ds.glm: Fits Generalized Linear Model

In datashield/dsBaseClient: DataSHIELD Client Functions

Fits Generalized Linear Model

Description

Fits a Generalized Linear Model (GLM) on data from single or multiple sources on the server-side.

Usage

ds.glm(
  formula = NULL,
  data = NULL,
  family = NULL,
  offset = NULL,
  weights = NULL,
  checks = FALSE,
  maxit = 20,
  CI = 0.95,
  viewIter = FALSE,
  viewVarCov = FALSE,
  viewCor = FALSE,
  datasources = NULL
)

Arguments

formula	an object of class formula describing the model to be fitted. For more information see Details.
data	a character string specifying the name of an (optional) data frame that contains all of the variables in the GLM formula.
family	identifies the error distribution function to use in the model. This can be set as "gaussian", "binomial" and "poisson". For more information see Details.
offset	a character string specifying the name of a variable to be used as an offset. ds.glm does not allow an offset vector to be written directly into the GLM formula. For more information see Details.
weights	a character string specifying the name of a variable containing prior regression weights for the fitting process. ds.glm does not allow a weights vector to be written directly into the GLM formula.
checks	logical. If TRUE ds.glm checks the structural integrity of the model. Default FALSE. For more information see Details.
maxit	a numeric scalar denoting the maximum number of iterations that are permitted before ds.glm declares that the model has failed to converge.
CI	a numeric value specifying the confidence interval. Default 0.95.
viewIter	logical. If TRUE the results of the intermediate iterations are printed. If FALSE only final results are shown. Default FALSE.
viewVarCov	logical. If TRUE the variance-covariance matrix of parameter estimates is returned. Default FALSE.
viewCor	logical. If TRUE the correlation matrix of parameter estimates is returned. Default FALSE.
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

Fits a GLM on data from a single source or multiple sources on the server-side. In the latter case, the data are co-analysed (when using ds.glm) by using an approach that is mathematically equivalent to placing all individual-level data from all sources in one central warehouse and analysing those data using the conventional glm() function in R. In this situation marked heterogeneity between sources should be corrected (where possible) with fixed effects. For example, if each study in a (binary) logistic regression analysis has an independent intercept, it is equivalent to allowing each study to have a different baseline risk of disease. This may also be viewed as being an IP (individual person) meta-analysis with fixed effects.

In formula most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glm.

Many GLMs can be fitted very simply using a formula such as:

y~a+b+c+d

which simply means fit a GLM with y as the outcome variable and a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

EVENT~1+TID+SEXF*AGE.60

In the above model the outcome variable is EVENT and the covariates TID (factor variable with level values between 1 and 6 denoting the period time), SEXF (factor variable denoting sex) and AGE.60 (quantitative variable representing age-60 in years). The term 1 forces the model to include an intercept term, in contrast if you use the term 0 the intercept term is removed. The * symbol between SEXF and AGE.60 means fit all possible main effects and interactions for and between those two covariates. This takes the value 0 in all males 0 * AGE.60 and in females 1 * AGE.60. This model is in example 1 of the section Examples. In this case the logarithm of the survival time is added as an offset (log(survtime)).

In the family argument can be specified three types of models to fit:

"gaussian"

: conventional linear model with normally distributed errors

"binomial"

: conventional unconditional logistic regression model

"poisson"

: Poisson regression model which is the most used in survival analysis. The model used Piecewise Exponential Regression (PER) which typically closely approximates Cox regression in its main estimates and standard errors.

At present the gaussian family is automatically coupled with an identity link function, the binomial family with a logistic link function and the poisson family with a log link function.

The data argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d

The checks argument verifies that the variables in the model are all defined (exist) on the server-side at every study and that they have the correct characteristics required to fit the model. It is suggested to make checks argument TRUE if an unexplained problem in the model fit is encountered because the running process takes several minutes.

In maxit Logistic regression and Poisson regression models can require many iterations, particularly if the starting value of the regression constant is far away from its actual value that the GLM is trying to estimate. In consequence we often set maxit=30 but depending on the nature of the models you wish to fit, you may wish to be alerted much more quickly than this if there is a delay in convergence, or you may wish to all more iterations.

Privacy protected iterative fitting of a GLM is explained here:

(1) Begin with a guess for the coefficient vector to start iteration 1 (let's call it beta.vector[1]). Using beta.vector[1], run iteration 1 with each source calculating the resultant score vector (and information matrix) generated by its data - given beta.vector[1] - as the sum of the score vector components (and the sum of the components of the information matrix) derived from each individual data record in that source. NB in most models the starting values in beta.vector[1] are set to be zero for all parameters.

(2) Transmit the resultant score vector and information matrix from each source back to the clientside server (CS) at the analysis centre. Let's denote SCORE[1][j] and INFORMATION.MATRIX[1][j] as the score vector and information matrix generated by study j at the end of the 1st iteration.

