I develop some package using rstan::stan(). I make a function whose return value is an S4 class object generated by rstan::stan(). To access estimates comfortablely or to add an information for data, I want to make a new S4 class object which inherits S4 class of rstan::stan()so that there is new slots.
Furthermore, the new S4class object also can be available for any functions in rstan such as rstan::traceplot().
fit <- rstan::stan( model_name=scr, data=data) # This is a fictitious code.
Suppose we get S4 (stanfit) object named fit .
Define an extended class of stanfit
InheritedClass <- setClass("InheritedClass",
# New slots
representation(slotA="character",
slotB="character",
slotC="numeric"),
contains = "stanfit"
)
To create an S4 object of the inherited class using an existing S4 class object ,i.e., fit,
so what I need is only to input values for added new slots, i.e., slotA, slotB, slotC.
Using the following code, we can convert the S4 object for old class to inherited class:
fit2 <- as(fit,"InheritedClass")
Using this we can edit slot like following:
fit2#slotA <- "aaaaaaaaaaaa"
See help(setClass). I believe it would be something like
setClass("classname", slots = c(foo = "numeric", bar = "character"),
contains = "stanfit")
And I'm sure you would have to include rstan in the Imports: line of the DESCRIPTION file in your package in order for it to find the S4 class definition for stanfit.
Related
I am using rpy2 to import a library from CRAN repository called "MatrixEQTL" to run in within Python using importr, here is my attempt:
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
robjects.r('install.packages("MatrixEQTL")')
mtrql = importr('MatrixEQTL')
I am trying to access both class fields as well as class methods but I failed here is what the class looks like when printing into the python shell:
# to view class SlicedData of MatrixEQTL R package
print(mtrql.SlicedData)
Generator for class "SlicedData":
Class fields:
Name: dataEnv nSlices1 rowNameSlices
Class: environment numeric list
Name: columnNames fileDelimiter fileSkipColumns
Class: character character numeric
Name: fileSkipRows fileSliceSize fileOmitCharacters
Class: numeric numeric character
Class Methods:
"Clear", "show#envRefClass", "nSlices", "getRefClass", "export",
"initialize", "CombineInOneSlice", "callSuper", "initFields", "nCols",
"getClass", "RowStandardizeCentered", "import", "SaveFile", "RowReorder",
"setSlice", "getSlice", "RowReorderSimple", "CreateFromMatrix", "nRows",
"ResliceCombined", "LoadFile", "ColumnSubsample", "SetNanRowMean",
"setSliceRaw", "getSliceRaw", "copy", "RowMatrixMultiply", "usingMethods",
"GetAllRowNames", "RowRemoveZeroEps", "field", ".objectParent",
"IsCombined", "untrace", "trace", "Clone", "GetNRowsInSlice",
".objectPackage", "show", "FindRow"
Reference Superclasses:
"envRefClass"
I want to access for instance class field say fileDelimiter and also class Methods say LoadFile but I couldn't, here is also my attempt to access class method LoadFile and the error message that generated:
# If I try to run this without "()"
data = mtrql.SlicedData
load_my_file = data.LoadFile(file)
data = data.LoadFile(file)
AttributeError: 'DocumentedSTFunction' object has no attribute 'LoadFile'
# And that's my attempt for when adding "()" to the class name
data = mtrql.SlicedData
load_my_file = data.LoadFile(file)
data = data.LoadFile(file)
AttributeError: 'RS4' object has no attribute 'LoadFile'
I tried to look for a solution to this issue but I wasn't successful, please help me understand and solve this issue.
Thank you so much in advance.
mtrql.SlicedData is a "Generator", that is a constructor. In R that means a function (that will return an instance of the class), which is why mtrql.SlicedData is an R function with rpy2.
Consider the following example from the R documentation (https://rdrr.io/r/methods/Introduction.html):
import rpy2.robjects as ro
Pos = ro.r("""
setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric",
altitude = "numeric"))
""")
With rpy2, the object Pos is an R function:
>>> type(Pos)
rpy2.robjects.functions.SignatureTranslatedFunction
However that function object has an S3 class in R (there are several OOP systems in R, 2 of them coexisting in standard R unfortunately).
