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ds.rPois.R
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ds.rPois.R
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#' @title Generates Poisson distribution in the server-side
#' @description Generates random (pseudorandom) non-negative integers
#' with a Poisson distribution.
#' Besides, \code{ds.rPois} allows creating different vector lengths in each server.
#' @details Creates a vector of random or pseudorandom non-negative integer values
#' distributed with a Poisson distribution in each data source.
#' The \code{ds.rPois} function's arguments specify lambda,
#' the length and the seed of the output vector in each source.
#'
#' To specify different \code{lambda} value in each source, you can use a character vector
#' \code{(..., lambda = "vector.of.lambdas"...)} or the \code{datasources}
#' parameter to create the random vector for one source at a time,
#' changing \code{lambda} as required.
#' Default value for \code{lambda> = 1}.
#'
#' If \code{seed.as.integer} is an integer
#' e.g. 5 and there is more than one source (N) the seed is set as 5*N.
#' For example, in the first study the seed is set as 938*1,
#' in the second as 938*2
#' up to 938*N in the Nth study.
#'
#' If \code{seed.as.integer} is set as 0 all sources will start with the seed value
#' 0 and all the random number generators will, therefore, start from the same position.
#' Also, to use the same starting seed in all studies but do not wish it to
#' be 0, you can use \code{datasources} argument to generate the random number
#' vectors one source at a time.
#'
#' Server functions called: \code{rPoisDS} and \code{setSeedDS}.
#'
#' @param samp.size an integer value or an integer vector that defines the length of the
#' random numeric vector to be created in each source.
#' @param lambda the number of events mean per interval.
#' @param newobj a character string that provides the name for the output variable
#' that is stored on the data servers. Default \code{newObject}.
#' @param seed.as.integer an integer or a NULL value which provides the random seed
#' in each data source.
#' @param return.full.seed.as.set logical, if TRUE will return the full
#' random number seed in each data source (a numeric vector of length 626). If
#' FALSE it will only return the trigger seed value you have provided.
#' Default is FALSE.
#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login.
#' If the \code{datasources} argument is not specified
#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
#' @return \code{ds.rPois} returns random number vectors with a Poisson distribution for each study,
#' taking into account the values specified in each parameter of the function.
#' The created vectors are stored in the server-side.
#' If requested, it also returned to the client-side the full
#' 626 lengths random seed vector generated in each source
#' (see info for the argument \code{return.full.seed.as.set}).
#'
#' @examples
#'
#' \dontrun{
#'
#' ## Version 6, for version 5 see the Wiki
#' # Connecting to the Opal servers
#'
#' require('DSI')
#' require('DSOpal')
#' require('dsBaseClient')
#'
#' builder <- DSI::newDSLoginBuilder()
#' builder$append(server = "study1",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM1", driver = "OpalDriver")
#' builder$append(server = "study2",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM2", driver = "OpalDriver")
#' builder$append(server = "study3",
#' url = "http://192.168.56.100:8080/",
#' user = "administrator", password = "datashield_test&",
#' table = "CNSIM.CNSIM3", driver = "OpalDriver")
#' logindata <- builder$build()
#' # Log onto the remote Opal training servers
#' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
#'
#' # Generating the vectors in the Opal servers
#' ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different
#' lambda=as.character(c(2,3,4)), #different mean per interval (2,3,4) in each source
#' newobj="Pois.dist",
#' seed.as.integer=1234,
#' return.full.seed.as.set=FALSE,
#' datasources=connections) #all the Opal servers are used, in this case 3
#' #(see above the connection to the servers)
#' ds.rPois(samp.size=13,
#' lambda=5,
#' newobj="Pois.dist",
#' seed.as.integer=1234,
#' return.full.seed.as.set=FALSE,
#' datasources=connections[1]) #only the first Opal server is used ("study1")
#'
#' # Clear the Datashield R sessions and logout
#' datashield.logout(connections)
#' }
#' @author DataSHIELD Development Team
#' @export
ds.rPois<-function(samp.size=1,lambda=1, newobj="newObject", seed.as.integer=NULL, return.full.seed.as.set=FALSE, datasources=NULL){
##################################################################################
# look for DS connections
if(is.null(datasources)){
datasources <- datashield.connections_find()
}
# ensure datasources is a list of DSConnection-class
if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){
stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE)
}
########################
#TEST SEED PRIMING VALUE
seed.valid<-0
if(is.null(seed.as.integer)){
seed.as.text<-"NULL"
seed.valid<-1
}
if(is.numeric(seed.as.integer)){
seed.as.text<-as.character(seed.as.integer)
seed.valid<-1
}
if(seed.valid==0){
mess1<-("ERROR failed: seed.as.integer must be set as an integer [numeric] or left NULL")
return(mess1)
}
###################################################################################
#samp.size is either a numeric scalar or a numeric vector set
#by the user or derived as explained for "numobs" in the help
#for the samp.size parameter - and declared without inverted commas
#as it is a client-side vector lambda is specified either as a numeric scalar,
#or as a vector on the serverside which contains values that
#can vary from row to row of a dataset.
