Re: [R] Undocumented behaviour of diag when replacing the diagonal of a matrix?

2024-12-05 Thread Spencer Graves
he entries are no longer the indices of A as a vector. Does this fact make his example work for you? It does for me. Hope this helps. Spencer Graves I guess, Duncan Murdochs hint is crucial. I'll commen

Re: [R] x[0]: Can '0' be made an allowed index in R?

2024-04-22 Thread Spencer Graves
Convert to character: goofy <- 1:9 names(goofy) <- (-4):4 goofy[as.character(0)] goofy["-2"] sg On 4/22/24 10:31 AM, Ebert,Timothy Aaron wrote: You could have negative indices. There are two ways to do this. 1) provide a large offset. Offset <- 30 for (i in -29 to 120) { print(df[

Re: [R] understanding predict.lm

2023-11-06 Thread Spencer Graves
Doh! Thanks very much. sg On 11/6/23 5:17 PM, John Fox wrote: Dear Spencer, You need the t distribution with correct df, not the standard-normal distribution: > pt(-z.confInt/2, df=13)     1 2 3 4 5 6 7 8 9    10    11 0.025 0.025 0.025 0.025 0.025 0.

[R] understanding predict.lm

2023-11-06 Thread Spencer Graves
with(pred.w.plim, (fit[,3]-fit[,2])/s.pred)) pnorm(-z.predInt/2) ** This gives me 0.01537207. I do not understand why it's not 0.025 with level = 0.95. Can someone help me understand this? Thanks, Spencer Graves __ R-

Re: [R] simulating future observations from heteroscedastic fits

2023-08-31 Thread Spencer Graves
On 8/31/23 1:27 AM, Spencer Graves wrote: Hello, All:   I want to simulate future observations from fits to heteroscedastic data. A simple example is as follows: (DF3_2 <- data.frame(y=c(1:3, 10*(1:3)), gp=factor(rep(1:2, e=3 # I want to fit 4 mod

[R] simulating future observations from heteroscedastic fits

2023-08-30 Thread Spencer Graves
ed(fit21) # How can I do the same with either fit12 and fit22 # or fit12r and fit22r? Thanks, Spencer Graves __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] logLIk(lme(...))?

2023-08-29 Thread Spencer Graves
What I thought should have been a linear operation wasn't. Please excuse the waste of your time. Thanks, Spencer Graves On 8/29/23 11:15 AM, Spencer Graves wrote: Hello, all:   I have a dataset with 2 groups.  I want to estimate 2 means and 2 standard deviatio

[R] logLIk(lme(...))?

2023-08-29 Thread Spencer Graves
)) # Why isn't (ll22 = llGp1+llGp2)? (ll22 - llGp1-llGp2) # And secondarily, how can I get the residual standard deviations # within each gp from fit22? Thanks, Spencer Graves __ R-help@r-project.org mailing list -- To UNS

Re: [R] Book Recommendation

2023-08-28 Thread Spencer Graves
suggest you consider using findFn with SQL and applications of greatest interest to your target audience. Spencer Graves p.s. DISCLAIMER: I'm the lead author and maintainer of the sos package. On 8/28/23 1:48 PM, Hadley Wickham wrote: You might find this chapter of R

Re: [R] Book Recommendation

2023-08-28 Thread Spencer Graves
On 8/28/23 12:47 PM, Bert Gunter wrote: I presume you are familiar with the RSQL and RSQLite packages and their vignettes. Can't offer any help, but a point of clarification: When you say, "teach accomplishing SQL in R," do you explicitly mean using SQL syntax in R to manipulate data or do yo

Re: [R] Questions about R

2023-08-17 Thread Spencer Graves
his article, with good reason. Hope this helps. Spencer Graves On 8/17/23 11:48 AM, Bert Gunter wrote: Incidentally, you might be interested in the banner shown when R starts up: "R is free software and comes with ABSOLUTELY NO WARRANTY." I believe this is standar

