NPM NodeJS API is not well documented, but checking the code helps up.
Here we find the following string:
install.usage = "npm install"
              + "\nnpm install <pkg>"
              + "\nnpm install <pkg>@<tag>"
              + "\nnpm install <pkg>@<version>"
              + "\nnpm install <pkg>@<version range>"
              + "\nnpm install <folder>"
              + "\nnpm install <tarball file>"
              + "\nnpm install <tarball url>"
              + "\nnpm install <git:// url>"
              + "\nnpm install <github username>/<github project>"
              + "\n\nCan specify one or more: npm install ./foo.tgz bar@stable /some/folder"
              + "\nIf no argument is supplied and ./npm-shrinkwrap.json is "
              + "\npresent, installs dependencies specified in the shrinkwrap."
              + "\nOtherwise, installs dependencies from ./package.json."
My question is about the version, so we can do: hello-world@0.0.1 to install 0.0.1 version of hello-world.
var npm = require("npm");
npm.load({
    loaded: false
}, function (err) {
  // catch errors
  npm.commands.install(["hello-world@0.0.1"], function (er, data) {
    // log the error or data
  });
  npm.on("log", function (message) {
    // log the progress of the installation
    console.log(message);
  });
});
I didn't test, but I am sure that we can use any format of the install.usage solutions.
I wrote a function that converts the dependencies object in an array that can be passed to the install function call.
dependencies:
{
   "hello-world": "0.0.1"
}
The function gets the path to the package.json file and returns an array of strings.
function createNpmDependenciesArray (packageFilePath) {
    var p = require(packageFilePath);
    if (!p.dependencies) return [];
    var deps = [];
    for (var mod in p.dependencies) {
        deps.push(mod + "@" + p.dependencies[mod]);
    }
    return deps;
}