#Such serverside vectors must be named in inverted commas. These get
#stripped off when the vector name is passed to the serverside.
arguments.valid<-1
if(is.null(samp.size)||is.null(lambda)||is.null(newobj)){
arguments.valid<-0
}
if(!arguments.valid){
mess2<-("ERROR: appropriate values must be set for samp.size, lambda, and newobj name")
return(mess2)
}
lambda.valid<-1
if(is.numeric(lambda)){
if(lambda<=0){
lambda.valid<-0
}
}
if(!lambda.valid){
mess3<-("ERROR: lambda must be > 0")
return(mess3)
}
###################################################################################
#######################
#SET SEED IN EACH STUDY
ssDS.obj<-list()
numsources<-length(datasources)
single.integer.seed<-NULL
for(study.id in 1:numsources){
if(is.null(seed.as.integer)){
seed.as.text<-"NULL"
}
if(is.numeric(seed.as.integer)){
seed.as.integer.study.specific<-(seed.as.integer*study.id) #if set as 0 all studies will be the same
seed.as.text<-as.character(seed.as.integer.study.specific)
single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific)
}
if(seed.as.text=="NULL"){
cat("NO SEED SET IN STUDY",study.id,"\n\n")
}
calltext <- paste0("setSeedDS(", seed.as.text, ")")
ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext))
}
cat("\n\n")
##############################
#GENERATE PSEUDORANDOM NUMBERS
if(length(samp.size)==1){
samp.size<-rep(samp.size,numsources)
}
for(k in 1:numsources){
toAssign<-paste0("rPoisDS(",samp.size[k],",",lambda, ")")
if(is.null(toAssign)){
stop("Please give the name of object to assign or an expression to evaluate and assign.!\n", call.=FALSE)
}
# now do the business
DSI::datashield.assign(datasources[k], newobj, as.symbol(toAssign))
}
#############################################################################################################
#DataSHIELD CLIENTSIDE MODULE: CHECK KEY DATA OBJECTS SUCCESSFULLY CREATED #
#
#SET APPROPRIATE PARAMETERS FOR THIS PARTICULAR FUNCTION #
test.obj.name<-newobj #
# #
#
# CALL SEVERSIDE FUNCTION #
calltext <- call("testObjExistsDS", test.obj.name) #
#
object.info<-DSI::datashield.aggregate(datasources, calltext) #
#
# CHECK IN EACH SOURCE WHETHER OBJECT NAME EXISTS #
# AND WHETHER OBJECT PHYSICALLY EXISTS WITH A NON-NULL CLASS #
num.datasources<-length(object.info) #
#
#
obj.name.exists.in.all.sources<-TRUE #
obj.non.null.in.all.sources<-TRUE #
#
for(j in 1:num.datasources){ #
if(!object.info[[j]]$test.obj.exists){ #
obj.name.exists.in.all.sources<-FALSE #
} #
if(is.null(object.info[[j]]$test.obj.class) || ("ABSENT" %in% object.info[[j]]$test.obj.class)){ #
obj.non.null.in.all.sources<-FALSE #
} #
} #
#
if(obj.name.exists.in.all.sources && obj.non.null.in.all.sources){ #
#
return.message<- #
paste0("A data object <", test.obj.name, "> has been created in all specified data sources") #
#
#
}else{ #
#
return.message.1<- #
paste0("Error: A valid data object <", test.obj.name, "> does NOT exist in ALL specified data sources") #
#
return.message.2<- #
paste0("It is either ABSENT and/or has no valid content/class,see return.info above") #
#
return.message.3<- #
paste0("Please use ds.ls() to identify where missing") #
#
#
return.message<-list(return.message.1,return.message.2,return.message.3) #
#
} #
#
calltext <- call("messageDS", test.obj.name) #
studyside.message<-DSI::datashield.aggregate(datasources, calltext) #
#
no.errors<-TRUE #
for(nd in 1:num.datasources){ #
if(studyside.message[[nd]]!="ALL OK: there are no studysideMessage(s) on this datasource"){ #
no.errors<-FALSE #
} #
} #
#
#
if(no.errors && !return.full.seed.as.set){ #
validity.check<-paste0("<",test.obj.name, "> appears valid in all sources") #
return(list(integer.seed.as.set.by.source=single.integer.seed,random.vector.length.by.source=samp.size, #
is.object.created=return.message,validity.check=validity.check)) #
} #
#
if(no.errors && return.full.seed.as.set){ #
validity.check<-paste0("<",test.obj.name, "> appears valid in all sources") #
return(list(full.seed.as.set=ssDS.obj, #
integer.seed.as.set.by.source=single.integer.seed,random.vector.length.by.source=samp.size, #
is.object.created=return.message,validity.check=validity.check)) #
} #
#
if(!no.errors){ #
validity.check<-paste0("<",test.obj.name,"> invalid in at least one source. See studyside.messages:") #
return(list(is.object.created=return.message,validity.check=validity.check, #
studyside.messages=studyside.message)) #
} #
#
#END OF CHECK OBJECT CREATED CORECTLY MODULE #
#############################################################################################################
}
#ds.rPois