[R] Style guide when using "R" in a title

2023-07-26 Thread Wadsworth, Spencer G [STAT]
t for Basic Engineering Data Collection and Analysis by Vardeman and Jobe". Someone with whom I'm working on the booklet said that the "R" in the title might need to follow a specific style guide given by the R-project. Is this accurate? Is there a particular font I sho

Re: [R] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Spencer Graves
dramatically by use of appropriate artificial intelligence. Comments? Spencer Graves [1] https://en.wikipedia.org/wiki/Daniel_Kahneman [2] https://en.wikipedia.org/wiki/Behavioral_economics [3] https://www.researchgate.net/publication/26798603_Conditions_for_Intuitive_Expertise_A

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-31 Thread Spencer Graves
X.[, 3], ylab='accel (%)', axes=FALSE) axis(2) box(col='grey') axis(1) Best, Wolfgang That's exactly what I needed. Thanks, Spencer -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Spencer Graves Sent: Wednesday, 31 Ma

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-31 Thread Spencer Graves
t would make it feasible for a user to call axis(2, ...) once for each vertical axis to handle cases where someone wanted to a vertical scale different from linear and log. I'd want to make sure that lines.ts also works with this, because I want to add fits and predictions. Co

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-31 Thread Spencer Graves
b searches have so far failed to produce anything better than modifying plot.ts.R (and then submitting such with compatible changes to plot.ts.Rd), as I suggested earlier. ??? Thanks, Spencer On Tue, May 30, 2023 at 5:45 PM Spencer Graves wrote: On 5/30/23

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-30 Thread Spencer Graves
ab='vel (%)') plot(DAX.[, 3], ylab='accel (%)') This is what I want as three panels of a single plot. I think I could get it by modifying the code for plot.ts so it accepted ylab as a vector, etc., as I previously mentioned. What do you think?

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-30 Thread Spencer Graves
red to produce the default labeling. Then a user who wants a log scale for some but not all variables can get that easily and can further modify any of those scales further if they don't like the default. ??? Thanks very much. Spencer Graves On Tue, May 30

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-30 Thread Spencer Graves
diff(log(DAX)), diff(diff(log(DAX) colnames(logDAX) <- c('logDAX', 'vel', 'accel') plot(logDAX, axes=FALSE) axis(1) axis(2) I'm thinking of creating my own copy of "plot.ts", and changing it so it accepts the "log"

Re: [R] plot level, velocity, acceleration with one x axis

2023-05-29 Thread Spencer Graves
That's it. Thanks. sg HTH, Eric On Mon, May 29, 2023 at 7:57 AM Spencer Graves wrote: Hello, All: I want to plot level, velocity, and acceleration in three panels with only one x axis. The code below does this using "layout". However, I want the three plot areas

[R] plot level, velocity, acceleration with one x axis

2023-05-28 Thread Spencer Graves
es of the three panels changes. There's probably a way to do this with ggplot2, but I have yet to find it. Suggestions? Thanks, Spencer Graves str(AirTime <- as.numeric(time(AirPassengers))) str(AP <- as.numeric(AirPassengers)) def.par <- p

Re: [R] identify the distribution of the data

2023-02-08 Thread Spencer Graves
s of the product. This application to products is less well known and occasionally controversial. https://en.wikipedia.org/wiki/Gibrat%27s_law Spencer Graves 1) Try a simulation. Draw 5 values from a normal distribution, make a histogram. Then do it again. Is it easy

Re: [R] Plotmath isn't working for special characters

2023-01-24 Thread Spencer Graves
ave this behavior. plot(1,1,main=parse(text="x >= y")) Has anyone else seen this? What's your "sessionInfo()"? I got the symbol, not problem. Spencer Graves sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit)

Re: [R] R Certification

2023-01-02 Thread Spencer Graves
king the signature: pkgutil --check-signature R-4.2.2.pkg". Beyond that, RStudio and other companies will happily sell you a maintenance contract, which will get you more polite answers than from a list serve like this ;-) Spencer Graves On 1/2/23 11:24 AM, John Kane wrot

Re: [R] [External] Amazing AI

2022-12-21 Thread Spencer Graves
ing techniques. Let's use the best understandable model, and apply AI to the residuals from that. Then identify the variables that make the largest contributions to a useful AI model, and see if they can be added to the other model. Spencer Graves On Sun, Dec 18, 2022 at 7:01 PM Bori

Re: [R] cannot print a list with cat

2022-10-24 Thread Spencer Graves
1e-12 I don't know what you mean by "main program" vs. "the command t(mycontrol)". ??? Spencer Graves > sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.7 Matrix

Re: [R] ggplot2 install.package

2022-10-10 Thread Spencer Graves
il on this thread, "PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code." If you do that, it increases the chances that the help you get will actually be helpful ;-) Spencer

Re: [R] Parsing XML?

