I want to document a replacement function in R, but when I run R CMD check I get this error message:
Bad \usage lines found in documentation object 'timestamps':
<unescaped bksl>S4method{"timestamps<-"}{.MoveTrack}(this, value)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
the documentation looks like this:
\name{timestamps}
\alias{timestamps}
\alias{timestamps,.MoveTrack-method}
\alias{timestamps,.MoveTrackSingle-method}
\alias{"timestamps<-",.MoveTrack-method}
\docType{methods}
\title{Extract the timestamps of a Move or MoveStack object}
\description{The timestmaps method returns or sets the timestamps of a track from a Move or MovesStack object.}
\usage{
\S4method{timestamps}{.MoveTrackSingle}(this)
\S4method{timestamps}{.MoveTrack}(this)
\S4method{"timestamps<-"}{.MoveTrack}(this, value)
}
\arguments{
\item{this}{Move or MoveStack object}
\item{value}{timestamps from class POSIXct}
}
and the actual function is the following:
setGeneric("timestamps", function(this) standardGeneric("timestamps"))
setMethod("timestamps", ".MoveTrack",
function(this) {
this#timestamps
})
setMethod("timestamps", ".MoveTrackSingle",
function(this) {
this#timestamps
})
setGeneric("timestamps<-", function(this, value) standardGeneric("timestamps<-"))
setReplaceMethod("timestamps", ".MoveTrack",
function(this, value) {
this#timestamps <- value
this
})
I searched for the error message but all I found was about Roxygen documentation which didn't help me. I also tried different documentation styles like :
\S4method{"timestamps<-"}{.MoveTrack}(this, value)
\S4method{"timestamps<-."}{.MoveTrack}(this, value)
\S4method{"timestamps<-$"}{.MoveTrack}(this, value)
\S4method{'timestamps<-'}{.MoveTrack}(this, value)
\S4method{timestamps<-}{.MoveTrack}(this, value)
\S4method{"timestamps\<\-"}{.MoveTrack}(this, value)
\S4method{"timestamps\\<\\-"}{.MoveTrack}(this, value)
but non of them worked. Any idea?
Thanks a lot in advance.
best, marco
Try
\S4method{timestamps}{.MoveTrack}(this) <- value
with multiple dispatch in the second{} as a comma-separate list.
Related
I want to calculate the loan outstanding at valuation date for a data set. I define a function but when I call the function its giving an error saying the fifth argument is missing(term).
Function is as follows:
loan_outstanding<-function(c_date,v_date,l_amt,int ,pmt,term){
l_amt<-as.numeric(l_amt)
freq<-12
term_in_months<-as.numeric(term)*freq
c_date<-as.Date(c_date,"%d/%m/%Y")
Interest_Rate<-per_to_num(int)
v_date<-as.Date(v_date,"%Y-%m-%d")
date_<-numeric(500)
date_[1]<-as.character(c_date)
int_cal<-numeric(500)
cap_repay<-numeric(500)
loan_out<-numeric(500)
loan_out[1]<-l_amt
i<-2
while(as.Date(date_[i-1],"%Y-%m-%d")<v_date){
date_[i]<-as.character(AddMonths(as.Date(date_[i-1],"%Y-%m-%d"),1),"%Y-%m-%d")
int_cal[i]<-loan_out[i-1]*((1+Interest_Rate)^(1/freq)-1)
cap_repay[i]<-pmt-int_cal[i]
loan_out[i]<-max(loan_out[i-1]-cap_repay[i],0)
i<-i+1
}
val<- loan_out[i-2]
return(val)
}
The error :
>loan_outstanding("28/07/2011","2017-03-31",500000,7,9629.918)
argument "term" is missing, with no default
Is there a mistake in my code?
This is not a pretty solution, but I just made another variable and put it after the last one in the function definition:
...pmt, term, [new var]) {
It solved the problem for me.
Been going around for hours with this. My 1st question online on R. Trying to creat a function that contains a loop. The function takes a vector that the user submits like in pollutantmean(4:6) and then it loads a bunch of csv files (in the directory mentioned) and binds them. What is strange (to me) is that if I assign the variable id and then run the loop without using a function, it works! When I put it inside a function so that the user can supply the id vector then it does nothing. Can someone help ? thank you!!!
pollutantmean<-function(id=1:332)
{
#read files
allfiles<-data.frame()
id<-str_pad(id,3,pad = "0")
direct<-"/Users/ped/Documents/LearningR/"
for (i in id) {
path<-paste(direct,"/",i,".csv",sep="")
file<-read.csv(path)
allfiles<-rbind(allfiles,file)
}
}
Your function is missing a return value. (#Roland)
pollutantmean<-function(id=1:332) {
#read files
allfiles<-data.frame()
id<-str_pad(id,3,pad = "0")
direct<-"/Users/ped/Documents/LearningR/"
for (i in id) {
path<-paste(direct,"/",i,".csv",sep="")
file<-read.csv(path)
allfiles<-rbind(allfiles,file)
}
return(allfiles)
}
Edit:
Your mistake was that you did not specify in your function what you want to get out from the function. In R, you create objects inside of function (you could imagine it as different environment) and then specify which object you want it to return.
