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I didn't look at the code because I don't know perl, but I can offer some advice for the future. I work at a research group that collaborates with local and international governments on modelling various epidemics as a mathematician. I'm not bragging but letting you know my credentials and experience.


I mainly use MATLAB. Why? Everything is extremely well documented and well developed. The user interface is simple and the language is not so complicated either. There is also a very big, welcoming community which is extremely important. Don't know how to do something in MATLAB? Chances are someone has asked it and someone has answered it, now you don't have to spend hours developing your own solution or, in some cases, never coming up with a solution. It is true it may not be the fastest, but you don't necessarily always want the fastest programming language there is. There is always a trade off and MATLAB excels in other areas where other programming languages don't for this kind of thing. Also, pretty much everyone at the group uses MATLAB.


Use R for data visualization. This is a must. MATLAB has pretty subpar data visualization. Not many programming languages do and I really doubt perl does. From my experience in working with health scientists, doctors and government administrators, they seem to like what R produces the best and this was recommended to me by my supervisor. R is not too hard to learn, in fact I learned in one night how to transfer my output from MATLAB to R and then produce some pretty beautiful graphs.


If you're still learning and would like to learn more, check out Modeling Infectious Diseases in Humans and Animals link. Chapter 2 should be the main chapter for you and try to reproduce results.

I really like applied stats but think a good understanding of stats theory is important for any researcher. A good "litmus" test, I think, would be reading Mostly Harmless Econometrics (you can probably find a place to check the book out for free). It isn't about health statistics at all but it is a very good "applied" theory book. If you get into the first bit and go "this isn't for me," that is fine and epi probably won't be a problem. If you go "this is interesting," then you might be worth looking at doing the required pre-reqs for the MS biostats program.

Relatedly, check out this free biostatistics bootcamp on Coursera. Check out the first few weeks of lectures and if you decide that the stat theory is more than you care for, epi is a good place.

Epi is a good field, don't get me wrong, but if you are interested in statistics, then it might not be a great fit. MHE and a few of those lectures might be very helpful in deciding if you are at all unsure of how you lean.

Not entirely scientific, but Spillover by David Quammen is a really good read on diseases that have 'spilled over' from animals to humans. It covers lots of recent epidemics, from smaller ones like Q-fever to very big ones like HIV and ebola (not that ebola is quite as big as HIV, but it has been making big headlines).

It's one of the few books that I keep recommending to people 'cause it makes epidemiology sound very cool and explains lots of complicated concepts in a really engaging and understandable way. And it reads like a detective novel while not dumbing down the science.

It's also got a very detailed bibliography, so you'll find all the references you need to start writing a paper.

Sorry for being slow to respond!

Yes, probably the single best resource to look at is a book called Choosing to train in public health which gives a pretty great overview of the area and the application process.

There is also a lot of information from the UK Faculty of public health https://www.fph.org.uk/.

The final source of information is to consider contacting a Training Programme Director directly in the UK. The programme run out of Oxford has a strong international focus so that might be one to consider. This this is the website for the School.

Feel free to message me if you have any other questions.

You can't talk about public health/epi lit without bringing up The Hot Zone by Richard Preston. It's a really intriguing look at the known history of Ebola and the Ebola Reston outbreak at a monkey house in the US, but take a lot of his details with a grain of salt because he's on the record saying that he dramatized a number of details but its entertaining and informative nonetheless. Preston has a few other books that fall in a similar fold.

I'm currently reading Spillover by David Quammen and I'm really loving it! It's a more scientifically sound book about zoonosis and how infections make their way across species and into humans. I'm personally finding it to be a lot more entertaining than The Hot Zone as well.

I read the second edition of Studying a Study & Testing a Test by Riegelman and it was the best thing I did in preparation for my masters in biostatistics & clinical epidemiology. I specifically like the fifth edition (pink cover) because it has a brief statistics primer in the sixth section that is unmatched as a general / mostly non-technical overview, in my opinion. The rest of the book is not about statistics, per se, but is a great overview on study design and test fit diagnostics (sens/spec, PPV, ROC curves, etc.). That last section on stats, which won't take you more than a couple of afternoons to read, is worth the purchase alone. It has very helpful charts on how to select the appropriate statistic depending on your model construction and types of predictor / outcome variables. It is unfortunate that they removed this in the sixth edition. And yes, it is (only) available as a physical book. Here is a link:

http://www.amazon.com/Studying-Study-Testing-Test-Pediatrics/dp/0781745764/ref=sr_1_2?ie=UTF8&qid=1408634374&sr=8-2&keywords=studying+a+study

EDIT: sixth section, not third

Tom's River is a great book about a child cancer cluster in NJ.


Even though you mentioned a specific interest in infectious disease, I think Tom's River is a worthwhile addition for anyone in public health, not just those with an interest in environmental health.


It does a great job of tying together the broader scientific, political, environmental, and public health histories and critiques while using Tom's River as a specific case study.


Book: http://www.amazon.com/Toms-River-Story-Science-Salvation/dp/055380653X



NYT Review: http://mobile.nytimes.com/2013/03/19/health/on-the-trail-of-cancer-a-review-of-toms-river-by-dan-fagin.html?referer=

You should do a monthly PH book club too. There are lots of public health related books that are also very interesting and entertaining. I would recommend starting with The Barbary Plague by Marilyn Chase. The plot revolves around the epidemiologists trying to deal with the Plague outbreak of turn of the century San Fransisco. Remember that for these folks, the field of epidemiology was very new. They still admired Kochs lab since there was no direct equivalent anywhere in the USA. A large portion of the book is about Joseph Kinyoun, the physician and epidemiologist who went on to found the United States' Hygienic Laboratory. Ever heard of it? Today is called the National Institutes of Health.

