Version 4.0.0

Created by Former user (Deleted)
Last updated: 07 Jul, 2020 by Alex Westerberg


(Link back to Version 4 Archive)

Contents


 Click here to expand...



Functions amended

ds.glm

New parameters (i.e. arguments) added to the function: ds.glm: data, weights and offset, checks, startBetas.

  • data allows for user to specify the name of an optional data frame that holds the variables in the regression formula so one can can write for example:

    ds.glm(formula='DIS_DIAB~GENDER', data='D', family='binomial')

    which is equivalent to

    ds.glm(formula='D$DIS_DIAB~D$GENDER', family='binomial')

    In the previous release only the latter command was possible when the variables in the regression formula were held in a data frame 'D'.

  • weights to specify the name of a numeric variable of 'prior weights' to be used in the model fitting process.
  • offset to specify the name of a known component to be included in the linear predictor.
  • checks to help with error tracking. These checks are switched off by default. If set to TRUE thorough checks are carried out before the process starts.
  • startBetas to specify starting values for the parameters in the linear predictor. In earlier versions this parameter was named startCoeff.
ds.table1D and ds.table2D

The Functions were re-written from scratch to implement a new way of masking 'invalid' cells whilst reporting correct total counts (i.e. to address the issues raised in BioSHaRe annual meeting, Athens 2014).
The new versions of these two functions return a more tidy output with improved error reporting and improved flexibility.

ds.tTest

In the previous version of this function a t.test was only possible for two continuous vectors.
The new version allows for the comparison of the mean values of a continuous vector across the categories of factor as in the below example where both vectors are in a data frame 'D':

# The continuous vector is on the left of the formula whilst the factor is on the right side
ds.tTest(x='D$PM_BMICONTINUOUS~D$GENDER')
ds.dataframe

New parameter (i.e. argument) added to the function: completeCases:

  • completeCases if set to TRUE allows to construct a complete table (i.e. a data frame where rows with missing values are excluded)
ds.meanByClass

In the new version of this function it is possible to compute the mean and standard deviation of a continuous vector across the categories of a factor as follows:

# The continuous vector is on the left of the formula whilst the factor is on the right side. In the below example both vector are in a data frame named 'D'.
ds.meanByClass(x='D$LAB_HDL~D$GENDER')

This addition was implemented for improved flexibility and is equivalent to the below syntax which still works and should be used to specify more than one outcome or covariate.

ds.meanByClass(x='D', outvar=c('LAB_HDL'), covar=c('GENDER'))

New functions

ds.subsetByClass

This function replaces the previous ds.subclass

ds.numNA

Returns the number of missing values in a given vector.

ds.replaceNA

To replaces missing values in a given vector by specific value(s).

ds.ls

To display the names of the objects stored/defined on the server side.

Functions removed

ds.subclass

This function has been replaced by ds.subsetByClass

Actions required from users

  • Some of the changes listed above might affect your previous scripts/commands, particularly the change of function names and syntax (e.g. ds.subclass replaced by ds.subsetByClass). Please amend your previous scripts/commands to adopt the new functions names and syntax to avoid errors.
  • If you are faced with an error whilst using this new version please double check first that you are using the correct function name and syntax before contacting the support team. This will ensure our limited support resources are used efficiently.

Remarks:

  • If you are using the BioSHaRE Rstudio interface (http://rstudio.bioshare.eu/) you do not have to do anything. However you might experience errors with the cohorts that have not updated their server packages because the latest client functions work with their server side counterparts.
    We will keep you updated about the cohorts that have updated their servers so you only include those in your analysis.
  • If you are running horizontal-DataSHIELD locally using the test environment: Please install the latest server side functions the same way as mentioned above on your virtual machine. And get the latest client side functions by running the below command in R or Rstudio, see here how to install the client packages on the test environment.

Actions required from opal server administrators

If you are the administrator of the opal server for a cohort: Please deploy the new package in your servers. Install all the packages via opal as follows:

  • Login in to your opal interface
  • Go to Administration on top-right corner
  • select DataSHIELD
  • In the packages list:
    • remove remove all the packages
      2. click Add Package
      3. click Install
      4. wait...
      5. verify that all package version are 4.0.0
      6. next to each package and under the column Action, click on Publish methods

List of packages and functions in the version 4.0.0

A /wiki/spaces/DSDEV/pages/12943456 is available.