ammaraziz

"""
    This code pulls data from the WHO's influenza surveillance database:

        https://apps.who.int/flumart/Default?ReportNo=12

    This website is pretty tricky to parse; you must pass realistic headers to the POST requests, and you must also
    issue 3 total requests: 1) a GET request, 2) a POST request, and 3) another POST request. All 3 of these requests,
    in order, are required to actually collect the underlying data that's displayed in the table. See `get_table_data`
    for more documentation on this process.

ammaraziz

import argparse
import textwrap
import os
import sys
from datetime import timedelta, datetime


# function for reading a multifasta file
# returns a dictionary with sequence headers and nucleotide sequences
def get_seqs_from_fasta(filepath):

ammaraziz

mle <- function(data,start=NULL,eps=10**(-9),logit=FALSE,cov=NULL){
  # INPUT:
  # data: data matrix with
  # 1) observed outcome D (0: no; 1: yes)
  # 2) observed types at risk for (0: no; 1: yes)
  # start: starting vector for the algorithm
  # eps: accuracy parameter to stop the algorithm
  # logit: logical to indicate whether the logit model is used
  # (i.e. correct for a covariate)
  # cov: covariate vector to correct for (only if logit=TRUE)