Re: [R] matching similar character strings

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research

Re: [R] coxph won't converge when including categorical (factor) variables

--- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] abbreviating words in a model formula

Your cart is stuck in front of your horse. This will be WAY easier to accomplish if you rename your columns in your input data frame before fitting the model. --- Jeff Newmiller

Re: [R] Help with installing a .tar.gz package on windows

system so you need to learn that with Google. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Cannot access PDF manuals from R console

and follow the directions there. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live

Re: [R] Sparse matrix no longer sparse (Matrix Package)

It seems to me that this issue should be reproducible with a small matrix, since the concern is the representation rather than the values. --- Jeff NewmillerThe . . Go Live

Re: [R] Use R for data aggregation

This is off-topic here... you are looking for statistical advice, if not problem-domain-specific help. Please read the Posting Guide. --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] Matrix column flip when recycled

Only vectors recycle. If you don't want the behaviour if the matrix to reflect that of the underlying vector then don't use recycling. Instead use indexing. M.1 - M.2[rep(1:5,3),] --- Jeff Newmiller

Re: [R] file.stem?

Read the Posting Guide... use plain text email. help.search(file) --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Serialize data.frame to database

of this type. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO

Re: [R] Help: Error when installing R 2.8.1 in IBM AIX system from source code

there. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer

Re: [R] Linear regression repeat for each column

Sure. Read the Posting Guide, and provide a reproducible example with sample data. I suspect the basic idea will be to merge the data frames and then setup the model to refer to the desired columns. --- Jeff Newmiller

Re: [R] do not perform function if the outcome is NA

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O

Re: [R] Fwd: Why does impulse response function of VAR starts at zero and not at one?

parameters. Most likely, supplying just one of the options for each parameter will obtain best results. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] cannot install XML package - getting cannot open URL 'http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip' error

the file you want does exist, verify that your local network is functioning, and practice a little patience. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] readTiff - Sorry can't handle images with 32-bit samples

Try reading a different file. The error message says the existing code cannot read that file. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Is it possible (/reasonable) to write an as.RefClass function for R list class?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] Declare BASH Array Using R System Function

and off topic here. Once you do understand this difference, you might be interested in reading the R help file on Sys.setenv(). --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] cross-correlation with R

exchange.com for an example of a forum where such discussions may not be off-topic. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Intersecting two matrices

In that case, you should be looking at a relational inner join, perhaps with SQLite (see package sqldf). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] Intersecting two matrices

a code snippet when you got time. Thanks a lot! On Tue, Jul 30, 2013 at 10:36 AM, Jeff Newmiller jdnew...@dcn.davis.ca.uswrote: In that case, you should be looking at a relational inner join, perhaps with SQLite (see package sqldf

Re: [R] Error Help: duplicate?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing

Re: [R] use Vectorized function as range of for statement

to be applied to the computation phase. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] readBin into a data frame

I find the hexView package quite helpful for this. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] R runs on Windows Server 2012?

files non-interactively and serves them via a web page. I suggest you clarify your definition of run to prompt a more helpful response from the list. --- Jeff NewmillerThe . . Go Live

Re: [R] Write-table and dynamic access path

Or ?file.path for a more OS- independent approach. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] import function without overwriting function with the same name

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing

Re: [R] library XML in R version 2.15.1

? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O

Re: [R] memory size

specifically so you can ask more specific questions. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Lattice/panel.bwplot and Gviz: Boxplot question

Best to ask questions about Bioconductor packages on the bioconductor mailing list. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] [RCurl] HTTP 404 Status

(stackoverflow?). If you find a bug in RCurl, correspond with the package maintainer (see ?maintainer). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Help from DOS Command Prompt

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O

Re: [R] Function for ddply

write your own .FUN function if you are calling ddply within your own function. See the help for ddply for examples of how to do that. --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] Nearest Neighbors

Isn't the obvious solution to subtract the set for level n-1 from the set for level n? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] R doesn't recognize R_HOME value

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O

Re: [R] reshape - reshape 2: function cast changed?

? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research

Re: [R] internal error -3 in R_decompress1

try options (error= recover) and examine the stack frames. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] How to filter datetime from a dataframe

Please read the posting guide mentioned at the bottom of any message on this list. Your posts have issues: Reproducible example (use dput) desired output (use dput) Include context from previous messages --- Jeff Newmiller

Re: [R] Working with Numbers generated from Regression Output

). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research

Re: [R] On Reproducible Code

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries

Re: [R] Assigning a new name to object loaded with load()

Don't imagine too much, because R is pretty good about not doing deep copies unless it is necessary to change data. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] use R remotely (ssh / shell / emacs)

such software up is definitely off topic here. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] problem plotting in a grid

Did you actually read the help file for filled.contour? The image.plot call is being affected by the documented behavior of filled.contour. ggplot might be worth investigating. --- Jeff Newmiller

Re: [R] sprintf doesn't care of escape characters

) ) and print ( sprintf(a\bc\d) ) In a nutshell, print makes the string suitable for inclusion in source code, while cat sends the string directly as-is. --- Jeff NewmillerThe . . Go Live

Re: [R] Latest version of R on Ubuntu

are pretty good. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO

Re: [R] Ubuntu installation

to pick a different one to get the right combination of updated software and libraries. This changes over time, so I have never had the perfect storm of repository problems and new installation unfamiliarity to deal with. --- Jeff

Re: [R] Why the error is coming while extracting the data from sheet?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O

Re: [R] Best Programming Practices regarding data frames

frame. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO

Re: [R] timeBasedSeq stumbles over the year 2038 (xts package)

http://en.wikipedia.org/wiki/Year_2038_problem Workaround 1: Avoid collecting data in the future and processing it in the present. Workaround 2: Use a 64-bit build of R, as appropriate for such future data sets. --- Jeff

Re: [R] Head or Tails game

lack of reproducible (even if inefficient) code. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Package to remove collinear variables

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] Identify points that lie within polygon

This is off-topic (not about R), and a quick Web search of test within polygon yields many results, and adding R to the search when using Google provides hints about applying the algorithms in R. --- Jeff Newmiller

Re: [R] shading line plot

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research

Re: [R] Unable to download R package

Try a different repository? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live

Re: [R] Sum of vector elements

of positive and not-positive numbers) aggregate does the summation ans may be empty if x started with positive numbers. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] reshape2's dcast() Adds NAs to Data Frame

Need sample data, and code that demos the problem. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Outer product from matrix by row and a vector

Can you post what you want your answer to be for the a and b you have given already? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Can not find lme

(LME~WD, random=~1|Species, ML)Error: could not find function lme [[alternative HTML version deleted]] --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] R help

before changing it this way. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO

Re: [R] Pass Conditional loop argument into a function

the string directly to the output stream to prove this to yourself. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] reshape2's dcast() Adds NAs to Data Frame

converting to factors until I need them. Other people convert from factor to character and back to factor to get rid of unwanted factor levels on an as-needed basis. --- Jeff Newmiller

Re: [R] R help

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] reshape2's dcast() Adds NAs to Data Frame

] reshape2's dcast() Adds NAs to Data Frame On Wed, 8 Aug 2012, Jeff Newmiller wrote: The explanation is that this is normal and consistent with behavior of factors in general. If you don't want that, it is common to work with character data instead of factors, only converting to factor when needed

Re: [R] if else elseif for data frames

Maybe the cut function? ?cut --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live

Re: [R] Web scrabing - getURL with delay

Perhaps ?Sys.sleep between scrapes. If this slows things down too much you may be able to parallelize by host site with ?mclapply. --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] Basic question -loading data

for matrices. Tempting for naming time variables.) df (density of the f distribution. Tempting because data frames are very often used object classes.) --- Jeff NewmillerThe . . Go Live

