want ordering by the median (boxplot, and based on t

Re: [R] Problem with pairs() in nlme

2011-04-09 Thread Mark Difford
Apr 08, 2011; 11:05pm dgmaccon wrote: >> I get the same error: >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "lmList", for signature >> "formula", "nfnGroupedData" I get no such error. You need to provide more information (platform &c.) ##

Re: [R] glm: modelling zeros as binary and non-zeroes as coming from a continuous distribution

2011-03-30 Thread Mark Difford
On Mar 30, 2011; 11:41am Mikhail wrote: >> I'm wondering if there's any way to do the same in R (lme can't deal >> with this, as far as I'm aware). You can do this using the pscl package. Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/glm-modelling-zeros-as-bina

Re: [R] Tukey HSD test using Multcomp

2011-03-25 Thread Mark Difford
Mar 25, 2011; 12:58am Simon Bate wrote: >> I've been happily using the TukeyHSD function to produce Tukeys HSD tests >> but have decided to try >> out Multcomp instead. However when I carry out the test repeatedly I have >> found that Multcomp >> produces slightly different values each time. (se

Re: [R] [R-sig-ME] lmm WITHOUT random factor (lme4)

2011-03-19 Thread Mark Difford
On Mar 19, 2011; 01:39am Andrzej Galecki wrote: >> I agree with you that caution needs to be exercised. Simply because >> mathematically the same >> likelihood may be defined using different constant. Yes. But this is ensured by the implementation. If the call to anova() is made with the lm$obj

Re: [R] lmm WITHOUT random factor (lme4)

2011-03-18 Thread Mark Difford
On Mar 18, 2011; 10:55am Thierry Onkelinx wrote: >> Furthermore, I get an error when doing an anova between a lm() and a >> lme() model. Hi Thierry, You get this error because you have not done the comparison the way I said you should, by putting the lme$obj model first in the call to anova(). T

Re: [R] lmm WITHOUT random factor (lme4)

2011-03-18 Thread Mark Difford
Apologies to all for the multiple posting. Don't know what caused it. Maybe it _is_ time to stop using Nabble after all... Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/lmm-WITHOUT-random-factor-lme4-tp3384054p3386833.html Sent from the R help mailing list archive

Re: [R] lmm WITHOUT random factor (lme4)

2011-03-17 Thread Mark Difford
On Mar 17, 2011; 04:29pm Thierry Onkelinx wrote: >> You cannot compare lm() with lme() because the likelihoods are not the >> same. Use gls() instead of lm() And perhaps I should have added the following: First para on page 155 of Pinheiro & Bates (2000) states, "The anova method can be used to

Re: [R] lmm WITHOUT random factor (lme4)

2011-03-17 Thread Mark Difford
On Mar 17, 2011; 04:29pm Thierry Onkelinx wrote: >> You cannot compare lm() with lme() because the likelihoods are not the >> same. Use gls() instead of lm() Hi Thierry, Of course, I stand subject to correction, but unless something dramatic has changed, you can. gls() can be used if you need to

Re: [R] lmm WITHOUT random factor (lme4)

2011-03-17 Thread Mark Difford
On Mar 17, 2011; 11:43am Baugh wrote: >> Question: can I simply substitute a dummy var (e.g. populated by zeros) >> for "ID" to run the model >> without the random factor? when I try this R returns values that seem >> reasonable, but I want to be sure >> this is appropriate. If you can fit the

Re: [R] Problem implementing 'waldtest' when using 'mlogit' package

2011-03-13 Thread Mark Difford
On Mar 13, 2011; 03:44pm Gaurav Ghosh wrote: >> I have been working through the examples in one of the vignettes >> associated with the 'mlogit' >> package, 'Kenneth Train's exercises using the mlogit package for R.' In >> spite of using the code >> unchanged, as well as the data used in the ex

Re: [R] rms: getting adjusted R^2 from ols object

2011-03-09 Thread Mark Difford
On Mar 09, 2011; 11:09am Mark Seto wrote: >> How can I extract the adjusted R^2 value from an ols object (using rms >> package)? >> library(rms) >> x <- rnorm(10) >> y <- x + rnorm(10) >> ols1 <- ols(y ~ x) ## ols1$stats ols1$stats[4] Regards, Mark. -- View this message in context: http:/

Re: [R] Change panel background color in spplot()