2022-07-28 Thread Spencer Graves
te was unknown. My contact at the Library of Congress then suggested I parse the XML version. Thanks, Spencer What of this information do you actually want? The elements of the list should be what? On Thu, 28 Jul 2022 at 08:52, Spencer Graves <mailto:spencer.gra...@eff

Re: [R] A humble request

2022-07-03 Thread Spencer Graves
in the upper right. 7. Also, in the directory "~R/wmtsa/wmtsa/man" I found a file called "wavBestBasis.Rd". I opened that in R. To learn how to read that, you can type "help.start()", which will open a menu that includes, "Writing R Extensions".

Re: [R] A humble request

2022-07-02 Thread Spencer Graves
ubtle, Muhammad can use "debug", as I earlier suggested. Spencer Graves You might find as I did that the wmtsa package has some dependencies that are also archived, namely pkg:splus2R (provided generously by Insightful for many years but apparently no longer) and pkg:ifultools.

Re: [R] A humble request

2022-07-02 Thread Spencer Graves
invite you to walk through the function line by line. You can look at what it does, and change it as you like. Doing so should help you learn R while also making it easier for you to figure out how to make the function do what you want. Hope this helps. Spencer Graves

Re: [R] Is it possible to set a default working directory for all R consoles?

2022-06-17 Thread Spencer Graves
ing Directory". Then when I want to work on an existing project, I can do File > "Recent Projects" in RStudio. Or I can double click on the appropriate *.Rproj file in Finder or Windows Explorer. Hope this helps. Spencer Graves On 6/17/22 10:4

Re: [R] Exact 95% CI around the mean for LogNormal distribution

2022-03-16 Thread Spencer Graves
looks plausibly like a straight line, you are fine with a log-normal assumption. If not, my favorite reference is Titterington, Smith and Makov (1985) Statistical Analysis of Finite Mixture Distributions (Wiley). Hope this helps. Spencer Graves On 3/16/22 5:44 PM, Bert G

Re: [R] Is there a Truth Table Generator in R?

2022-03-12 Thread Spencer Graves
t matches. The second is a summary by package. Hope this helps. Spencer Graves On 3/12/22 10:42 AM, Paul Bernal wrote: Dear friends, Hope you are doing great. I have been searching for a truth table generator in R, but everything I find has a Python implementation inst

Re: [R] Searching for packages

2022-02-28 Thread Spencer Graves
There is also sos::findFn, discussed in a vignette included in that package. When I created that package, I felt it was the fastest literature search for anything statistical: It will identify all help pages that match a search string and sort them by package. It creates an object so rela

Re: [R] nlme::lme sigma parameter standard deviation or variance?

2021-12-18 Thread Spencer Graves
n: Standard deviation, as indicated in help('lmeObject'). Hope this helps. Spencer Graves On 12/18/21 4:00 AM, Eric Berger wrote: You can run a test. Multiply all your data by a scalar, say 2. If this changes the result lme_mod$sigma by a factor of 2, then it i

Re: [R] Date read correctly from CSV, then reformatted incorrectly by R

2021-11-22 Thread Spencer Graves
it can be improved. It's on GitHub in case anyone would like to take the time to suggest improvements: https://github.com/sbgraves237/Ecfun Hope this helps. Spencer Graves On 11/20/21 4:13 PM, Avi Gross via R-help wrote: This seems to be a topic that comes up pe