There was a fantastically terrifying bit where they were looking for evidence of plague among animals in the park and ended up stumbling upon a squirrel that had obviously died of plague. After a few seconds of examination, they realized they were absolutely covered in fleas... too many to possibly shake off, moments later, little specks of blood started to appear...

[spoilers] By amazing luck, the fleas were all very young instars that had hatched after the squirrel had died. Since the squirrel was cold when they were born, they never tried to feed on it. The fleas were waiting on the squirrel for another host to come by, but they had never been infected themselves. There is evidence of vertical transmission of other pathogens in such fleas, but thankfully not plague.

Rabid, by Bill Wasik and Monica Murphy. It is an engaging history of rabies in the context of social history and epidemiological development. I loved it!

https://www.amazon.com/Rabid-Cultural-History-Worlds-Diabolical/dp/0143123572/ref=sr_1_2?ie=UTF8&qid=1491805903&sr=8-2&keywords=rabid

By IDE I assume you are referring to Infectious Disease Epidemiology. I'm currently taking a course in that, and I found Infectious Disease Epidemiology by Nelson and Williams a great book, although it doesn't cover the 'stats side'.

I really liked The Fever by Sonia Shah about the history of malaria, I'd also liked Rabid, Beating Back the Devil and The Coming Plague. I also really liked Spillover

Richard Wenzel, who's a kind of a prolific epidemiologist on several fronts wrote a fiction book that I've had on my short list for curiosity's sake:Labrynth of Terror.

Here's his academic profile: http://www.people.vcu.edu/~rwenzel/

Workbook of Epidemiology (Norrell): https://www.amazon.com/Workbook-Epidemiology-Staffan-Norell/dp/0195074912/ref=sr_1_1?s=books&ie=UTF8&qid=1518227129&sr=1-1&keywords=workbook+for+epidemiology

Interpreting Epidemiologic Evidence (Savitz): https://www.amazon.com/Interpreting-Epidemiologic-Evidence-Strategies-Analysis/dp/019510840X/ref=sr_1_2?s=books&ie=UTF8&qid=1518227195&sr=1-2&keywords=interpreting+epidemiologic+evidence

Epidemiology, 5th Edition (Gordis): https://www.amazon.com/Epidemiology-STUDENT-CONSULT-Online-Access/dp/145573733X/ref=sr_1_1?s=books&ie=UTF8&qid=1518227238&sr=1-1&keywords=epidemiology+5th+edition+by+leon+gordis

Beyond The Basics, 3rd Edition (Szklo & Nieto): https://www.amazon.com/Epidemiology-Beyond-Basics-Moyses-Szklo/dp/1449604692/ref=sr_1_2?s=books&ie=UTF8&qid=1518227273&sr=1-2&keywords=szklo+m.+and+nieto+j.+epidemiology+beyond+the+basics&dpID=515BdoQV9QL&preST=_SY291_BO1,204,203,200_QL40_&dpSrc=srch

Rabid... straddles the line between epi and medical anthropology.

Assuming your speaking of the statistical language "R," I cannot recommend anything. I have never used "R." But here is Amazon's top result: http://www.amazon.com/The-Book-Michael-J-Crawley/dp/0470973927

tl;dr: I am not helpful. Sorry OP.

I've found this one interesting: "The Woman Who Knew Too Much" by Gayle Greene.

This book tells the story of Alice Stewart (physician and epidemiologist), who with her assistant, connected fetal x-rays with the risk of cancer. There's a good discussion on risk and epidemiologic process--but it's as much a study on social issues, the struggles of female scientists and leadership. The book isn't written by an epidemiologist, so the details aren't too technical, which might frustrate some, but the narrative is strong and much can be learned from its pages.

Deadly Medicine: Why Tens of Thousands of Heart Patients Died in America's Worst Drug Disaster

Dr. Garth Nicolson has testified to U.S. Congress 7+ times, and wrote the outstanding book "Project Day Lily: An American Biological Warfare Tragedy," in honor of his murdered cancer research partner (Dr. Fred Conrad, who was shot in broad daylight in a Houston, TX hospital. It was national news.). Nicolson also runs the Institute for Molecular Medicine (in California, USA).

https://www.amazon.com/Project-Lily-Garth-Nicolson-Nancy/dp/1413485197

GOVERNMENT RECOGNIZES DR. NICOLSON'S WORK!

"Dr. Nicolson's daughter served in the Persian Gulf War and came back very ill along with most of her platoon.. Mycoplasma incognitus found by Drs. Nicolson has a piece of the HIV envelope, but HIV is not found inside the envelope. Instead, a mix of different bacteria from other illnesses is present. This is not something... natural... man-made!"

http:// ncf-net.org/forum/nicholson.htm

Meaning: People would be testing HIV+ but not really have it. Meaning: HIV is not the cause of AIDS.

Have a nice day.

Randomly enough, I just asked Dr. Joe McCormick (http://www.amazon.com/Level-4-Virus-Hunters-CDC/dp/0760712085) about this a few hours ago in a lecture.

He was there for the first Ebola outbreak and seems to be somewhat of an international expert on these "hot" viruses. He said that this outbreak is unique in that it has moved into large cities, but didn't seem to be overly concerned about the threat of pandemic or spread beyond the region. It's really only spread by close contact with infectious patients, so it's fairly hard to catch from others.