2011-03-05 Thread Mark Difford
Marcel, Here is one way: spplot(meuse.grid, zcol = "part.a", par.settings = list(panel.background=list(col="grey"))) ## trellis.par.get() trellis.par.get()$panel.background Regards, Mark. > On 03/05/2011 01:06 PM, Marcel J. wrote: >> Hi! >> >> How does one change the background color of th

Re: [R] mlogit.data

2011-03-01 Thread Mark Difford
My previous posting seems to have got mangled. This reposts it. On Mar 01, 2011; 03:32pm gmacfarlane wrote: >> workdata.csv >> The code I posted is exactly what I am running. What you need is this >> data. Here is the code again. > hbwmode<-mlogit.data("worktrips.csv", shape="long", choice="CHOS

Re: [R] mlogit.data

2011-02-28 Thread Mark Difford
On Feb 28, 2011; 10:33pm Gregory Macfarlane wrote: >> It seems as though the mlogit.data command tries to reassign my >> row.names, >> and doesn't do it right. Is this accurate? How do I move forward? Take the time to do as the posting guide asks you to do (and maybe consider the possibility tha

Re: [R] Set size of plot: in pdf() or par() ?

2011-02-23 Thread Mark Difford
On Feb 23, 2011; 03:32pm Matthieu Stigler wrote: >>> I want to have a rectangular plot of size 0.5*0.3 inches. I am having >>> surprisingly a difficult time to do it... <...snip...> >>> If I specifz this size in pdf(), I get an error... >>> >>> pdf("try.pdf", height=0.3, width=0.5) >>> >>> p

Re: [R] NPMC - replacement has 0 rows (multiple comparisons)

2011-02-21 Thread Mark Difford
On 2011-02-20 20:02, Karmatose wrote: >> I'm trying to include multiple variables in a non-parametric analysis >> (hah!). So far what I've managed to >> figure out is that the NPMC package from CRAN MIGHT be able to do what I >> need... Also look at packages nparcomp and coin (+ multcomp). Both

Re: [R] FW: multivariate regression

2011-02-07 Thread Mark Difford
Deniz, >> There are 3 F statistics, R2 and p-values. But I want just one R2 and >> pvalue for my multivariate >> regression model. Which is as it should. Maybe the following will help, but we are making the dependent variables the independent variables, which may or may not be what you really

Re: [R] different results in MASS's mca and SAS's corresp

2011-02-06 Thread Mark Difford
>> When I came to David's comment, I understood the theory, but not the >> numbers in his answer. I wanted to see the MASS mca answers "match >> up" with SAS, and the example did not (yet). I am inclined to write, "O yea of little faith." David showed perfectly well that when the results of th

Re: [R] Preparing dataset for glmnet: factors to dummies

2011-02-02 Thread Mark Difford
Hi Frank, >> I believe that glmnet scales variables by their standard deviations. >> This would not be appropriate for categorical predictors. That's an excellent point, which many are likely to forget (including me) since one is using a model matrix. The default argument is to standardize inpu

Re: [R] Factor rotation (e.g., oblimin, varimax) and PCA

2011-01-26 Thread Mark Difford
Finn, >> But when I use 'principal' I do not seem to be able to get the same >> results >> from prcomp and princomp and a 'raw' use of eigen: < ...snip... > >> So what is wrong with the rotations and what is wrong with 'principal'? I would say that nothing is wrong. Right at the top of the hel

Re: [R] Problem with factor analysis

2011-01-24 Thread Mark Difford
>> Does anyone know what I am doing wrong? Could be a lot or could be a little, but we have to guess, because you haven't given us the important information. That you are following Crawley is of little or no interest. We need to know what _you_ did. What is "model" and what's in it? ## str(mode

Re: [R] Discriminant Correspondence Analysis

2010-12-14 Thread Mark Difford
Wayne, >> I don't know how to assign a name for the df, or what to put for "fac", >> and what is worse, >> I get an error message saying that the program cannot find the >> "discrimin.coa" command. Before you can use a package you have downloaded you need to "activate" it. There are different w

Re: [R] remove quotes from the paste output

2010-12-11 Thread Mark Difford
Bob, >> Does anybody know how to eliminate the double quotes so that I can use >> the >> variable name (generated with the paste function) further in the code... ?noquote should do it. ## > "varName" [1] "varName" > noquote("varName") [1] varName Regards, Mark. -- View this message in contex

Re: [R] Tukey Test, lme, error: less than two groups

2010-12-03 Thread Mark Difford
Lilith, >> No the big mystery is the Tukey test. I just can't find the mistake, it >> keeps telling me, that >> there are " less than two groups" >> ... >> ### Tukey test ## >> summary(glht(PAM.lme, linfct = mcp(Provenancef = "Tukey"))) >> >> Error message: >> Fehler in glht.matrix(model = li

Re: [R] pca analysis: extract rotated scores?

