ds.getWGSR {dsBaseClient}

R Documentation

Computes the WHO Growth Reference z-scores of anthropometric data

Description

Calculate WHO Growth Reference z-score for a given anthropometric measurement This function is similar to R function getWGSR from the zscorer package.

Usage

ds.getWGSR(
  sex = NULL,
  firstPart = NULL,
  secondPart = NULL,
  index = NULL,
  standing = NA,
  thirdPart = NA,
  newobj = NULL,
  datasources = NULL
)

Arguments

sex	the name of the binary variable that indicates the sex of the subject. This must be coded as 1 = male and 2 = female. If in your project the variable sex has different levels, you should recode the levels to 1 for males and 2 for females using the ds.recodeValues DataSHIELD function before the use of the ds.getWGSR.
firstPart	Name of variable specifying: Weight (kg) for BMI/A, W/A, W/H, or W/L Head circumference (cm) for HC/A Height (cm) for H/A Length (cm) for L/A MUAC (cm) for MUAC/A Sub-scapular skinfold (mm) for SSF/A Triceps skinfold (mm) for TSF/A Give a quoted variable name as in (e.g.) "weight". Be careful with units (weight in kg; height, length, head circumference, and MUAC in cm; skinfolds in mm).
secondPart	Name of variable specifying: Age (days) for H/A, HC/A, L/A, MUAC/A, SSF/A, or TSF/A Height (cm) for BMI/A, or W/H Length (cm) for W/L Give a quoted variable name as in (e.g.) "age". Be careful with units (age in days; height and length in cm).
index	The index to be calculated and added to data. One of: bfa BMI for age hca Head circumference for age hfa Height for age lfa Length for age mfa MUAC for age ssa Sub-scapular skinfold for age tsa Triceps skinfold for age wfa Weight for age wfh Weight for height wfl Weight for length Give a quoted index name as in (e.g.) "wfh".
standing	Variable specifying how stature was measured. If NA (default) then age (for "hfa" or "lfa") or height rules (for "wfh" or "wfl") will be applied. This must be coded as 1 = Standing; 2 = Supine; 3 = Unknown. Missing values will be recoded to 3 = Unknown. Give a single value (e.g."1"). If no value is specified then height and age rules will be applied.
thirdPart	Name of variable specifying age (in days) for BMI/A. Give a quoted variable name as in (e.g.) "age". Be careful with units (age in days). If age is given in different units you should convert it in age in days using the ds.make DataSHIELD function before the use of the ds.getWGSR. For example if age is given in months then the transformation is given by the formula $age_days=age_months*(365.25/12)$.
newobj	a character string that provides the name for the output variable that is stored on the data servers. Defaults getWGSR.newobj.
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

The function calls the server-side function getWGSRDS that computes the WHO Growth Reference z-scores of anthropometric data for weight, height or length, MUAC (middle upper arm circumference), head circumference, sub-scapular skinfold and triceps skinfold. Note that the function might fail or return NAs when the variables are outside the ranges given in the WGS (WHO Child Growth Standards) reference (i.e. 45 to 120 cm for height and 0 to 60 months for age). It is up to the user to check the ranges and the units of their data.

Value

ds.getWGSR assigns a vector for each study that includes the z-scores for the specified index. The created vectors are stored in the servers.

Author(s)

Demetris Avraam for DataSHIELD Development Team

Examples

## Not run: 

  # Connecting to the Opal servers

  require('DSI')
  require('DSOpal')
  require('dsBaseClient')

  builder <- DSI::newDSLoginBuilder()
  builder$append(server = "study1", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "ANTHRO.anthro1", driver = "OpalDriver")
  builder$append(server = "study2", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "ANTHRO.anthro2", driver = "OpalDriver")
  builder$append(server = "study3",
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "ANTHRO.anthro3", driver = "OpalDriver")
                 
  logindata <- builder$build()
  
  # Log onto the remote Opal training servers
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Example 1: Generate the weight-for-height (wfh) index
  ds.getWGSR(sex = "D$sex", firstPart = "D$weight", secondPart = "D$height",
           index = "wfh", newobj = "wfh_index", datasources = connections)

  # Example 2: Generate the BMI for age (bfa) index
  ds.getWGSR(sex = "D$sex", firstPart = "D$weight", secondPart = "D$height",
           index = "bfa", thirdPart = "D$age", newobj = "bfa_index", datasources = connections)

  # clear the Datashield R sessions and logout
  datashield.logout(connections) 


## End(Not run)

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