Re: [R] Date

2021-11-04 Thread Spencer Graves
year 2019. However, if it were "09/06/2019", we would not know if it were September 6 or 9 June of 2019. If it were "09/06/08", we would have the added possibility with the year first, followed by month and day: June 8, 2009. This ambiguity is resolved most forcefully by IS

Re: [R] about L-BFGS-B

2021-08-15 Thread Spencer Graves
g., by giving a more informative error message. Hope this helps, Spencer Graves On 8/15/21 7:26 AM, J C Nash wrote: You have the answer in the error message: the objective function has been calculated as +/-Inf somehow. You are going to have to figure out where the functi

Re: [R] SOS package: findFn does not work

2021-08-07 Thread Spencer Graves
e GitHub version to CRAN. However, it would help me if I understood your configuration and if the GitHub version fixes the problem for you. Thanks for the report. I apologize for the inconvenience. Spencer Graves On 8/7/21 2:57 AM, hp wan wrote: Dear All, Recently, I

Re: [R] Sin curve question

2021-07-24 Thread Spencer Graves
ope this helps. Spencer On 7/24/21 2:04 PM, Eric Berger wrote: Alternatively with base graphics N <- 500 ## number of points (arbitrary) degrees <- seq(from=0,to=180,length=N) degreesToRadians <- function(d) { pi * d / 180.0} ## vectorIzed! plot(x=degrees,y=sin(degrees

Re: [R] MAC version 10

2021-07-08 Thread Spencer Graves
What web site did you go to? Have you tried: https://cran.r-project.org/bin/macosx/ Then click on "R-4.1.0.pkg". That should download as normal. Then double click on that, etc. Spencer Graves On 7/6/21 3:52 PM, Farrah T wrote: Hello, I have Mac

[R] input string ... cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?

2021-04-22 Thread Spencer Graves
)" and detailed instructions below on the precise file I dowloaded from the web and tried to read. I may be able to get what I want just ignoring this. However, I'd like to know how to fix this. Thanks, Spencer Graves sessionInfo() R version 4.0.5 (2021-03-

Re: [R] about a p-value < 2.2e-16

2021-03-19 Thread Spencer Graves
t uses the permutation distribution, though I could be mistaken.  If it's NOT a permutation distribution, I don't know what it is.   Spencer Best, Jiefei On Fri, Mar 19, 2021 at 10:01 PM Jiefei Wang wrote: Hey, I just want to point out that the word "exact" has

Re: [R] about a p-value < 2.2e-16

2021-03-19 Thread Spencer Graves
is case sensitive, so "EXACT" is a different variable from "exact". It is interpreted as an optional argument, which is not recognized and therefore ignored in this context. Hope this helps. Spencer > On Thu, Mar 18, 2021 at 10:47 PM Vivek Das wrote:

Re: [R] about a p-value < 2.2e-16

2021-03-18 Thread Spencer Graves
asking makes sense:  There is is no such thing as an "exact p value" except to the extent that certain assumptions hold, and all models are wrong (but some are useful), as George Box famously said years ago.[1]  Truth only exists in mathematics, and that's because it's a fict

Re: [R] Very slow optim()

2021-03-13 Thread Spencer Graves
Hi, Deepayan: On 2021-03-13 01:27, Deepayan Sarkar wrote: On Sat, Mar 13, 2021 at 10:08 AM Spencer Graves wrote: TWO COMMENTS: 1. DID YOU ASSIGN THE OUTPUT OF "optim" to an object, like "est <- optim(...)"? If yes and if "optim" terminated normally, the

Re: [R] Very slow optim()

2021-03-12 Thread Spencer Graves
optim" actually ended normally. However, if the problem is sufficiently important to justify more work, then I'd want to cast it as some kind if mixed-effects model, per "2" -- perhaps using an analysis of "1" as a first step towards "2".

Re: [R] forecast accuracy

2021-02-17 Thread Spencer Graves
u can get his email from help("fda"). Hope this helps. Spencer Graves On 2021-02-17 06:02, Faheem Jan via R-help wrote: I am new in the functional time series,  my question may be stupid as  I am new, I am  functional forecasting one year a head, Know I want to ch

Re: [R] Is there anyone who uses both R and Python here? How do you debug? Perhaps in RStudio?

