madlib.glm: Generalized Linear Regression by MADlib in databases

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/madlib-glm.R View source: R/madlib-glm.R

Description

The wrapper function for MADlib's generzlized linear regression [7] including the support for multple families and link functions. Heteroskedasticity test is implemented for linear regression. One or multiple columns of data can be used to separate the data set into multiple groups according to the values of the grouping columns. The requested regression method is applied onto each group, which has fixed values of the grouping columns. Multinomial logistic regression is not implemented yet. Categorical variables are supported. The computation is parallelized by MADlib if the connected database is Greenplum/HAWQ database. The regression computation can also be done on a column which contains an array as its value in the data table.

Usage

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Arguments

formula

An object of class formula (or one that can be coerced to that class): a symbolic description of the model to be fitted. The details of model specification are given under ‘Details’.

data

An object of db.obj class. Currently, this parameter is mandatory. If it is an object of class db.Rquery or db.view, a temporary table will be created, and further computation will be done on the temporary table. After the computation, the temporary will be dropped from the corresponding database.

family

A string which indicates which form of regression to apply. Default value is “gaussian”. The accepted values are: gaussian(identity) (default for gaussian family), gaussian(log), gaussian(inverse), binomial(logit) (default for binomial family), binomial(probit), poisson(log) (default for poisson family), poisson(identity), poisson(sqrt), Gamma(inverse) (default for Gamma family), Gamma(identity), Gamma(log), inverse.gaussian(1/mu^2) (default for inverse.gaussian family), inverse.gaussian(log), inverse.gaussian(identity), inverse.gaussian(inverse).

na.action

A string which indicates what should happen when the data contain NAs. Possible values include na.omit, "na.exclude", "na.fail" and NULL. Right now, na.omit has been implemented. When the value is NULL, nothing is done on the R side and NA values are filtered on the MADlib side. User defined na.action function is allowed.

control

A list, extra parameters to be passed to linear or logistic regressions.

na.as.level: A logical value, default is FALSE. Whether to treat NA value as a level in a categorical variable or just ignore it.

For the linear regressions, the extra parameter is hetero. A logical, deafult is FALSE. If it is TRUE, then Breusch-Pagan test is performed on the fitting model and the corresponding test statistic and p-value are computed.

For logistic regression, one can pass the following extra parameters:

method: A string, default is "irls" (iteratively reweighted least squares [3]), other choices are "cg" (conjugate gradient descent algorithm [4]) and "igd" (stochastic gradient descent algorithm [5]). These algorithm names for logistic regression, namely family=binomial(logit) and use.glm=FALSE in the control list.

max.iter: An integer, default is 10000. The maximum number of iterations that the algorithms will run.

tolerance: A numeric value, default is 1e-5. The stopping threshold for the iteration algorithms.

use.glm: Whether to call MADlib's GLM function even when the family is gaussian(identity) or binomial(logit). For these two cases, the default behavior is to call MADlib's linear regression or logistic regression respectively, which might give better performance under certain circumstances. However, if use.glm is TRUE, then the generalized linear function will be used.

...

Further arguments passed to or from other methods. Currently, no more parameters can be passed to the linear regression and logistic regression.

Details

See madlib.lm for more details.

Value

For the return value of linear regression see madlib.lm for details.

For the logistic regression, the returned value is similar to that of the linear regression. If there is no grouping (i.e. no | in the formula), the result is a logregr.madlib object. Otherwise, it is a logregr.madlib.grps object, which is just a list of logregr.madlib objects.

If MADlib's generalized linear regression function is used (use.glm=TRUE for family=binomial(logit)), the return value is a glm.madlib object without grouping or a glm.madlib.grps object with grouping.

A logregr.madlib or glm.madlib object is a list which contains the following items:

grouping column(s)

When there are grouping columns in the formula, the resulting list has multiple items, each of which has the same name as one of the grouping columns. All of these items are vectors, and they have the same length, which is equal to the number of distinct combinations of all the grouping column values. Each row of these items together is one distinct combination of the grouping values. When there is no grouping column in the formula, none of such items will appear in the resulting list.

coef

A numeric matrix, the fitting coefficients. Each row contains the coefficients for the linear regression of each group of data. So the number of rows is equal to the number of distinct combinations of all the grouping column values.

log_likelihood

A numeric array, the log-likelihood for each fitting to the groups. Thus the length of the array is equal to grps.

std_err

A numeric matrix, the standard error for each coefficients. The row number is equal to grps.

z_stats,t_stats

A numeric matrix, the z-statistics or t-statistics for each coefficient. Each row is for a fitting to a group of the data.

p_values

A numeric matrix, the p-values of z_stats. Each row is for a fitting to a group of the data.

odds_ratios

Only for logregr.madlib object. A numeric array, the odds ratios [6] for the fittings for all groups.

