topicLasso {stm}

Plot predictions using topics

Description

Use the glmnet package to plot LASSO based estimates of relationship between an arbitrary dependent variable with topics and additional variables as predictors. This function is experimental (see below).

Usage

topicLasso(
  formula,
  data,
  stmobj = NULL,
  subset = NULL,
  omit.var = NULL,
  family = "gaussian",
  main = "Topic Effects on Outcome",
  xlab = expression("Lower Outcome Higher Outcome"),
  labeltype = c("prob", "frex", "lift", "score"),
  seed = 2138,
  xlim = c(-4, 4),
  standardize = FALSE,
  nfolds = 20,
  ...
)

Arguments

formula

Formula specifying the dependent variable and additional variables to included in the LASSO beyond the topics present in the stmobj. Just pass a 1 on the right-hand side in order to run without additional controls.

data

Data file containing the dependent variable. Typically will be the metadata file used in the stm analysis. It must have a number of rows equal to the number of documents in the stmobj.

stmobj

The STM object, and output from the stm function.

subset

A logical statement that will be used to subset the corpus.

omit.var

Pass a character vector of variable names to be excluded from the plot. Note this does not exclude them from the calculation, only the plot.

family

The family parameter used in glmnet. See explanation there. Defaults to "gaussian"

main

Character string for the main title.

xlab

Character string giving an x-axis label.

labeltype

Type of example words to use in labeling each topic. See labelTopics. Defaults to "prob".

seed

The random seed for replication of the cross-validation samples.

xlim

Width of the x-axis.

standardize

Whether to standardize variables. Default is FALSE, which is different from the glmnet default because the topics are already standardized. Note that glmnet standardizes the variables by default but then projects them back to their original scales before reporting coefficients.

nfolds

the number of cross-validation folds. Defaults to 20.

...

Additional arguments to be passed to glmnet. This can be useful for addressing convergence problems.

Details

This function is used for estimating the most important topical predictors of an arbitrary outcome. The idea is to run an L1 regularized regression using cv.glmnet in the glmnet package where the document-level dependent variable is chosen by the user and the predictors are the document-topic proportions in the stm model along with any other variables of interest.

The function uses cross-validation to choose the regularization parameter and generates a plot of which loadings were the most influential in predicting the outcome. It also invisibly returns the glmnet model so that it can be used for prediction.

NOTE: This function is still very experimental and may have stability issues. If stability issues are encountered see the documentation in glmnet for arguments that can be passed to improve convergence. Also, it is unlikely to work well with multivariate gaussian or multinomial families.

References

Friedman, Jerome, Trevor Hastie, and Rob Tibshirani. "Regularization paths for generalized linear models via coordinate descent." Journal of statistical software 33.1 (2010): 1.

See Also

glmnet

Examples

#Load the poliblog data
data(poliblog5k)
#estimate a model with 50 topics
stm1 <- stm(poliblog5k.docs, poliblog5k.voc, 50,
            prevalence=~rating + blog, data=poliblog5k.meta,
            init.type="Spectral")
#make a plot of the topics most predictive of "rating"
out <- topicLasso(rating ~ 1, family="binomial", data=poliblog5k.meta,stmobj=stm1)
#generate some in-sample predictions
pred <- predict(out, newx=stm1$theta,type="class")
#check the accuracy of the predictions
table(pred, poliblog5k.meta$rating)