Re: [R] which() function not finding certain numbers

FAQ 7.31 ?is.equal --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO

Re: [R] sample() from (un-)sorted vectors

such a thing is possible. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO

Re: [R] How to plot data in logarithmic scale

to use the help system, e.g. ?ecdf --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Error: level sets of factors are different?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] Opinion: Why I find factors convenient to use

delay conversion until late in the game... but usually I do eventually convert in most cases. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Upgrading Ubuntu from 11.10 to 12.04: Problem with r-base-dev?

by the uninstall/install of R. disclaimer: It works for me. As always, YMMV so backup anything you are concerned about losing due to Ubuntu coding errors or your own errors. --- Jeff Newmiller

Re: [R] apply question

What is wrong with utilizing the vectorized nature of paste? zz[[1]] - paste(zz[[1]],zz[[2]],sep=_) --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] Why was my R process killed spontaneously?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] Why was my R process killed spontaneously?

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer

Re: [R] error type

to HTML corruption or whether you actually typed that in. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] total CPU time in Matlab - what is the equivalent in R?

Google is your friend http://www.ats.ucla.edu/stat/r/faq/timing_code.htm http://r.research.att.com/benchmarks/ --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us

Re: [R] Course

a course my work paid for, and I have purchased CDROMs of Linux distributions before. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live

Re: [R] variable scope

--- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO

Re: [R] Conditional merging in R if then statement

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software

Re: [R] Computing 'exp(1e3)*0' correctly....

to pursue that conversation here. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live

Re: [R] a newbie seeking for a simple problem

Read the posting guide... you need to provide more specific information such as sample data (?dput). For this problem you should probably read ?merge --- Jeff NewmillerThe . . Go

Re: [R] adding points to a point pattern

Perhaps. What does this have to do with R? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] RES: adding points to a point pattern

Then why don't you follow the posting guide and provide an R sample data set and R sample result? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] POSIXlt and daylight savings time

of analysis. c) Use the format argument if you want consistent results. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Revolution Analytics

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing

Re: [R] Improvement of Regression Model

, but you provide no data or reproducible, self-contained R code, so even if it is not homework you are not providing us with a sporting chance at understanding your questions. Read the Posting Guide. --- Jeff Newmiller

Re: [R] Simulating key-press or keyword events on a Mac

This is very off-topic here. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live

Re: [R] merge a list of data frames

in the combined data frame? If you really want the column names to stay the same, perhaps you want to stack the data frames vertically with rbind? --- Jeff NewmillerThe . . Go Live

Re: [R] How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?

Perhaps what you want to explore is the object returned from the summary method rather than the fit object? coef(summary(kinfit)) --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] use of ddply() within function

function of your own as the help page for ddply describes. Too many layers of syntactic sugar are involved for summarise to work within a function. --- Jeff NewmillerThe . . Go Live

Re: [R] merge a list of data frames

combine computations on groups of rows instead of on columns. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go

Re: [R] Query on how to do maximum likelihood fitting of a functional (MLFR)

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O

Re: [R] Why the error is coming, can anyone help?

benefit from (re)reading the Introduction to R document. Without a reproducible example or an idea of what you want to accomplish, I don't know what _is_ going to work. --- Jeff Newmiller

Re: [R] Problem with duplicates in row.names

You cannot have duplicate row names. You have to do something to address that, such as remove duplicates or aggregate your data. --- Jeff NewmillerThe . . Go Live... DCN:jdnew

Re: [R] how to save a heatmap.2 in png /jpeg /tiff

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research

Re: [R] use subset to trim data but include last per category

, and eventually you may want to use that function yourself. One solution is to use DF for your variables... another is to use more descriptive names. --- Jeff NewmillerThe . . Go Live

Re: [R] plot: x and y chromosomes are missing

-reproducible-example In particular note the recommendation to use the dput function to send us sample data. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics

Re: [R] CRAN, install packages problem on networked PC

. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar

Re: [R] R equivalent of python module structure and functionality?

It is my normal practice to install R libraries without root. Just use your own library directory instead of the system library. --- Jeff NewmillerThe . . Go Live... DCN:jdnew

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