With my comment about accepting my answer, I meant this: (...To mark an answer as accepted, click on the check mark beside the answer to toggle it from greyed out to filled in...).
Consider even an lapply and do.call which would not need return being last line of function:
pollutantmean <- function(id=1:332) {
id <- str_pad(id,3,pad = "0")
direct_files <- paste0("/Users/ped/Documents/LearningR/", id, ".csv")
# READ FILES INTO LIST AND ROW BIND
allfiles <- do.call(rbind, lapply(direct_files, read.csv))
}
ok, I got it. I was expecting the files that are built to be actually created and show up in the environment of R. But for some reason they don't. But R still does all the calculations. Thanks lot for the replies!!!!
pollutantmean<-function(directory,pollutant,id)
{
#read files
allfiles<-data.frame()
id2<-str_pad(id,3,pad = "0")
direct<-paste("/Users/pedroalbuquerque/Documents/Learning R/",directory,sep="")
for (i in id2) {
path<-paste(direct,"/",i,".csv",sep="")
file<-read.csv(path)
allfiles<-rbind(allfiles,file)
}
#averaging polutants
mean(allfiles[,pollutant],na.rm = TRUE)
}
pollutantmean("specdata","nitrate",23:35)
I am trying to delete all values in a list that have the tag ".dsw". My list is a list of files using the function list.files. This is my code:
for (file in GRef) {
if (strsplit(file, "[.]")[[1]][3] == "dsw") {
#GRef=GRef[-file]
for(n in 1:length(GRef)){
if (GRef[n] == file){
GRef=GRef[-n]
}
}
}
}
Where GRef is the list of file names. I get the error listed above, but I dont understand why. I have looked at this post: Error .. missing value where TRUE/FALSE needed, but I dont think it is the same thing.
You shouldn't attempt to to modify a vector while you are looping over it. The problem is your are removing items you are then trying to extract later which is causing the missing values. It's better to identify all the items you want remove first, then remove them. For example
GRef <- c("a.file.dsw", "b.file.txt", "c.file.gif", "d.file.dsw")
exts <- sapply(strsplit(GRef, "[.]"), `[`, 3)
GRef <- GRef[exts!="dsw"]
I'd like to get the unique elements from a column. That seems straight forward. Both of these work, but I'm not getting the object type I'd like:
userlist <- as.list(somebigdf$username)
userlist <- unique(userlist)
or
userlist <- unique(somebigdf$username)
When I iterate through, I'm not getting the names:
for(i in 1:length(userlist)){
cat(names(userlist[i]), '\n')
}
Returns blank spaces.
for(i in userlist){
cat(i, '\n')
}
Returns integers.
The above function is just an example. I'll be using that but also matching the returned name in an if-else function.
The object types seem to be integers or an extended data.frame with lots of values for each name - which isn't what I want. I would really just like a list of strings something along the lines of userlist = c( the results from unique).
Edit -
This code will iterate correctly through the names:
for(name in unique(somebigdf$username)){
cat(name, '\n')
}
I'm accepting my own answer. Namely, a working solution - this code will iterate correctly through the names:
for(name in unique(somebigdf$username)){
cat(name, '\n')
}
If someone at a later date has a better answer that seems more in keeping with the question, I will be happy to accept that as the answer.
I have a function in R that looks somewhat like this:
setMethod('[', signature(x="stack"),definition=function(x,i,j,drop){
new('class', as(x, "SpatialPointsDataFrame")[i,]) })
I use it to get a single element out of a stacked object. For the package I'm building I need a .Rd file to document the function. I stored it as [.Rd but somehow the R CMD check does not see this. It returns:
Undocumented S4 methods: generic '[' and siglist 'MoveStack,ANY,ANY'
The [.Rd file starts with these lines:
\name{[}
\alias{[}
\alias{[,stack,ANY,ANY-method}
\docType{methods}
\title{Returns an object from a stack}
\description{Returning a single object}
\usage{
\S4method{\[}{stack,ANY,ANY}(x,i,y,drop)
}
Any idea how I make R CMD check aware of this file?
If you look at the source code of the sp package, for example SpatialPolygons-class.Rd, the Methods section:
\section{Methods}{
Methods defined with class "SpatialPolygons" in the signature:
\describe{
\item{[}{\code{signature(obj = "SpatialPolygons")}: select subset of (sets of) polygons; NAs are not permitted in the row index}
\item{plot}{\code{signature(x = "SpatialPolygons", y = "missing")}:
plot polygons in SpatialPolygons object}
\item{summary}{\code{signature(object = "SpatialPolygons")}: summarize object}
\item{rbind}{\code{signature(object = "SpatialPolygons")}: rbind-like method}
}
}
method for [ is defined.
Name and class of the file are
\name{SpatialPolygons-class}
\alias{[,SpatialPolygons-method}
If you look at the help page for ?SpatialPolygons you should see
> Methods
>
> Methods defined with class "SpatialPolygons" in the signature:
>
> [ signature(obj = "SpatialPolygons"): select subset of (sets of)
> polygons; NAs are not permitted in the row index
>
So I would venture a guess that if you specify a proper (ASCII named) file name, give it an alias as in the above example, you should be fine.