similar to: Running an error-prone R script using 'source' command

Hi All, I am running an Rscript with a bunch of algorithms that are UNSTABLE under some parameter settings. At a certain point one of them sends error massage and my whole run STOPS! What I would like is to save the error massage in some file or variable and carry on to the next command line without stopping this run... Any help or ideas would be welcome, please, with a concrete example (not

Hi, is there a way to retrieve the line number of where en error occurred when sourcing a file in a tryCatch statement? Is it stored somewhere accessible? It is not found in the error object. Consider the following code/output and note the difference in the traceback between source (has line number) and sys.source (has no line number). Thank you, Renaud ######## # code ######## codefile <-

Usage data(gasoline) Format A data frame with 60 observations on the following 2 variables. octane a numeric vector. The octane number. NIR a matrix with 401 columns. The NIR spectrum and I see the gasoline data to see below NIR.1686 nm NIR.1688 nm NIR.1690 nm NIR.1692 nm NIR.1694 nm NIR.1696 nm NIR.1698 nm NIR.1700 nm 1 1.242645 1.250789 1.246626 1.250985 1.264189 1.244678 1.245913

I have two ideas about it. 1- i) Entering variables in quadratic form is done with the command I (variable ^ 2) - plsr (octane ~ NIR + I (nir ^ 2), ncomp = 10, data = gasTrain, validation = "LOO" You could also use a new variable NIR_sq <- (NIR) ^ 2 ii) To insert a square variable, use syntax I (x ^ 2) - it is very important to insert I before the parentheses. iii) If you want to

Below. -- Bert Bert Gunter On Thu, Jul 13, 2017 at 3:07 AM, Luigi Biagini <luigi.biagini at gmail.com> wrote: > I have two ideas about it. > > 1- > i) Entering variables in quadratic form is done with the command I > (variable ^ 2) - > plsr (octane ~ NIR + I (nir ^ 2), ncomp = 10, data = gasTrain, validation = > "LOO" > You could also use a new variable

> On Jul 13, 2017, at 7:43 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > > Below. > > -- Bert > Bert Gunter > > > > On Thu, Jul 13, 2017 at 3:07 AM, Luigi Biagini <luigi.biagini at gmail.com> wrote: >> I have two ideas about it. >> >> 1- >> i) Entering variables in quadratic form is done with the command I >>

?? If I haven't misunderstood, they are completely different! 1) NIR must be a matrix, or poly(NIR,...) will fail. 2) Due to the previously identified bug in poly, degree must be explicitly given as poly(NIR, degree =2,raw = TRUE). Now consider the following example: > df <-matrix(runif(60),ncol=3) > y <- runif(20) > mdl1 <-lm(y~df*I(df^2)) > mdl2

Hi list, I am looking at the data yarn in package, I don't understand what is dimension of this data set. I did the following: > library(pls) > data(yarn) > dim(yarn) [1] 28 3 > head(yarn) NIR.1 NIR.2 NIR.3 NIR.4 NIR.5 NIR.6 NIR.7 NIR.8 NIR.9 NIR.10 NIR.11 1 3.06630 3.08610 3.10790 3.09720 2.99790 2.82730 2.62330 2.40390 2.19310 2.00580 1.83790 2

Hello, I'm playing around with the PLS package and found a data set (NIR) whose structure I don't understand. Forgive me if this is a stupid question, as I feel like it must be since I am less experienced with aspects of modeling. My problem, the pls NIR data frame does not seem to be a typical data frame as, while it is a list, its variables are not of equal length. Furthermore, I have

Dear all, I am using the pls package of R to perform partial least square on a set of multivariate data. Instead of fitting a linear model, I want to fit my data with a quadratic function with interaction terms. But I am not sure how. I will use an example to illustrate my problem: Following the example in the PLS manual: ## Read data data(gasoline) gasTrain <- gasoline[1:50,] ## Perform

> On Jul 12, 2017, at 6:58 PM, Ng, Kelvin Sai-cheong <kscng at connect.hku.hk> wrote: > > Dear all, > > I am using the pls package of R to perform partial least square on a set of > multivariate data. Instead of fitting a linear model, I want to fit my > data with a quadratic function with interaction terms. But I am not sure > how. I will use an example to

> On Jul 13, 2017, at 10:43 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > > poly(NIR, degree = 2) will work if NIR is a matrix, not a data.frame. > The degree argument apparently *must* be explicitly named if NIR is > not a numeric vector. AFAICS, this is unclear or unstated in ?poly. I still get the same error with: library(pld) data(gasoline) gasTrain <-

Dear All, I'm using "reg.finalizer" in a function that is to be called in R scripts to do some cleanup on success. I have not found a way to run the function only if the script run without errors, so when the exit code is expected to be 0. What I've tried is checking "geterrmessage()", but unfortunately it's not perfect: if an error was handled with eg

The following example involves a function whose on.exit() expression both generates an error and catches the error. The body of the function also generates an error. When calling the function wrapped in a tryCatch, should that tryCatch's error function be given the error from the body of the function, since the one from the on.exit has already been dealt with? Currently the outer tryCatch

Bert, The 'degree' argument follows the "..." argument in the function declaration: poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Generally, any arguments after the "..." must be explicitly named, but as per the Details section of ?poly: "Although formally degree should be named (as it follows ...), an unnamed second argument of length 1

poly(NIR, degree = 2) will work if NIR is a matrix, not a data.frame. The degree argument apparently *must* be explicitly named if NIR is not a numeric vector. AFAICS, this is unclear or unstated in ?poly. -- Bert 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

Marc: 1. I am aware of the need to explicitly name arguments after ... -- see the R Language definition where this can be inferred from the argument matching rules. 2. I am aware of the stated exception for poly(). However: > x1 <- runif(20) > x2 <- runif(20) > mx <- cbind(x1,x2) > poly(mx,2) Error in poly(dots[[i]], degree, raw = raw, simple = raw) : 'degree'

G'day Federico, On Wed, 17 May 2023 10:42:17 +0000 "Calboli Federico (LUKE)" <federico.calboli at luke.fi> wrote: > sexsnp = rep(NA, 1750) > for(i in 1:1750){tryCatch(sexsnp[i] = fisher.test(table(data[,3], > data[,i + 38]))$p, error = function(e) print(NA))} Error: unexpected > '=' in "for(i in 1:1750){tryCatch(sexsnp[i] =" Try: R> for(i in

I'm confused by the page documenting tryCatch and friends. I think it describes 3 separate mechanisms: tryCatch (in which control returns to the invoking tryCatch), withCallHandlers (in which control goes up to the calling handler/s but then continues from the point at which signalCondition() was invoked), and withRestarts (I can't tell where control ends up). For tryCatch the docs say

Hello, I run a fisher.test() in a loop, with the issue that some of the data will not be useable. To protect the loop I used tryCatch but: sexsnp = rep(NA, 1750) for(i in 1:1750){tryCatch(sexsnp[i] = fisher.test(table(data[,3], data[,i + 38]))$p, error = function(e) print(NA))} Error: unexpected '=' in "for(i in 1:1750){tryCatch(sexsnp[i] =" But this works: for(i in