similar to: reproducing scaling used in biplot(pc.biplot=TRUE)

Hello, I would like to remove the last 8 digists of character strings in a vector. Below I added a couple of elements from that vector. I have a problem defining a pattern to replace the digits using for example "sub". Removing the ".tif" part works fine using sub('.tif',"",x), but how do I get rid of the four preceding digits? Thanks for your help, Kim

Hello, I would like to use R to process a list of text strings. The text strings are filenames, encoding experimental settings. Based on the information in there I'd like to select certain files and copy only the selected files to another directory. The files are images and there is no need, actually no desire, to open them. Is there a way to use R for copying and pasting files with any

Hello, I have a time series of data as a data.frame. Occasionally there is one or more days missing (e.g. data available for days 2, 3, 4, 8, 9, 10 --> missing days between 4 and 8). The experimental time information can be found in the 2nd column of "data". I would like to have a continuous time line with one time point per day. Therefore I try to insert lines for the missing

Hi, I'd like to construct a somewhat unusual barplot. In "barplot" I use beside=F as I'd like to have stacked bars. The height of each bar is always the same. Information in my plot is coded in the color of the bar. I therefore need to be able so assign a different combination (or order) of colors to each individual stacked bar. In the example below, the combination of

Dear help-list, I would like to perform a linear regression on the log10 of the two vectors ov.mag.min and res.600nm. The slope and intercept of the regression I use to plot a wider range of ov.mag.min in a double log plot. For a linear regression on only tow points, wouldn't I expect the results for two.points.min to match pretty exactly res.600nm? It does not seem to be the case here.

Hello, in a three dimensional coordinate system, I'd like to find all my experimental data points that fall within an ellipsoid around a fixed coordinate. The fixed point is defined by (x.coord.point, y.coord.point, z.coord.point). The coordinates of the ellipsoid are given by the three vectors x,y,z. In a previous version of my code, I simply used a box instead of an ellipsoid to sort

Hello, I very much enjoy rgl! But when converting the screen output to pdf using rgl.postscript I have encountered three problems: (1) I don't seem to have control over font sizes and point sizes (of added points) in the pdf output. I tried cex from "plot" but that does not have an effect. Initially I got some plots where fonts and especially points were far too small. But now

Hello, in the data.frame "resultsfuzzy" I would like to replace the characters in the second column ("5a", "5b", ... "5e") with numbers from 1 to 5. The data.frame has 39150 entries. I seems to work on samples that are << nrow(resultsfuzzy) but it takes suspicously long. Do you have any suggestions how to make the character replacing more

Dear all, I've been learning biplot (Gabriel, 1971) and some days ago I sent for this list a procedural function with invitation for a collaborative package. Jari Oksanen made some suggestions and I agree with all. So, I reworked the function under the object-oriented programming (OOP/S3). I think it is now a good frame for more resources. Below it is the function and a small script to

Hi, I am trying to understand how the biplot.prcomp is constructed so I can manipulate it to emphasise particular observations and reduce the number of variables shown. The prcomp model I have ran has cor=TRUE and scale=TRUE I have worked out from looking at str(prcomp.model) that... prcomp.model$x = the observations ploted in the biplot prcomp.model$rotation = the variables that form the

I'm attempting to modify how biplot draws its red vectors (among other things). This is how I've started: Biplot <- function(xx, comps = c(1, 2), cex = c(.6, .4)) { ## Purpose: Makes a biplot with princomp() object to not show arrows ## ---------------------------------------------------------------------- ## Arguments: xx is an object made using princomp() ##

I'm using R for PCA and? factor analysis. I want to create biplots of varimax rotated factors that color-code points by their classification. My research is on streams that are urban and rural. So, I want to color code them by this classification. If you just do a biplot from prcomp or princomp, you cannot add this color. So, I have used some code developed by a graduate student in our

Hi, I think that the documentation for the biplot function `biplot.princomp' is inconsistent with what it actually does. Here is what the documentation states: pc.biplot If true, use what Gabriel (1971) refers to as a "principal component biplot", with lambda = 1 and observations scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner products between

Hello, I am trying to run some AMOVA analyses with the amova function in the package ade4. When running the example dataset provided in ade4, I noticed a difference between the published results from the same data (Excoffier et al. 1992) and what ade4 calculates. Below are the data for "within sample/population" from ade4 and from the haplotypic distance matrix in the paper:

Dear R-users, I would like to create pdf files with varying paper sizes. The paper size is determine by the number of plots that I squeeze on a page using par(mfcol). I also add text to each of these plots. I observed that depending on the number of plots per page, the default character size is changing, leading to differing font sizes in my plot annotations. I would like to use cex to

Dear all, >From the documentation of biplot.prcomp: scale: The variables are scaled by 'lambda ^ scale' and the observations are scaled by 'lambda ^ (1-scale)' where 'lambda' are the singular values as computed by 'princomp'. >From the source code of prcomp: lam <- x$sdev[choices] n <- NROW(scores) lam <- lam * sqrt(n)

Dears, I've been learning biplot (Gabriel, 1971) and I found the function 'biplot', inside of the package 'stats', useful but, a bit limited. So, I'm thinking to start a colaborative package to enhance this methods to other multivariate methods. In this way, I would like to start it, making public a new function (biplot.pca, still in development, but running) that make

Hi, I recently uploaded a package called "calibrate" to CRAN. This package contains routines for the calibration of (oblique) axes in biplots and scatter plots. Documentation provides examples for ordinary scatter plots with additional axes, biplots from principal component analysis, correspondence analysis, canonical correlation analysis and redundancy analysis. Jan Graffelman --

Hi everybody, Excuse me for this silly question, but after searching the help archives I'm still unable to find my way to read the source code of the "biplot" function in R. I have installed the mvbutils package, and tried: > fixr(biplot) which only gives me: function (x, ...) UseMethod("biplot") with no further details.... I'd like to read the code to see if

Hello, we have a large data set of water quality data and want to identify influence variables or *why* different groups of data are different (in an explorative sense). We consider to use biplots, however there are only the common PCA-Biplots available in R (biplot.princomp). We consider to use transformations (log-type, x^a, Box-Cox), but are seeking for alternatives. Are there