ds.tapply {dsBaseClient}R Documentation

Applies a Function Over a Server-Side Ragged Array

Description

Apply one of a selected range of functions to summarize an outcome variable over one or more indexing factors. The resultant summary is written to the client-side.

Usage

ds.tapply(
  X.name = NULL,
  INDEX.names = NULL,
  FUN.name = NULL,
  datasources = NULL
)

Arguments

X.name

a character string specifying the name of the variable to be summarized.

INDEX.names

a character string specifying the name of a single factor or a vector of names of factors to index the variable to be summarized. For more information see Details.

FUN.name

a character string specifying the name of one of the allowable summarizing functions. This can be set as: "N" (or "length"), "mean","sd", "sum", or "quantile". For more information see Details.

datasources

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Details

This function is similar to a native R function tapply(). It applies one of a selected range of functions to each cell of a ragged array, that is to each (non-empty) group of values given by each unique combination of a series of indexing factors.

The range of allowable summarizing functions for DataSHIELD ds.tapply function is much more restrictive than for the native R tapply function. The reason for this is the protection against disclosure risk.

Should other functions be required in the future then, provided they are non-disclosive, the DataSHIELD development team could work on them if requested.

To protect against disclosure the number of observations in each summarizing group in each source is calculated and if any of these falls below the value of nfilter.tab (the minimum allowable non-zero count in a contingency table) the tapply analysis of that source will return only an error message. The value of nfilter.tab is can be set and modified only by the data custodian. If an analytic team wishes the value to be reduced (e.g. to 1 which will allow any output from tapply to be returned) this needs to formally be discussed and agreed with the data custodian.

If the reason for the tapply analysis is, for example, to break a dataset down into a small number of values for each individual and then to flag up which individuals have got at least one positive value for a binary outcome variable, then that flagging does not have to be overtly returned to the client-side. Rather, it can be written as a vector to the server-side at each source (which, like any other server-side object, cannot then be seen, abstracted or copied). This can be done using ds.tapply.assign which writes the results as a newobj to the server-side and does not test the number of observations in each group against nfilter.tab. For more information see the help option of ds.tapply.assign function.

The native R tapply function has optional arguments such as na.rm = TRUE for FUN = mean which will exclude any NAs from the outcome variable to be summarized. However, in order to keep DataSHIELD's ds.tapply and ds.tapply.assign functions straightforward, the server-side functions tapplyDS and tapplyDS.assign both starts by stripping any observations which have missing (NA) values in either the outcome variable or in any one of the indexing factors. In consequence, the resultant analyses are always based on complete cases.

In INDEX.names argument the native R tapply function can coerce non-factor vectors into factors. However, this does not always work when using the DataSHIELD ds.tapply or ds.tapply.assign functions so if you are concerned that an indexing vector is not being treated correctly as a factor, please first declare it explicitly as a factor using ds.asFactor.

In FUN.name argument the allowable functions are: N or length (the number of (non-missing) observations in the group defined by each combination of indexing factors); mean; SD (standard deviation); sum; quantile (with quantile probabilities set at c(0.05,0.1,0.2,0.25,0.3,0.33,0.4,0.5,0.6,0.67,0.7,0.75,0.8,0.9,0.95)).

Server function called: tapplyDS

Value

ds.tapply returns to the client-side an array of the summarized values. It has the same number of dimensions as INDEX.

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") 
  
  # Apply a Function Over a Server-Side Ragged Array
  
  ds.assign(toAssign = "D$LAB_TSC",
            newobj = "LAB_TSC",
            datasources = connections)
            
  ds.assign(toAssign = "D$GENDER",
            newobj =  "GENDER",
            datasources = connections)
            
  ds.tapply(X.name = "LAB_TSC",
            INDEX.names = c("GENDER"),
            FUN.name = "mean",
            datasources = connections)
                 
  # Clear the Datashield R sessions and logout                 
  datashield.logout(connections) 
  

## End(Not run) 

[Package dsBaseClient version 6.1.1 ]