Migrate from pbkdf2

Let's users be your collection of registered users. Each of those users should have a salt, a secret, a number of iterations, a keylen and a digest algorithm stored in some manner. (It really depends on how you have implemented it)

users.forEach(user => {
  var hash = JSON.stringify({
    hash: JSON.stringify({
      salt: user.salt,
      secret: user.secret, // Should be encoded in base64. If secret was saved with
                           // another base, convert it to base64.
      iterations: user.iterations,
      keylen: user.keylen,
      digest: user.digest // 'sha1' or 'sha256' or 'sha512'
    }),
    func: 'pbkdf2'
  });
  user.hash = hash;  // Now you can pass user.hash to the verify function of
                     // this package.
})

Base conversion utilies

hex -> base64

function hexToBase64(str) {
  return btoa(String.fromCharCode.apply(null,
    str.replace(/\r|\n/g, "")
      .replace(/([\da-fA-F]{2}) ?/g, "0x$1 ")
      .replace(/ +$/, "").split(" "))
  );
}

function btoa(bin) {
  var tableStr = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
  var table = tableStr.split("");
  for (var i = 0, j = 0, len = bin.length / 3, base64 = []; i < len; ++i) {
    var a = bin.charCodeAt(j++), b = bin.charCodeAt(j++), c = bin.charCodeAt(j++);
    if ((a | b | c) > 255) throw new Error("String contains an invalid character");
    base64[base64.length] = table[a >> 2] + table[((a << 4) & 63) | (b >> 4)] +
                            (isNaN(b) ? "=" : table[((b << 2) & 63) | (c >> 6)]) +
                            (isNaN(b + c) ? "=" : table[c & 63]);
  }
  return base64.join("");
}