2021-01-27 Thread Spencer Graves
hon since. However, this is described in the book Xie, Allaire, and Grolemund (2020) R Markdown: The Definitive Guide (Chapman & Hall and available for free at the above link). Spencer Graves On 2021-01-27 10:31, Robert Knight wrote: An iterative process works well. Python to

Re: [R] merging multiple .csv files

2020-12-15 Thread Spencer Graves
. It may not work as written. However, I've done things like this in the past. "merge" and "dplyr" have seemed too much like black magic for me. Spencer On 2020-12-15 16:13, pooja sinha wrote: I know that but I do not want to merge them sequentially because

Re: [R] Google Summer of Code 2021

2020-12-08 Thread Spencer Graves
roposal was not funded, but documentation of the basic idea is still available: https://en.wikiversity.org/wiki/Draft_Proposal_for_improving_the_ability_of_R_users_to_search_R_packages See also: https://en.wikiversity.org/wiki/Searching_R_Packages Hope this helps.

Re: [R] How to save Results in svg format

2020-12-04 Thread Spencer Graves
tried 300 pixels/in, and I think that worked, though I'm not 100% certain. hope this helps. Spencer Graves On 2020-12-03 23:21, David Carlson wrote: If you look at the examples on the manual pages for the upgma() and NJ() functions you will see that the results are generally se

Re: [R] Inappropriate color name

2020-11-17 Thread Spencer Graves
lar topics. If the name of that article were changed, then it should be a lot easier to pursue a similar name change elsewhere. Spencer Graves On 2020-11-17 15:25, Mitchell Maltenfort wrote: What about just amputating the final "n?" "Indian" might mean one of two

Re: [R] WG: Packages for mathematics

2020-11-16 Thread Spencer Graves
tation.org"; to be most useful. Many functions are included in base R. Many more are provided in contributed packages. Spencer Graves On 2020-11-16 04:02, ELLENBERGER Mihaela via R-help wrote: Von: ELLENBERGER Mihaela Gesendet: Monta

Re: [R] analyzing results from Tuesday's US elections

2020-11-08 Thread Spencer Graves
tter for the 2024 US presidential elections. Thanks for asking. Spencer Graves [1] https://github.com/sbgraves237 [2] https://en.wikiversity.org/wiki/Electoral_integrity_in_the_United_States __ R-help@r-project.org mailing

[R] analyzing results from Tuesday's US elections

2020-11-01 Thread Spencer Graves
inner from NC-09 to the US House in 2018 was detected by a college prof, who accessed the data two weeks after the election.[2] Spencer Graves [1] https://github.com/sbgraves237 [2] https://en.wikiversity.org/wiki/Local_Journalism_Sustainabilit

Re: [R] CRAN R For Windows 3.6.3

2020-09-19 Thread Spencer Graves
encounter problems, you can ask someplace on StackExchange or one of the R email lists like this or a package maintainer, as Duncan said. Spencer On 2020-09-19 12:44, Duncan Murdoch wrote: On 18/09/2020 1:39 p.m., Shapira, Leeor via R-help wrote: Can you please let me know the End of Life

Re: [R] [External] Re: help with web scraping

2020-07-25 Thread Spencer Graves
Dear Rasmus Liland et al.: On 2020-07-25 11:30, Rasmus Liland wrote: On 2020-07-25 09:56 -0500, Spencer Graves wrote: Dear Rasmus et al.: It is LILAND et al., is it not? ... else it's customary to put a comma in there, isn't it? ... The APA Style recommends "Sharp et al.,

Re: [R] [External] Re: help with web scraping

2020-07-25 Thread Spencer Graves
Dear Rasmus et al.: On 2020-07-25 04:10, Rasmus Liland wrote: > On 2020-07-24 10:28 -0500, Spencer Graves wrote: >> Dear Rasmus: >> >>> Dear Spencer, >>> >>> I unified the party tables after the >>> first summary table like this: >>>

[R] prevent XML::readHTMLTable from suppressing

2020-07-24 Thread Spencer Graves
<- xml2::read_html(sosChars) MOcan2 <- rvest::html_table(sosPointers) MOcan2[[2]][1, 2] [1] "4476 FIVE MILE RDSENECA MO 64865"   MOcan2 does not have names, and some of the fields are automatically converted to integers, which I think is not smart in this application.

