I'm using R Studio based on R 3.4.3. However, when I tried to call the forecast.HoltWinters function, R told me that "could not find function "forecast.HoltWinters"". Inspect the installed package (v8.2) told me that it's true, there is no forecast.HoltWinters. But the manual in https://cran.r-project.org/web/packages/forecast/ clearly stated that forecast.HoltWinters is still available.
I have also tried stats::HoldWinters, but it's working wrong. The code run fine on another computer, but it couldn't run at all on mine. Is there any solution?
Here is the code. Book2.csv has enough data to last more than 3 periods.
dltt <- read.csv("book2.csv", header = TRUE)
dltt.ts <- ts(dltt$Total, frequency=12, start=c(2014,4))
dltt.ts.hw <- HoltWinters(dltt.ts)
library(forecast)
dltt.ts.hw.fc <- forecast.HoltWinters(dltt.ts.hw) //Error as soon as I run this line
Fit a HoltWinters model using the HoltWinters function and then use forecast. Its all in the help for HoltWinters and forecast, namely "The function invokes particular _methods_ which depend on the class of the first argument". I'll copy the guts of it here:
m <- HoltWinters(co2)
forecast(m)
Note this will call the non-exported forecast.HoltWinters function, which you should never call directly using triple-colon notation as some may suggest.
Related
can someone please help me understand this:
I encountered an error when calling a function from a library, specifically "steinertree" from the "SteinerNet" package. When stepping into the function with debug(steinertree), I see that the error occurs, when the function in turn calls "steinertree3". When I try debug(steinertree3), I get "object 'steinertree3' not found". Similarly, I can get the code for 'steinertree' by typing it in the terminal, but not for 'steinertree3'.
So it seems to me that there are some "higher-level" functions and "hidden" functions in packages. I did eventually find the error by finding a file "steinertree.R" in the package at CRAN, which contains both 'steinertree' and 'steinertree3', but I`m wondering how to properly go about debugging such "hidden" functions.
Here is a simple example:
library(igraph)
library(SteinerNet)
set.seed(1)
g= erdos.renyi.game(n=10,p.or.m=0.2)
plot(g)
steinertree(type= 'KB', terminals= c(1,3), graph= g)
Thank you!
Use triple colon ::: to execute a function that is not exported by the package/namespace:
package:::hidden_function()
I am trying to run a power analysis using a MonteCarlo approach in R.
I have created a function of two parameters that does output a boolean (tested manually for all relevant values of the parameters). I also have run baby-examples of the MonteCarlo function to make sure that I understand it and that it works well.
Yet when I try to run the real thing, I get the following error message:
Error in parse(text = all_funcs_found[i]) : <text>:1:1: unexpected '::'
1: ::
I read through the source code of the MonteCarlo function (which I found here) and found
#loop through non-primitive functions used in func and check from which package they are
for(i in 1:length(all_funcs_found)){
if(environmentName(environment(eval(parse(text=all_funcs_found[i]))))%in%env_names){
packages<-c(packages,env_names[which(env_names==environmentName(environment(eval(parse(text=all_funcs_found[i])))))])
}
}
which doesn't really make sense to me - why should there be a problem there?
Thank you for any ideas.
I found the answer: the function I wrote was calling a function from a specific library in the form libraryname::functionname.
This works OK if you use the function once manually, but makes MonteCarlo break.
I solved the problem by first loading the relevant library, then removing the 'libraryname::' part from the definition of the main function. MonteCarlo then runs just fine.
Goal: mas5 normalize data.
Problem: when I try the following R code, I get this
error: unable to find an inherited method for function bg.correct for signature ExpressionFeatureSet, character
I have looked on SO, and found the following: What does this mean: unable to find an inherited method for function ‘A’ for signature ‘"B"’, but I am not exactly sure how to fix my specific problem and use the mas5 function properly. I have also looked at this affy manual but still stuck...
installpkg("affy")
library('affy')
setwd("/Users/er/Desktop/DesktopFolders/DataSets/CD8Helios/Microarray/CELfiles/CEL")
cel_Files <- list.celfiles()
affyRaw <- read.celfiles(cel_Files)
eset <- mas5(affyRaw)
If you are sure that the .cel files were created based on experiments performed on the type of array that works with affy package than you should try this workflow using ReadAffy from affy package.
cel_Files <- list.celfiles()
affyRaw <- affy::ReadAffy(filenames=cel_Files)
eset <- mas5(affyRaw)
However, it might be the case that the affy package is not designed for your array type. Then, you should switch to the oligo and oligoClasses packages and normalize with analogous function rma
cel_Files <- oligoClasses::list.celfiles()
affyRaw <- oligo::read.celfiles(cel_Files)
eset <- oligo::rma(affyRaw)
I am using R version 3.3.2 and the package copula version 0.999-15 to evaluate the fitting of the normal copula to my data. My data and code are:
Data: https://www.dropbox.com/s/tdg8bfzmy4nd1dd/jumps.dat?dl=0
library(copula)
data <- read.csv(file="jumps.dat", head=F, sep="")
cop_model <- ellipCopula("normal", dim = 2)
m <- pobs(as.matrix(data))
fitCopula(cop_model, m, method = 'mpl')
After I run the code I receive the following error:
Error in `freeParam<-`(`*tmp*`, value = estimate) : the length of 'value' is not equal to the number of free parameters
Calls: fitCopula ... fitCopula.ml -> fitCopStart -> fitCopula.icor -> freeParam<-
Execution halted
I have no idea what is happening here. The fitting for Clayton and Gumbel is pretty fine. Searching for similar errors in the web, I have found nothing. Reading the documentation (https://www.rdocumentation.org/packages/copula/versions/0.999-15/topics/fitCopula?) for some specificity for ellipCopula, I have found an specific option for posDef, but it did not returns any solution at all.
Old question, but I found this, so will share my solution.
Try to run the following, this is a minimum working example:
library(copula)
print("-----------")
mycop <- ellipCopula("normal", dim=4)
data <- matrix(runif(400), nrow=4)
fitCopula(mycop, t(data))
print("-----------")
For me, this works fine if I open R and type in the lines one by one, but fails if I run as a script with Rscript. The solution is that you need library(methods) as well.
For some reason this worked with copula v0.999-v14, but was broken by v0.999-v16. Alas.
Suppose I'm curious about the workings of the R function, say HoltWinters. I typed HoltWinters and it shows me R source for the function. On inspection, the source shows the function is a wrapper around a second function:
final.fit <- hw(alpha, beta, gamma)
Presumably, the serious work happens in the function hw. However, I can't find this function anywhere to read its source
> hw
Error: object 'hw' not found
How can I read the source?
Edit: Ok, so now I've read hw , I see it's a wrapper around C_HoltWinters. How can I read that?
As you successfully found, there are lines
hw <- function(alpha, beta, gamma)
.C(C_HoltWinters,
....
in the source of HoltWinters function. Which means that we need to look at C files: you can find all the source code of R here, or just go straight here.