ds.make.RdThis function defines a new object in the server-side via an allowed function or an arithmetic expression.
ds.make function is equivalent to ds.assign, but runs slightly faster.
ds.make(toAssign = NULL, newobj = NULL, datasources = NULL)a character string specifying the function or the arithmetic expression.
a character string that provides the name for the output
variable that is stored on the data servers. Default make.newobj.
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.
ds.make returns the new object which is written to the
server-side. Also a validity message is returned to the client-side indicating whether the new object has been correctly
created at each source.
If the new object is created successfully, the function will verify its
existence on the required servers. Please note there are certain modes of failure
where it is reported that the object has been created but it is not there. This
reflects a failure in the processing of some sort and warrants further exploration of the
details of the call to ds.make and the variables/objects which it invokes.
TROUBLESHOOTING: please note we have recently identified an error that makes ds.make
fail and DataSHIELD crash.
The error arises from a call such as
ds.make(toAssign = '5.3 + beta*xvar', newobj = 'predvals').
This is a typical call you
may make to get the predicted values from a simple linear regression model where
a y variable is regressed against an x variable (xvar)
where the estimated regression intercept is 5.3
and beta is the estimated regression slope.
This call appears to
fail because in interpreting the arithmetic function which is its first argument
it first encounters the (length 1) scalar 5.3
and when it then encounters the xvar vector
which has more than one element it fails - apparently because it does not recognise
that you need to replicate the 5.3 value the appropriate number of times
to create a vector
of length equal to xvar with each value equal to 5.3.
There are two work-around solutions here:
(1) explicitly create a vector of appropriate length with each
value equal to 5.3. To do this there is a useful trick. First identify
a convenient numeric variable with no missing values (typically a numeric
individual ID) let us call it indID equal in length to xvar (xvar may include NAs
but that doesn't matter provided indID is the same total length). Then issue the call
ds.make(toAssign = 'indID-indID+1',newobj = 'ONES'). This creates a vector of ones (called ONES)
in each source equal in length to the indID vector in that source. Then issue
the second call ds.make(toAssign = 'ONES*5.3',newobj = 'vect5.3') which creates the required
vector of length equal to xvar with all elements 5.3. Finally, you can
now issue a modified call to reflect what was originally needed:
ds.make(toAssign = 'vect5.3+beta*xvar', 'predvals').
(2) Alternatively, if you simply swap the original call around:
ds.make(toAssign = '(beta*xvar)+5.3', newobj = 'predvals')
the error seems also to be circumvented. This is presumably because the first element
of the arithmetic function is of length equal to xvar and it then knows to
replicate the 5.3 that many times in the second part of the expression.
The second work-around is easier, but it is worth knowing about the
first trick because creating a vector of ones of equal length to another vector
can be useful in other settings. Equally the call:
ds.make(toAssign = 'indID-indID',newobj = 'ZEROS')
to create a vector of zeros of that same length may also be useful.
Server function : messageDS
The ds.make function is a wrapper for the DSI package function datashield.assign
if (FALSE) {
## Version 6, for version 5 see the Wiki
# connecting to the Opal servers
require('DSI')
require('DSOpal')
require('dsBaseClient')
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver")
builder$append(server = "study2",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver")
builder$append(server = "study3",
url = "http://192.168.56.100:8080/",
user = "administrator", password = "datashield_test&",
table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver")
logindata <- builder$build()
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
##Example 1: arithmetic operators
ds.make(toAssign = "D$age.60 + D$bmi.26",
newobj = "exprs1",
datasources = connections)
ds.make(toAssign = "D$noise.56 + D$pm10.16",
newobj = "exprs2",
datasources = connections)
ds.make(toAssign = "(exprs1*exprs2)/3.2",
newobj = "result.example1",
datasources = connections)
##Example 2: miscellaneous operators within functions
ds.make(toAssign = "(D$female)^2",
newobj = "female2",
datasources = connections)
ds.make(toAssign = "(2*D$female)+(D$log.surv)-(female2*2)",
newobj = "output.test.1",
datasources = connections)
ds.make(toAssign = "exp(output.test.1)",
newobj = "output.test",
datasources = connections)
# clear the Datashield R sessions and logout
datashield.logout(connections)
}