condition_no

Only for logregr.madlib object. A numeric array, the condition number for all combinations of the grouping column values.

num_iterations

An integer array, the itertion number used by each fitting group.

grp.cols

An array of strings. The column names of the grouping columns.

has.intercept

A logical, whether the intercept is included in the fitting.

ind.vars

An array of strings, all the different terms used as independent variables in the fitting.

ind.str

A string. The independent variables in an array format string.

call

A language object. The function call that generates this result.

col.name

An array of strings. The column names used in the fitting.

appear

An array of strings, the same length as the number of independent variables. The strings are used to print a clean result, especially when we are dealing with the factor variables, where the dummy variable names can be very long due to the inserting of a random string to avoid naming conflicts, see as.factor,db.obj-method for details. The list also contains dummy and dummy.expr, which are also used for processing the categorical variables, but do not contain any important information.

model

A db.data.frame object, which wraps the result table of this function.

terms

A terms object, describing the terms in the model formula.

nobs

The number of observations used to fit the model.

data

A db.obj object, which wraps all the data used in the database. If there are fittings for multiple groups, then this is only the wrapper for the data in one group.

origin.data

The original db.obj object. When there is no grouping, it is equal to data above, otherwise it is the "sum" of data from all groups.

Note that if there is grouping done, and there are multiple logregr.madlib objects in the final result, each one of them contains the same copy model.

Note

See madlib.lm's note for more about the formula format.

For logistic regression, the dependent variable MUST be a logical variable with values being TRUE or FALSE.

Author(s)

Author: Predictive Analytics Team at Pivotal Inc.

Maintainer: Frank McQuillan, Pivotal Inc. [email protected]

References

[1] Documentation of linear regression in lastest MADlib, http://doc.madlib.net/latest/group__grp__linreg.html

[2] Documentation of logistic regression in latest MADlib, http://doc.madlib.net/latest/group__grp__logreg.html

[3] Wikipedia: Iteratively reweighted least squares, http://en.wikipedia.org/wiki/IRLS

[4] Wikipedia: Conjugate gradient method, http://en.wikipedia.org/wiki/Conjugate_gradient_method

[5] Wikipedia: Stochastic gradient descent, http://en.wikipedia.org/wiki/Stochastic_gradient_descent

[6] Wikipedia: Odds ratio, http://en.wikipedia.org/wiki/Odds_ratio

[7] Documentation of generalized linear regression in latest MADlib, http://doc.madlib.net/latest/group__grp__glm.html

See Also

madlib.lm, madlib.summary, madlib.arima are MADlib wrapper functions.

as.factor creates categorical variables for fitiing.

delete safely deletes the result of this function.

Examples

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## Not run: 



## set up the database connection
## Assume that .port is port number and .dbname is the database name
cid <- db.connect(port = .port, dbname = .dbname, verbose = FALSE)

source_data <- as.db.data.frame(abalone, conn.id = cid, verbose = FALSE)

lk(source_data, 10)

## linear regression conditioned on nation value
## i.e. grouping
fit <- madlib.glm(rings ~ . -id | sex, data = source_data, heteroskedasticity = T)
fit

## logistic regression

## logistic regression
## The dependent variable must be a logical variable
## Here it is y < 10.
fit <- madlib.glm(rings < 10 ~ . - id - 1 , data = source_data, family = binomial)

fit <- madlib.glm(rings < 10 ~ sex + length + diameter,
data = source_data, family = "logistic")

## 3rd example
## The table has two columns: x is an array, y is double precision
dat <- source_data
dat$arr <- db.array(source_data[,-c(1,2)])
array.data <- as.db.data.frame(dat)

## Fit to y using every element of x
## This does not work in R's lm, but works in madlib.lm
fit <- madlib.glm(rings < 10 ~ arr, data = array.data, family = binomial)

fit <- madlib.glm(rings < 10 ~ arr - arr[1:2], data = array.data, family = binomial)

fit <- madlib.glm(rings < 10 ~ arr[1:7] + sex | id 

fit <- madlib.glm(rings < 10 ~ arr - arr[8] + sex | id 

## 4th example
## Step-wise feature selection
start <- madlib.glm(rings < 10 ~ . - id - sex, data = source_data, family = "binomial")
## step(start)

## ------------------------------------------------------------
## Examples for using GLM model

fit <- madlib.glm(rings < 10 ~ . - id - sex, data = source_data, family = binomial(probit),
                  control = list(max.iter = 10))

fit <- madlib.glm(rings ~ . - id | sex, data = source_data, family = poisson(log),
                  control = list(max.iter = 10))

fit <- madlib.glm(rings ~ . - id, data = source_data, family = Gamma(inverse),
                  control = list(max.iter = 10))

db.disconnect(cid, verbose = FALSE)

## End(Not run)

PivotalR documentation built on May 30, 2017, 8:18 a.m.