>>> tuple(Pos.rclass)
('classGeneratorFunction',)
A specific print function is implemented for this S3 class, and it will use the attributes package and className for the object (the R function-that-is-in-fact-a-Generator) to display all the info about the clas you are seeing.
Since this is a constructor, to create an instance you can do:
pos = Pos()
or
pos = Pos(latitude=0, longitude=0, altitude=-10)
The instance will have instance attributes (and methods)
>>> tuple(pos.list_attrs())
('latitude', 'longitude', 'altitude', 'class')
>>> tuple(pos.do_slot('altitude'))
(-10,)
With your specific example, you probably want something like:
slidata = mtrql.SlicedData()
slidata.do_slot('LoadFile')(file)
The documentation can provide more information about R S4 classes in rpy2, and how to make wrapper classes in Python that map attributes and methods.
https://rpy2.github.io/doc/v3.3.x/html/robjects_oop.html#s4-objects
I can't figure out what I'm missing. Following Situation:
I wrote a R-Package lets call it "pkg_A"
It depends on "Rcpp" and I have a Module loaded and a class set up like :
Rcpp::loadModule("pkg_A_modul", what = "pkg_A_cppClass_A")
cppClass_A <- setRcppClass(
Class = "pkg_A_cppClass_A",
CppClass = "pkg_A_cppClass_A",
module = "pkg_A_modul",
fields = c(
remark = "character"
)
)
and a additional constructor
classA <- function(a,b){
# some stuff
tmpObj <- cppClass_A()
# some more stuff
return(tmpObj)
}
class(classA ) <- "classA "
The only Thing what I export to the NAMESPACE is the classA function/class.
That all works fine and I can build that package without any warnings and even can check it with "--as-cran" flag.
Now I want to build a second package on top of that package, lets call that "pkg_B" Therefore I list "pkg_A" in the DESCRIPTION Depends of "pkg_B"
as well as I load the class with importFrom(pkg_A, classA) in the NAMESPACE of "pkg_B".
Now I want to implement a class
classB <- setRefClass(
"classB",
contains = c("classA"),
fields = c( b = "numeric)
)
But when I now want to build "pkg_B" I get the error:
Error in getClass(what, where = where) : "classA" is not a defined
class
I also tried to use the "pkg_A_cppClass_A" instead or imprt the whole pkg_A or use pkg_A::classA. Nothing changed.
Hope the question is complete enough. If you missing some info let me know.
Thankful for any suggestions!
I am currently creating a new S4 class which uses a S3 zoo object. I can create a class
setOldClass("zoo")
setClass("rollingSD", slot = c(rollPeriod = "numeric", tsOutput = "zoo"))
This code works fine. Now if I want to create an object as
riskSD <- new("rollingSD")
This also works fine. However, the following generates an error
riskSD <- new("rollingSD", rollPeriod = 12)
Error in validObject(.Object) :
invalid class “rollingSD” object: invalid object for slot "tsOutput" in class
"rollingSD": got class "S4", should be or extend class "zoo"
This not clear for me why a default object of the zoo class is not inititated. I also do not know how to fix this.
The problem is caused because R's class mechanism doesn't know how to make a new zoo object. You can fix this by specifying a "prototype":
setClass(
"rollingSD",
slot = c(rollPeriod = "numeric", tsOutput = "zoo"),
prototype=prototype(
tsOutput=some_zoo_object
)
)
where some_zoo_object is of class zoo. The default prototype for a numeric slot is numeric(), but because you defined the (S4) class zoo yourself, the default is new("zoo") and this isn't defined.
I am pretty new using R in an advanced way...so apologize for futile questions!
I want to create a object of class S4, defined by 3 slots. Thing is that I can't manage to create these attributes as a list. Here is my code :
test<-setClass("dblist",representation(df.list="list", df.para="list",df.coups="list"))
new("dblist",representation(df.list="list", df.para="list",df.coups="list"))
and the error I get :
Error in initialize(value, ...) : cannot use object of class “list” in new(): class
“dblistpgn” does not extend that class
Could you please explain how creating an object with list plot?
Thx!
try this:
new("dblist", df.list = list(), df.para = list(), df.coups = list())
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.