ds.dataFrameSubset: Sub-sets data frames in the server-side

In datashield/dsBaseClient: DataSHIELD Client Functions

Sub-sets data frames in the server-side

Description

Subsets a data frame by rows and/or by columns.

Usage

ds.dataFrameSubset(
  df.name = NULL,
  V1.name = NULL,
  V2.name = NULL,
  Boolean.operator = NULL,
  keep.cols = NULL,
  rm.cols = NULL,
  keep.NAs = NULL,
  newobj = NULL,
  datasources = NULL,
  notify.of.progress = FALSE
)

Arguments

df.name	a character string providing the name of the data frame to be subseted.
V1.name	A character string specifying the name of the vector to which the Boolean operator is to be applied to define the subset. For more information see details.
V2.name	A character string specifying the name of the vector to compare with V1.name.
Boolean.operator	A character string specifying one of six possible Boolean operators: '==', '!=', '>', '>=', '<' and '<='.
keep.cols	a numeric vector specifying the numbers of the columns to be kept in the final subset.
rm.cols	a numeric vector specifying the numbers of the columns to be removed from the final subset.
keep.NAs	logical, if TRUE the missing values are included in the subset. If FALSE or NULL all rows with at least one missing values are removed from the subset.
newobj	a character string that provides the name for the output object that is stored on the data servers. Default dataframesubset.newobj.
datasources	a list of DSConnection-class objects obtained after login. If the datasources the default set of connections will be used: see datashield.connections_default.
notify.of.progress	specifies if console output should be produced to indicate progress. Default FALSE.

Details

Subset a pre-existing data frame using the standard set of Boolean operators (==, !=, >, >=, <, <=). The subsetting is made by rows, but it is also possible to select columns to keep or remove. Instead, if you wish to keep all rows in the subset (e.g. if the primary plan is to subset by columns and not by rows) the V1.name and V2.name parameters can be used to specify a vector of the same length as the data frame to be subsetted in each study in which every element is 1 and there are no missing values. For more information see the example 2 below.

Server functions called: dataFrameSubsetDS1 and dataFrameSubsetDS2

Value

ds.dataFrameSubset returns the object specified by the newobj argument which is written to the server-side. Also, two validity messages are returned to the client-side indicating the name of the newobj which has been created in each data source and if it is in a valid form.

Author(s)

DataSHIELD Development Team

Examples

## Not run: 

 ## 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()
  
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Subsetting a data frame
  #Example 1: Include some rows and all columns in the subset
  ds.dataFrameSubset(df.name = "D",
                     V1.name = "D$LAB_TSC",
                     V2.name = "D$LAB_TRIG",
                     Boolean.operator = ">",
                     keep.cols = NULL, #All columns are included in the new subset
                     rm.cols = NULL, #All columns are included in the new subset
                     keep.NAs = FALSE, #All rows with NAs are removed
                     newobj = "new.subset",
                     datasources = connections[1],#only the first server is used ("study1")
                     notify.of.progress = FALSE)
  #Example 2: Include all rows and some columns in the new subset
    #Select complete cases (rows without NA)
    ds.completeCases(x1 = "D",
                     newobj = "complet",
                     datasources = connections)
    #Create a vector with all ones
    ds.make(toAssign = "complet$LAB_TSC-complet$LAB_TSC+1",
            newobj = "ONES",
            datasources = connections) 
    #Subset the data
    ds.dataFrameSubset(df.name = "complet",
                       V1.name = "ONES",
                       V2.name = "ONES",
                       Boolean.operator = "==",
                       keep.cols = c(1:4,10), #only columns 1, 2, 3, 4 and 10 are selected
                       rm.cols = NULL,
                       keep.NAs = FALSE,
                       newobj = "subset.all.rows",
                       datasources = connections, #all servers are used
                       notify.of.progress = FALSE)                
                     
  # Clear the Datashield R sessions and logout                 
  datashield.logout(connections) 
  

## End(Not run)   

datashield/dsBaseClient documentation built on May 16, 2023, 10:19 p.m.