Description Fields Methods See Also Examples
A class for storing data in multiple interrelated tables. Each table relates to the other tables through keys.
A function used to combine covariates of the same key/val pair.
This is the full array. For extensibility, it cannot be written to directly and must be modified through methods.
A list of metadata associated with the cells of the data.
The names of columns in the data.
A list of metadata associated with the columns of the data.
The data associated with each dimension of the array.
The size of the array.
The size of the array.
Long form data.
This is the matrix. For extensibility, it cannot be written to directly and must be modified through methods.
Any data not part of the main data structure.
The number of columns in the data.
The number of dimensions of the array.
The number of rows in the data
The names of rows in the data.
A list of metadata associated with the rows of the data.
A function for debugging the methods of this class. It calls the browser command. In order for methods to opt into to debugging, they need to implement the following code at the beginning: if(<method_name> %in% private$.debug){browser()}. This method exists, because the debugger is not always intuitive when it comes to debugging R6 methods.
string | - | The name(s) of methods to debug as a character vector |
This method must be extended. In order to use an ObservationList as an ArrayData, you need to select which columns to use to form the dimensions of the array. Optionally, you can also assign some of the columns to be associated with each dimension (or cell). Note that aggregate
is used to determine how to deal with multiple observations associated with a particular grouping.
val | - | The attribute of frame to use for the values of the array (must aggregate _ to a numeric type) |
... | - | Column names of columns which, in order should form the dimensions of the array |
metaData | - | The attribute(s) of frame to store in metaData so they can be accessed by methods expecting a MatrixData object. |
This function should be extended. Create a new instance of this class.
... | - | This function should take in any arguments just in case. |
A function for ceasing to debug methods. Normally a method will call the browser command every time it is run. This command will stop it from doing so.
string | - | The name(s) of the methods to stop debugging. |
Inherits from : FrameData
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ObservationList<- R6Class(
classname= "ObservationList",
inherit = AbstractObservationList,
private = list(
.aggregate = NULL,
.frame = data_frame(),
aCurrent = FALSE,
.aDims = list(),
.aVal = '',
.slice = 1,
.aDimData = list(),
na.rm = FALSE,
updateArray = function(na.rm = private$na.rm){
if('updateArray' %in% private$.debug){
browser()
}
if(length(self$aDims) == 0){
warning("Form array with formArray first")
private$.arr = array(as.numeric(NA),c(0,0))
private$.ndim = 2
private$.dims = c(0,0)
private$.dimData = list(list(),list())
private$.dnames = list()
return()
}
if(nrow(private$.frame) == 0){
warning("The frame is empty.")
private$.arr = array(as.numeric(NA),c(1:self$aDims*0))
private$.ndim = length(self$aDims)
private$.dims = 1:length(self$aDims)*0
private$.dimData = lapply(self$aDims,list())
private$.dnames = list()
return()
}
private$.dnames = lapply(self$aDims,function(name){
as.character(unique(private$.frame[[name]]))
})
private$.dims = sapply(private$.dnames,length)
private$.ndim = length(private$.dims)
private$.arr <- private$.frame %>%
select_(
.dots = setNames(
c(unlist(self$aDims),self$aVal),
nm=c(unlist(self$aDims),self$aVal)
)
) %>%
group_by_(.dots=setNames(self$aDims,NULL)) %>%
self$aggregate() %>%
ungroup() %>%
acast(as.formula(paste(self$aDims,collapse='~')),value.var=self$aVal)
mode(private$.arr) = 'numeric'
private$.dnames = dimnames(private$.arr)
if(class(self$aDimData) == 'list'){
if(length(self$aDimData) < length(self$aDims)){
self$aDimData[length(self$aDims)] = list(NULL)
}
} else {
stop("array metadata should be a list of columns in the data frame.")
}
private$.dimData = mapply(dim=self$aDims,data=self$aDimData,function(dim,data){
self$frame %>%
group_by_(dim) %>%
self$aggregate() %>%
ungroup() %>%
select_(.dots=data) %>%
as.list()
})
if(length(private$.dimData) < private$.ndim){
private$.dimData = lapply(1:private$.ndim,function(x){
if(length(private$.dimData >= x)){
private$.dimData[[x]]
} else {
list()
}
})
}
private$aCurrent <- TRUE
}
),
public = list(
initialize = function(data=data_frame(),...){
self$frame <- as_data_frame(data)
self$formArray(...)
private$.aggregate = function(input_data){
if('aggregate' %in% private$.debug){
browser()
}
grouping = groups(input_data)
input_data %>%
input_data <- summarize_all(funs(
sum = if(is.numeric(.) || is.logical(.)){
sum(.,na.rm=private$na.rm)
} else{NA},
unique = if(length(unique(.))==1){unique(.)} else{list(unique(.))}))
input_data <- input_data %>%
group_by_(.dots=grouping)
if('sum' %in% names(input_data)){
input_data <- input_data %>%
rename_(.dots=setNames('sum',paste(private$.aVal,'_sum',sep='')))
}
if('unique' %in% names(input_data)){
input_data <- input_data %>%
rename_(
.dots=setNames('unique',paste(private$.aVal,'_unique',sep=''))
)
}
column_names = c(
unlist(
sapply(private$.aDimData,function(x){paste(x,"_unique",sep='')})
),
paste(private$.aVal,'_sum',sep=''))
column_names = column_names[column_names %in% names(input_data)]
input_data %>%
select_(.dots=column_names) ->
input_data
input_data %>%
rename_(.dots=setNames(
names(input_data)[grepl(names(input_data),pattern='_unique')],
lapply(
names(input_data)[grepl(names(input_data),pattern='_unique')],
function(x){substr(x,1,nchar(x)-7)}
)
)) %>%
rename_(.dots=setNames(
names(input_data)[grepl(names(input_data),pattern='_sum')],
lapply(
names(input_data)[grepl(names(input_data),pattern='_sum')],
function(x){substr(x,1,nchar(x)-4)}
)
)) %>%
return()
}
},
formArray = function(...,val,dimData=list(),metaData=list()){
if('formArray' %in% private$.debug){
browser()
}
if(missing(val)){
if(length(list(...))==0){
return()
} else{
stop("val must be supplied in order to form the incidenceArray")
}
}
private$aCurrent=FALSE
private$.dnames = NULL
self$aDims = list(...)