Re: [R] [External] Re: help with web scraping

2020-07-24 Thread Spencer Graves
Dear Rasmus: On 2020-07-24 09:16, Rasmus Liland wrote: > On 2020-07-24 08:20 -0500, luke-tier...@uiowa.edu wrote: >> On Fri, 24 Jul 2020, Spencer Graves wrote: >>> On 2020-07-23 17:46, William Michels wrote: >>>> On Thu, Jul 23, 2020 at 2:55 PM Spencer Graves

Re: [R] [External] Re: help with web scraping

2020-07-24 Thread Spencer Graves
but I believe I'll be able to get what I want from the single character string using, e.g., gregexpr and other functions.   Thanks again,   Spencer Graves Best, luke On Fri, 24 Jul 2020, Spencer Graves wrote: Hi Bill et al.:   That broke the dam:  It gave me a chara

Re: [R] help with web scraping

2020-07-24 Thread Spencer Graves
columns of the former are all character;  that's not true for the latter.   Sadly, it's not quite what I want:  It's one table for each office-party combination, but it's lost the office designation. However, I'm confident I can figure out how to hack that.       Tha

[R] help with web scraping

2020-07-23 Thread Spencer Graves
ines, xml2::read_html, and XML::readHTMLTable; see summary below.   Suggestions?   Thanks,       Spencer Graves sosURL <- "https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975"; str(baseURL <- base::url(sosURL)) # this might give me s

Re: [R] R 4.0.2 is released

2020-06-22 Thread Spencer Graves
Thank you and all the core R team.  Spencer Graves On 2020-06-22 03:21, Peter Dalgaard via R-help wrote: The build system rolled up R-4.0.2.tar.gz (codename "Taking Off Again") this morning. The list below details the changes in this release. You can get the source code from htt

Re: [R] Rtools required

2020-04-29 Thread Spencer Graves
se binaries for some packages are not (yet) available for R 4.0.0.   Hope this helps.   Spencer Graves On 2020-04-29 21:02, Bert Gunter wrote: Wouldn't packages that have to be built from source on installation require Rtools? Bert Gunter "The trouble with having an open m

[R] Statistical Analysis of an Exchange Rate

2020-03-04 Thread spencer davis
So I've been researching statistical analysis for a considerable amount of time and still haven't really found what I've been looking for and am hoping that by getting help answering this question it will send me down the right path to answering all of my questions. So I am hoping that someone will

Re: [R] R 3.6.2 is released

2019-12-12 Thread Spencer Graves
Ditto.  Spencer Graves On 2019-12-12 07:54, Rich Shepard wrote: On Thu, 12 Dec 2019, Peter Dalgaard via R-help wrote: The build system rolled up R-3.6.2.tar.gz (codename "Dark and Stormy Night") this morning. Peter, My thanks to all of you on the R core team. Rega

Re: [R] transforming dates

2019-11-03 Thread Spencer Graves
and 64ths.       Spencer Graves __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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

Re: [R] transforming dates

2019-11-03 Thread Spencer Graves
tric units.    Binary, octal or hex is superior to decimal, except for the fact that most humans have 10 digits on hands and feet.  And decimal is vastly superior to arithmetic in mixed bases, e.g., adding miles, rods, yards, feet, inches, and 64ths.       Spen

[R] Using read.table for importing gz file

2019-08-10 Thread Spencer Brackett
haps a way to use read.table with fread in some way to do this? Many thanks, Spencer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE d

[R] Determining survival correlation among probes

2019-08-02 Thread Spencer Brackett
association with survival. Best, Spencer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org

Re: [R] Loading large tar.gz XenaHub Data into R

2019-08-01 Thread Spencer Brackett
You may also >> prefer to search (e.g. at rseek.org) on "read a gzipped file" or >> similar for possible alternatives. >> >> Of course, if they're not gzipped files, then ignore the above. If >> they are, your current approach is hopeless. >> >> &