2010-12-01 Thread Mark Difford
Hi He Zhang, >> Is the following right for extracting the scores? >> ... >> pca$loadings >> pca$score Yes. But you should be aware that the function principal() in package psych is standardizing your data internally, which you might not want. That is, the analysis is being based on the correla

Re: [R] pca analysis: extract rotated scores?

2010-12-01 Thread Mark Difford
Hi Liviu, >> However, I'm still confused on how to compute the scores when rotations >> (such as 'varimax' or other methods in GPArotation) are applied. PCA does an orthogonal rotation of the coordinate system (axes) and further rotation is not usually done (in contrast to factor analysis). Nei

Re: [R] Compute polychoric matrix for more than 2 variables

2010-11-30 Thread Mark Difford
Hi Raquel, >> routine in R to compute polychoric matrix to more than 2 categorical >> variables? I tried polycor >> package, but it seems to be suited only to 2-dimensional problems. Bur surely ?hetcor (in package polycor) does it. Regards, Mark. -- View this message in context: http://r.789

Re: [R] Factor analysis and cfa with asymptotically distributed data

2010-11-24 Thread Mark Difford
Jane, >> Does someone know how to do fa and cfa with strong skewed data? Your best option might be to use a robustly estimated covariance matrix as input (see packages robust/robustbase). Or you could turn to packages FAiR or lavaan (maybe also OpenMx). Or you could try soft modelling via packa

Re: [R] Wilcoxon Rank Sum in R with a multiple testing correction

2010-11-24 Thread Mark Difford
Hi Selthy, >> I'd like to use a Wilcoxon Rank Sum test to compare two populations of >> values. Further, I'd like >> to do this simultaneously for 114 sets of values. Well, you read your data set into R using: ## ?read.table ?read.csv There are other ways to bring in data. Save the import to

Re: [R] changing the limits of a secondary y-axis in a barplot

2010-11-17 Thread Mark Difford
Hi Anna, >> How can I change the barplot so that the left hand axis scales from 0 to >> 15 and the right hand >> axis from 0 to 5? Try this: par(mfrow=c(1,1), mai=c(1.0,1.0,1.0,1.0)) Plot1<-barplot(rbind(Y1,Y2), beside=T, axes=T, names.arg=c("a","b"), ylim=c(0,15), xlim=c(1,9), space=c(0,1), c

Re: [R] ANOVA table and lmer

2010-11-04 Thread Mark Difford
mary(Aov.mod) anova(Lme.mod) anova(Lmer.mod) HTH, Mark Difford. -- View this message in context: http://r.789695.n4.nabble.com/ANOVA-table-and-lmer-tp3027546p3027662.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org m

Re: [R] getting all contrasts from glm

2010-10-22 Thread Mark Difford
Jim, >> In the glm object I can find the contrasts of the main treats vs the >> first i.e. 2v1, 3v1 and >> 4v1 ... however I would like to get the complete set including 3v2, 4v2, >> and 4v3 ... along with >> the Std. Errors of all contrasts. Your best all round approach would be to use the m

Re: [R] Creating publication-quality plots for use in Microsoft Word

2010-09-15 Thread Mark Difford
>> I'd prefer to stick with JPEG, TIFF, PNG, or the like. I'm not sure EPS would fly. Preferring to stick with bitmap formats (like JPEG, TIFF, PNG) is likely to give you the jagged lines and other distortions you profess to want to avoid. EPS (encapsulated postscript, which handles vector+bitm

Re: [R] path analysis

2010-09-07 Thread Mark Difford
Guy, For a partial least squares approach look at packages plspm and pathmox. Also look at sem.additions. Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/path-analysis-tp2528558p2530207.html Sent from the R help mailing list archive at Nabble.com. ___

Re: [R] Coinertia randtest

2010-08-23 Thread Mark Difford
Hi Petar, >> I dunno why, but I cannot make randtes[t].coinertia() from ade4 package >> working. I have two nice distance matrices (Euclidean): >> Could anyone help with this? Yes (sort of). The test has not yet been implemented for dudi.pco, as the message at the end of your listing tells you.