(3) CS sums the score vectors, and equivalently the information matrices, across all studies (i.e. j = 1:S, where S is the number of studies). Note that, given beta.vector[1], this gives precisely the same final sums for the score vectors and information matrices as would have been obtained if all data had been in one central warehoused database and the overall score vector and information matrix at the end of the first iteration had been calculated (as is standard) by simply summing across all individuals. The only difference is that instead of directly adding all values across all individuals, we first sum across all individuals in each data source and then sum those study totals across all studies - i.e. this generates the same ultimate sums

(4) CS then calculates sum(SCORES)%*% inverse(sum(INFORMATION.MATRICES)) - heuristically this may be viewed as being "the sum of the score vectors divided (NB 'matrix division') by the sum of the information matrices". If one uses the conventional algorithm (IRLS) to update generalized linear models from iteration to iteration this quantity happens to be precisely the vector to be added to the current value of beta.vector (i.e. beta.vector[1]) to obtain beta.vector[2] which is the improved estimate of the beta.vector to be used in iteration 2. This updating algorithm is often called the IRLS (Iterative Reweighted Least Squares) algorithm - which is closely related to the Newton Raphson approach but uses the expected information rather than the observed information.

(5) Repeat steps (2)-(4) until the model converges (using the standard R convergence criterion). NB An alternative way to coherently pool the glm across multiple sources is to fit each glm to completion (i.e. multiple iterations until convergence) in each source and then return the final parameter estimates and standard errors to the CS where they could be pooled using study-level meta-analysis. An alternative function ds.glmSLMA allows you to do this. It will fit the glms to completion in each source and return the final estimates and standard errors (rather than score vectors and information matrices). It will then rely on functions in the R package metafor to meta-analyse the key parameters.

Server functions called: glmDS1 and glmDS2

Value

Many of the elements of the output list returned by ds.glm are equivalent to those returned by the glm() function in native R. However, potentially disclosive elements such as individual-level residuals and linear predictor values are blocked. In this case, only non-disclosive elements are returned from each study separately.

The list of elements returned by ds.glm is mentioned below:

Nvalid: total number of valid observational units across all studies.

Nmissing: total number of observational units across all studies with at least one data item missing.

Ntotal: total of observational units across all studies, the sum of valid and missing units.

disclosure.risk: risk of disclosure, the value 1 indicates that one of the disclosure traps has been triggered in that study.

errorMessage: explanation for any errors or disclosure risks identified.

nsubs: total number of observational units used by ds.glm function. nb usually is the same as nvalid.

iter: total number of iterations before convergence achieved.

family: error family and link function.

formula: model formula, see description of formula as an input parameter (above).

coefficients: a matrix with 5 columns:

First

: the names of all of the regression parameters (coefficients) in the model

second

: the estimated values

third

: corresponding standard errors of the estimated values

fourth

: the ratio of estimate/standard error

.

fifth

: the p-value treating that as a standardised normal deviate

dev: residual deviance.

df: residual degrees of freedom. nb residual degrees of freedom + number of parameters in model = nsubs.

output.information: reminder to the user that there is more information at the top of the output.

Also, the estimated coefficients and standard errors expanded with estimated confidence intervals with % coverage specified by ci argument are returned. For the poisson model, the output is generated on the scale of the linear predictor (log rates and log rate ratios) and the natural scale after exponentiation (rates and rate ratios).

Author(s)

DataSHIELD Development Team

Examples

## Not run: 

 ## Version 6, for version 5 see Wiki
  # Connecting to the Opal servers
  
  require('DSI')
  require('DSOpal')
  require('dsBaseClient')
  
  # Example 1: Fitting GLM for survival analysis
  # For this analysis we need to load survival data from the server 
  
  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()
  
  # Log onto the remote Opal training servers
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Fit the GLM 
  
  # make sure that the outcome is numeric 
  ds.asNumeric(x.name = "D$cens",
               newobj = "EVENT",
               datasources = connections)
               
  # convert time id variable to a factor 
               
  ds.asFactor(input.var.name = "D$time.id",
              newobj = "TID",
              datasources = connections)
              
  # create in the server-side the log(survtime) variable
         
  ds.log(x = "D$survtime",
         newobj = "log.surv",
         datasources = connections)
  
  ds.glm(formula = EVENT ~ 1 + TID + female * age.60,
         data = "D",
         family = "poisson", 
         offset = "log.surv",
         weights = NULL,
         checks = FALSE,
         maxit = 20,
         CI = 0.95,
         viewIter = FALSE,
         viewVarCov = FALSE,
         viewCor = FALSE,
         datasources = connections)
         
  # Clear the Datashield R sessions and logout
  datashield.logout(connections) 
  
  # Example 2: run a logistic regression without interaction
  # For this example we are going to load another dataset  
  
  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()
  
  # Log onto the remote Opal training servers
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Fit the logistic regression model

  mod <- ds.glm(formula = "DIS_DIAB~GENDER+PM_BMI_CONTINUOUS+LAB_HDL",
                data = "D",
                family = "binomial",
                datasources = connections)
                
  mod #visualize the results of the model

# Example 3: fit a standard Gaussian linear model with an interaction
# We are using the same data as in example 2. 

mod <- ds.glm(formula = "PM_BMI_CONTINUOUS~DIS_DIAB*GENDER+LAB_HDL",
              data = "D",
              family = "gaussian",
              datasources = connections)
mod

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

## End(Not run)

datashield/dsBaseClient documentation built on Nov. 16, 2024, 2:07 p.m.