[R] Loading large tar.gz XenaHub Data into R

2019-08-01 Thread Spencer Brackett
ve attempts failed with warning messages from R### Methyl <-read.delim(" https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz ") ##This attempt is still processing, but has been doing so for quite some time## Any ideas as to wh

Re: [R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
, am not familiar > with the specific functions you are using, and don't have time to > become familiar. You need to both improve your R understanding and > seek out guidance, ideally from someone whose job it is to help you. > > Best, > Sarah > > On Fri, Jul 19, 2019 a

Re: [R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
t; >phenoData(Dilution) On Fri, Jul 19, 2019 at 1:32 PM Sarah Goslee wrote: > You don't need fake.data or rnorm(), which was used to generate the fake > data. > > You need to use your real data for the analysis, not anything randomly > generated for example purposes, or

Re: [R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
ndom.affyid <- sample(geneNames(Dilution), 1) > # random.affyid <- '34803_at' > ps <- probeset(Dilution, random.affyid)[[1]] How would I substitute in my anno object to achieve this? On Fri, Jul 19, 2019 at 1:47 PM Spencer Brackett < spbracket...@saintjosephhs.com> w

Re: [R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
;t that just print the data or a subset thereof into my R console? On Fri, Jul 19, 2019 at 10:46 AM Spencer Brackett < spbracket...@saintjosephhs.com> wrote: > Sarah, > > I am trying to extract phenoData (ie sample information) from the object > as part of a procedure to analyz

Re: [R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
ad in through data(Dilution) which was made an object of the AnnotatedDataFrame via >phenoData(Dilution) My apologies in advance as I know the above info. pertains to functions carried out strictly through BioConducor, but is the only context I can provide for what I am trying to do. Best, Spen

[R] How to create a data set from object/data frame?

2019-07-19 Thread Spencer Brackett
need to transpose the object to a data set. Any ideas as to how I might do this? For reference, my next step in manipulating the data contained in the object is data(), which evidently does not work for reading in data frame objects as data(“file/object name). Best, Spencer [[alternative

Re: [R] Accessing/Visualizing Probe Sets to determine Data Association

2019-07-18 Thread Spencer Brackett
ng. > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Thu, Jul 18, 2019 at 12:55 PM Spencer Brac

[R] Accessing/Visualizing Probe Sets to determine Data Association

2019-07-18 Thread Spencer Brackett
trying to run a few different methods such as microarray probe set mapping through Ensembl, but without avail. Would anyone perhaps know of a procedure/workflow that I could use to achieve this? Best, Spencer [[alternative HTML version deleted

Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

2019-07-17 Thread Spencer Brackett
The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Wed, Jul 17, 2019 at 1:20 PM Spencer Brackett < > spbracket...@saintjosephhs.c

Re: [R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

2019-07-17 Thread Spencer Brackett
eStartupMessages({ library(Biobase) }) > > AnnotatedDataFrame() > An object of class 'AnnotatedDataFrame': none > > Biobase is a Bioconductor package, so support questions should more > appropriately go to https://support.bioconductor.org > > Martin > > On 7/17/19, 4:20 PM, "R

[R] Trying to coerce an AnnotatedDataFrame in order to access Probeset Info

2019-07-17 Thread Spencer Brackett
"annotatedDataFrameFrom" >as(data.frame, "AnnotatedDataFrame") Error in as(data.frame, "AnnotatedDataFrame") : no method or default for coercing “function” to “AnnotatedDataFrame” Best, Spencer [[alternative HTML version deleted]]

Re: [R] R 3.6.1

2019-07-17 Thread Spencer Graves
  What might be the likely outcomes of an attempt to reinstall 3.6.1?   And might that depend on whether the current 3.6.1 was uninstalled first?   Spencer On 2019-07-17 07:17, Jeff Newmiller wrote: It would never make sense for such messages to reflect normal and expected

Re: [R] random truncation

2019-07-13 Thread Spencer Graves
lysis with corrections that attempt to respond to Spurdle's most recent concerns.  Thanks, Spencer Graves On 2019-07-12 22:31, Abby Spurdle wrote: > The distribution of the randomly truncated variable has thus four > parameters: a, b, mu and sigma.  I was able to write down the