Re: [R] reading lmer table

2010-08-19 Thread Mark Difford
Hi Nicola, >> In few word: does this row indicate a global effect of the predictor >> 'cat' >> or a more specific passage? It indicates a more specific passage. Use anova(m7) for global/omnibus. Check this for yourself by fitting the model with different contrasts. The default "contrasts" in R

Re: [R] [Fwd: Re: Plotting log-axis with the exponential base to

2010-05-11 Thread Mark Difford
Hi All, You can also add a line using lines() if you transform in the call using the same log-base---but not via R's log="y" argument (because of what's stored in par("yaxp")). ## par(mfrow=c(1,3)) plot(1:10, log="y") lines(log10(1:10)) par("yaxp") plot(log10(1:10), yaxt="n") axis(side=2, at=sa

Re: [R] [Fwd: Re: Plotting log-axis with the exponential base to a plot with the default logarithm base 10]

2010-05-11 Thread Mark Difford
Elisabeth, You should listen to Ted (Harding). He answered your question with: >> the vertical axis is scaled logarithmically with the >> numerical annotations corresponding to the *raw* values of Y, >> not to their log-transformed values. Therefore it does not matter >> what base of logarith

Re: [R] Logistic and Linear Regression Libraries

2009-10-31 Thread Mark Difford
tdm wrote: >> OK, I think I've figured it out, the predict of lrm didn't seem to pass >> it through the logistic >> function. If I do this then the value is similar to that of lm. Is this >> by design? Why would it >> be so? Please take some time to read the help files on these functions so th

Re: [R] a publication quality table for summary.zeroinfl()

2009-10-31 Thread Mark Difford
Hi Chris, >> My ideal would be to gather the information onto the clipboard so I >> could paste it into Excel and do the formatting there, but any approach >> would be better than what I have now. I would never use Excel for this since there are far superior tools available. But it is very eas

Re: [R] Logistic and Linear Regression Libraries

2009-10-31 Thread Mark Difford
Hi Phil, >> So far for logistic regression I've tried glm(MASS) and lrm (Design) and >> found there is a big >> difference. Be sure that you mean what you say, that you are saying what you mean, and that you know what you mean when making such statements, especially on this list. glm is not in

Re: [R] Lost all script

2009-10-28 Thread Mark Difford
Hi David, >> Now when I turn on R again the script is now completely blank. This happened to me about 4--5 months ago under Vista. I cannot quite remember what I did but I think I got the script working by opening it in another editor (a hex editor would do) and removing either the first few byt

Re: [R] Missing data and LME models and diagnostic plots

2009-10-21 Thread Mark Difford
gt;>> understand it, one of the strengths of this sort of model is how well >>>> it >>>> deals with missing >>>> data, yet lme requires nonmissing data. >> > > Mark Difford replied > >>You are confusing missing data with an unbalanc

Re: [R] Missing data and LME models and diagnostic plots

2009-10-21 Thread Mark Difford
Peter Flom wrote: >> I am puzzled by the performance of LME in situations where there are >> missing data. As I >> understand it, one of the strengths of this sort of model is how well it >> deals with missing >> data, yet lme requires nonmissing data. You are confusing missing data with an

Re: [R] Re posting various problems with two-way anova, lme, etc.

2009-10-20 Thread Mark Difford
Hi Michael, >> How do you control what is the (intercept) in the model returned by the >> lme function and is there a way to still be able to refer to all groups >> and >> timepoints in there without referring to intercept? Here is some general help. The intercept is controlled by the contrast

Re: [R] What is the difference between prcomp and princomp?

2009-10-19 Thread Mark Difford
Peng Yu wrote: >> Some webpage has described prcomp and princomp, but I am still not >> quite sure what the major difference between them is. The main difference, which could be extracted from the information given in the help files, is that prcomp uses the singular value decomposition [i.e. do

Re: [R] Trendline for a subset of data

2009-10-09 Thread Mark Difford
Hi Steve, >> However, I am finding that ... the trendline ... continues to run beyond >> this data segment >> and continues until it intersects the vertical axes at each side of the >> plot. Your "best" option is probably Prof. Fox's reg.line function in package car. ## library(car) ?reg.line

Re: [R] trouble with html() in Hmisc

2009-10-03 Thread Mark Difford
and to the preamble of the *.tex file: \providecommand{\tabularnewline}{\\} Regards, Mark. Liviu Andronic wrote: > > Hello > > On 10/3/09, Mark Difford wrote: >> This has nothing to do with Hmisc or hevea. >> > Although I have LyX installed, I don't quite underst

