Multiple imputation using R

R has a long list of packages for multiple imputation. The main problem is integration: statistical procedures in other packages may or may not work with the imputation procedures. I have been using Amelia together with Zelig. Because they were written by the same group, they work well together. However, I have been having trouble with making multiple imputation to work with the plm package. After searching the internet, here comes the solution:

1. Impute the missing data using Amelia or Mice.
2. Estimate the model on each imputed data.
3. Use the mitools package to extract and combine results. 

For example, here is a simple example:

...

imp <- mice(d)

mydata <- imputationList(lapply(1:5, complete, x = imp))

fit <- lapply(mydata$imputations, function(x){

plm(cog3pl ~ oc + grade9 + boy + han + ruralbirth, data = x,

index = c("schids"), model = "pooling")})

betas <- MIextract(fit, fun = coef)

vars <- MIextract(fit, fun = vcov)

summary(MIcombine(betas, vars))

I bet this will work for most, if not all, estimation procedures in R.

Another text analysis package

Quanteda seems to be a serious contender for analyzing textual data using R.

Rstudio 0.99.878 becomes official

Rstudio 0.99.878 becomes official. There is server version in AUR that can be used. However, the pandoc that comes with that version seems to have problems on Arch/Manjora. The discussion here is very helpful. One easy solution is to replace the built-in pandoc with the one that comes with the system:

sudo mv /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/lib/rstudio-server/bin/pandoc/pandoc_old
sudo mv /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc_old

sudo ln -s /usr/bin/pandoc /usr/lib/rstudio-server/bin/pandoc/pandoc
sudo ln -s /usr/bin/pandoc-citeproc /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc

Alternate R Markdown Templates

These alternative R Markdown templates look great.

ggplot2 extensions

Here is a list of ggplot2 extension packages.