Re: [R] random truncation

2019-07-13 Thread Spencer Graves
maximized over variations in "b", "s" and "t" given "c".  I can get starting values for "b" and "s" from "lm", ignoring the truncation.  And I can first fit the model assuming t = s, then test whether it's different usin

[R] random truncation

2019-07-12 Thread Spencer Graves
tively easy to model the truncation as a function of "d" and / or publication that described someone doing it in R.  (I also have a couple of other variables that influence the distribution of Y.)   Thanks,   Spencer Graves [1] https://en.wikipedia.org/wiki/Truncated_

Re: [R] Using options(max.print = 1000000) to read in data

2019-07-09 Thread Spencer Brackett
My apologies! I made this much to complicated and allowed myself to become confused with the straightforward advice given. I tried running the lines Mr. Barradas suggested after receiving the output for as.matrix() and I understand now. Thank you all again for your patience. Best, Spencer On

Re: [R] Using options(max.print = 1000000) to read in data

2019-07-09 Thread Spencer Brackett
concerned that perhaps if I had to set the data in the data frame as a matrix (if not already), then I would not achieve this result. Thanks, Spencer On Tue, Jul 9, 2019 at 6:21 AM Michael Friendly wrote: > Why do you need it to be a matrix? A data.frame is like a matrix, but > allows colu

Re: [R] Using options(max.print = 1000000) to read in data

2019-07-08 Thread Spencer Brackett
ame" Is this to say that the object is set as a 'data frame', opposed to a 'matrix' ? I will try running ?is.matrix now On Mon, Jul 8, 2019 at 10:33 AM Rui Barradas wrote: > Hello, > > Inline. > > Às 15:26 de 08/07/19, Spencer Brackett escreveu: > >

Re: [R] Using options(max.print = 1000000) to read in data

2019-07-08 Thread Spencer Brackett
:16 AM Kevin Thorpe wrote: > > > On Jul 8, 2019, at 10:06 AM, Spencer Brackett < > spbracket...@saintjosephhs.com> wrote: > > > > Hello, > > > > I am trying to reload some data into R in order to check to see if it is > > formatted as a matrix.

[R] Using options(max.print = 1000000) to read in data

2019-07-08 Thread Spencer Brackett
the rows to test for a matrix? Best, Spencer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.

Re: [R] Problems with closing R

2019-07-07 Thread Spencer Brackett
on this list of bugs in RStudio related to > incompatibility with R 3.6, [1] which might be related to your problems so > upgrading RStudio to beta or downgrading R to 3.5.3 may make a difference. > > [1] https://stat.ethz.ch/pipermail/r-help/2019-July/463226.html > > On July 7, 20

[R] Problems with closing R

2019-07-07 Thread Spencer Brackett
environments saved on my desktop be deleted? Not sure if any other solutions to this issue. Best, Spencer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman

Re: [R] Reloading old R Environments/Workspaces

2019-07-04 Thread Spencer Brackett
Partly because the procedure itself is incomplete, but yes I see the illogic nature of my position. On Thu, Jul 4, 2019 at 4:22 PM Jeff Newmiller wrote: > If you can't reproduce them, how do you know they are correct? > > On July 4, 2019 11:34:53 AM PDT, Spencer Brackett

Re: [R] Reloading old R Environments/Workspaces

2019-07-04 Thread Spencer Brackett
Thank you for the clarification. So should I not rely on importing a saved environment from now on? I am currently experiencing some difficulties with reproducing the output (aka the objects listed in my environment), which is why I was trying to load them all at once. Best, Spencer On Thu, Jul

Re: [R] Reloading old R Environments/Workspaces

2019-07-04 Thread Spencer Brackett
when I last worked on, sufficient? Best, Spencer On Wed, Jul 3, 2019 at 8:44 PM Spencer Brackett < spbracket...@saintjosephhs.com> wrote: > Very interesting I will have to take a look. Thank you very much for > the reference to these resources! They will be of great help to me. >

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