Re: [R] trouble with html() in Hmisc

2009-10-03 Thread Mark Difford
Hi Liviu, >> > tmp <- latex(.object, cdec=c(2,2), title="") >> > class(tmp) >> [1] "latex" >> > html(tmp) >> /tmp/RtmprfPwzw/file7e72f7a7.tex:9: Warning: Command not found: >> \tabularnewline >> Giving up command: \...@hevea@amper >> /tmp/RtmprfPwzw/file7e72f7a7.tex:11: Error while reading

Re: [R] PCA or CA

2009-09-29 Thread Mark Difford
Hi Paul, >> I have a data set for which PCA based between group analysis (BGA) gives >> significant results but CA-BGA does not. >> I am having difficulty finding a reliable method for deciding which >> ordination >> technique is most appropriate. Reliability really comes down to you thinking

Re: [R] How to do a PCA with ordered variables?

2009-09-17 Thread Mark Difford
P. Branco wrote: >> I have used the dudi.mix method from the ade4 package, but when I do the >> $index it shows >> me that R has considered my variables as quantitative. >> What should I do? You should make sure that they are encoded as ordered factors, which has nothing to do with ade4's dud

Re: [R] hel with factorial analysis with mixed data

2009-09-15 Thread Mark Difford
andreiabb wrote: >> the message that I am getting is >> Error in AFDM (all_data_sub.AFDM, type=c(rep("s",1), rep("n",1), rep("n", >> : >> unused arguments (s) (type=c("s", "n","n")) >> Can someone help me? If you are in hel[l] then it is entirely your own fault. The error message is clear a

Re: [R] Triangular distribution for kernel regression

2009-09-12 Thread Mark Difford
Hi Brian, >> I am trying to get fitted/estimated values using kernel regression and a >> triangular kernel. Look at Loader's locfit package. You are likely to be pleasantly surprised. Regards, Mark. Bryan-65 wrote: > > Hello, > > I am trying to get fitted/estimated values using kernel regr

Re: [R] could not find function "Varcov" after upgrade of R?

2009-09-12 Thread Mark Difford
Hi Zhu, >> could not find function "Varcov" after upgrade of R? Frank Harrell (author of Design) has noted in another thread that Hmisc has changed... The problem is that functions like anova.Design call a function in the _old_ Hmisc package called Varcov.default. In the new version of Hmisc thi

Re: [R] Alternative to Scale Function?

2009-09-11 Thread Mark Difford
>> The scale function will return the mean and sd of the data. By default. Read ?scale. Mark. Noah Silverman-3 wrote: > > I think I just answered my own question. > > The scale function will return the mean and sd of the data. > > So the process is fairly simple. > scale training data varai

Re: [R] Omnibus test for main effects in the face ofaninteraction containing the main effects.

2009-09-08 Thread Mark Difford
Hi John, >> When Group is entered as a factor, and the factor has two levels, the >> ANOVA table gives a p value for each level of the factor. This does not (normally) happen so you are doing something strange. ## From your first posting on this subject fita<-lme(Post~Time+factor(Group)+fact

Re: [R] How can I appoint a small part of the whole data

2009-09-05 Thread Mark Difford
Yichih, Answer 2 is "correct," because your indexing specification for 1 is wrong. You also seem to have left out a comma. ## mu1990$wage[mu1990$edu==2|mu1990$edu==3|mu1990$edu==4, ] ## like this mu1990$wage[mu1990$edu%in%2:4, ] You really could have worked this out for yourself by looking at t

Re: [R] Problem with xtabs(), exclude=NULL, and counting NA's

2009-09-05 Thread Mark Difford
>> I must say that this is slightly odd behavior to require both >> na.action= AND exclude=. Does anyone know of a justification? Not strange at all. ?options na.action, sub head "Options set in package stats." You need to override the default setting. ws-7 wrote: > >>> xtabs(~wkhp, x, excl

r-help@r-project.org

2009-08-31 Thread Mark Difford
Hi John, >> Has a test for bimodality been implemented in R? You may find the code at the URL below useful. It was written by Jeremy Tantrum (a PhD of Werner Stuetzle's). Amongst other things there is a function to plot the unimodal and bimodal Gaussian smoothers closest to the observed data. A

Re: [R] adding factor scores back to an incomplete dataset...

2009-08-29 Thread Mark Difford
Hi David, Phil, Phil Spector wrote: >> David - >> Here's the easiest way I've been able to come up with. Easiest? You are making unnecessary work for yourselves and seem not to understand the purpose of ?naresid (i.e. na.action = na.exclude). Why not take the simple route that I gave, which rea

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