self$aVal = val
self$aDimData = dimData
metaDataKeys <-
names(private$.metaData)[!(names(private$.metaData) %in% names(metaData))]
self$metaData = c(private$.metaData[metaDataKeys],metaData)
}
),
active = list(
frame = function(value){
if('frame' %in% private$.debug){
browser()
}
private$aCurrent = FALSE
if(!missing(value)){
private$.rnames = NULL
private$.cnames = NULL
}
private$defaultActive('.frame','private',value)
},
arr = function(value){
if('arr' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.arr)
}
stop("Do not write directly to the array.")
},
dims = function(value){
if('dims' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dims)
}
stop("Do not write directly to the dimensions.")
},
ndim = function(value){
if('ndim' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.ndim)
}
stop("Do not write directly to the number of dimensions.")
},
dimData = function(value){
if('dimData' %in% private$.debug){
browser()
}
if(private$aCurrent == FALSE){
private$updateArray()
}
if(missing(value)){
return(private$.dimData)
}
if(is.null(value)){
private$.dimData=NULL
} else if(class(value) == 'list'){
nval = length(value)
if(nval == 0){
private$.dimData = value
} else if(nval <= private$.ndim){
if(all(mapply(function(self,other){
is.null(other) ||
all(sapply(other,function(x){self==length(x)}))
},
self = private$.dims[1:nval],
other=value
))){
private$.dimData[!sapply(value,is.null)] = value[!sapply(value,is.null)]
} else {
stop("The dimensions don't match up.")
}
} else {
stop("Invalid number of dimensions.")
}
} else {
stop(paste(
"Not sure how to make dimension metaData from object of class",
class(value)
))
}
},
dnames = function(value){
if('dnames' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dnames)
}
stop("Do not write directly to the dimension names.")
},
nrow = function(value){
if('nrow' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dims[1])
}
stop("Do not write directly to the number of rows.")
},
ncol = function(value){
if('ncol' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dims[2])
}
stop("Do not write directly to the number of columns.")
},
rnames = function(value){
if('rnames' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dnames[[1]])
}
stop("Do not write directly to the row names.")
},
cnames = function(value){
if('cnames' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(private$.dnames[[2]])
}
stop("Do not write directly to the column names.")
},
colData = function(value){
if('colData' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(self$dimData[[2]])
}
self$dimData[[2]] <- value
},
rowData = function(value){
if('rowData' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
return(self$dimData[[1]])
}
self$dimData[[1]] <- value
},
aDims = function(value){
if('aDims' %in% private$.debug){
browser()
}
if(missing(value)){
return(private$.aDims)
}
lapply(value,function(value){
if(!all(value %in% colnames(private$.frame))){
stop(paste(value,"is not a column of the frame"))
}
})
private$.aDims = value
private$aCurrent = FALSE
},
aVal = function(value){
if('aVal' %in% private$.debug){
browser()
}
if(missing(value)){
return(private$.aVal)
}
if(!(value %in% colnames(private$.frame))){
stop(paste(value,"is not a column of the frame"))
}
private$.aVal = value
private$aCurrent = FALSE
},
aDimData = function(value){
if('aDimData' %in% private$.debug){
browser()
}
if(missing(value)){
return(private$.aDimData)
}
lapply(value,function(value){
for(val in value){
if(!(val %in% colnames(private$.frame))){
stop(paste(val,"is not a column of the frame"))
}
}
})
private$.aDimData = value
private$aCurrent = FALSE
},
mat = function(value){
if('mat' %in% private$.debug){
browser()
}
if(missing(value)){
if(private$aCurrent == FALSE){
private$updateArray()
}
if(private$.ndim == 2){
return(as.matrix(private$.arr))
}
return(apply(private$.arr,c(1,2),function(x){x[slice]}))
}
stop(paste(
"Do not write directly to the mat, because it is automatically",
"calculated. The Observation List is called frame"
))
},
slice = function(value){
if(missing(value)){
return(private$.slice)
}
if(any(c(1,1,value) > self$dims)){
stop("Value must be between 1 and length in that dimension.")
}
private$.slice = matrix(value,1)
},
aggregate = function(value){
if(missing(value)){
return(private$.aggregate)
}
private$aCurrent = FALSE
if(class(value) != 'function'){
stop(paste(
"Not a function. aggregate should be a function taking a single",
"data_frame argument called input_data"
))
}
if(length(names(formals(fun=value))) != 1){
stop(paste(
"Not a valid function for aggregation. A valid aggregation function",
"must take a single data_frame argument."
))
}
private$.aggregate = value
}
)
)
|
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