Day 3 – 5 days 5 meals – how to stay healthy while busy

This is a great vegan Sandwich, that will fill you up with healthy veggies.

IMG_20170329_214854

 

Ingredients:

1 Aubergine
1 large courgette
2 large carrots
Hummus (or unsweetened peanut butter if you’re adventurous)
Wholemeal toast (8 slices)
Salt & Pepper

IMG_20170329_191546Slice the Aubergine and courgette and bake on a no-stick frying pan with some salt and pepper, no oil needed, until light brown and soft. Cut the whole carrot with a peeler, so you get thin slices. Toast the toast, spread hummus on it, top with carrot, Aubergine and courgette slices and top with another slice of toast. The amount should be enough for 4 double Sandwiches – two for dinner – two for lunch the next day!

 

 

 

STATA tricks for epidemiologists /// The Data Do-file

I believe, Do-files should be the core of your statistical analyses and literally everything you do. Do-files allow you to recap each and every step, to keep track about changes and to automatize your work. And the best thing of all you can search (Ctrl+F) and replace within a do-file using Ctrl+H.

1. Do-file basics – Visual structure & commenting

Find do files here:

dofilecommentry

2. The data-do file

To avoid any accidental changes in the original data I suggest using a data-do-file that you can run before every analysis. Also it ensures the safety of your data, because you do not need to save the dataset locally

datado_start

This is how you open a dataset:

data_indoThe IDENTIFIERVARIABLE is for example id, referring to each participant in a study, keepusing again allows you to choose specific variables, if not identified the entire dataset will be merged. Generating a variable: merge1 gives you a way to check if your files were merged.

Now we come to the interesting part – what do you want to have in your initial dataset – do-file? I suggest sections on outcome, exposures, covariates and exclusion/inclusion
Have a clear idea how you want to name your variables. Having a consistent data-collection wave identifier like w01 or fup0 aso. will make it much easier to work with variables later on. Further adding “bin” for binary variables or “cont” can make it easier to know which variable you work with. You want to make them as easy to remember and use as possible.

The following commands are shown in a example dataset in STATA (bpwide.dta):
data_content
Remember the operators for generating new variables and if -clauses:
+ addition; – subtraction; * multiplication; / division; ^ power;
& and; | or ( you can find that sign next to the Z-key, “Shift+\”)
== equal; > greater than;< less than; >= > or equal; ; ! not; != not equal (instead of ! you can also use ~)

For more complicated variables and summaries I use egen command, full description here Stata manual: egen  – some examples here, plus xtile command:

egen newvar=rowtotal (var1 var2 ..) sums up the variables even if some of them are missing (! this does not happen when using gen=var1+var2..)
egen newvar=rowmiss (var1) counts missing variables
egen newvar=std(var1) Standardized z-score
xtile newvar=var if…, nquantiles (X) command to make n-tiles, e.g. tertiles (X=3)

Be very careful in choosing your egen command, because they differ how missing values are handled!

Finally add as much commentary as possible to your command, you can use your data do-file to detect changes in the data, mistakes in coding (! which are awful, because they mess up all your work – therefore always tab and sum variables and see if they look reasonable), but also you can share your do files with other researchers when you constructed them understandable. And this is a rare moment where I take some time to make something look nice – because the prettier the easier to handle – change indent levels and add some clear structure by using signs – and as soon as you have one you can use it as a template for future Data- do-files.

Making a nice data do-file can take some time (a whole day or even several days) BUT this is a great investment. If you add references and clear comments, you can answer many questions on your methods by only using your data-do-file. If you then mark revisions at the start you can also track when and what you changed, so you keep it pretty and up to date.

3. How to run a Do-file

There are two options how to run a do-file – (A) select and click “Execute (do)” (B) use do “filelocation\name” – which will show you the output, (C) using run “filelocation\name” –  will not show you any output. I recommend using do when your file is fresh and you want to check everything, also I would recommend saving a  Log-file with your data-do file using the option (A/B) so you can  check changes at later stages and have a record of what you’ve done. When you are familiar with your data – option (C) is a great fast way. You can then add the run-command at the beginning of further do files for example for analysis you create.

data_run

 

Zotero tricks for epidemiologists

Coloured study design tags

A core question in epidemiological research is the study design. To have an easy overview on study design I recommend using color coding of keywords or “tags”. Assigning tags to each publication sounds like tedious work, but especially regarding study design it is absolutely worth it! Use simple tags- like case-control or prospective, so you don’t accidently assign different names that represent the study design.

Find a tutorial how to tag here: https://www.zotero.org/support/screencast_tutorials/tags

zotero1

When you assigned tags they can be shown on in a small box on the bottom left hand side.

If you right-click on the tag you can “Assign Color”. The colors will now be shown in front of the publication name and will give you a great overview about the evidence.

Filter publications

By clicking on a tag – you can now filter your studies by tag, and therefore by study design. Showing you how many for example trialevidence you have.

zotero2

Folders

As you can see in my example I ordered my library by topics. This can be done by simply creating new folders. But, to see the same publications of a subfolder in the main folder you need to change a hidden preference in Zotero by going to Preference – General- Miscallaneous- Open about:config – search for recursive – the one that should show up is called extensions.zotero.recursiveCollections and change the value from false to true!

Find further info on how to use zotero here:

https://www.zotero.org/support/collections_and_tags

 

 

How to present Odds ratios in a graph on a log-scale

When presenting Odds ratios in a graph, they should be presented on a log-scale. Unfortunately excel isn’t very straightforward on this. So a few tweaks are needed to get a smooth graph.

Imagine following Odds ratios: Result 1 1.2, 95%-CI: 1.1, 1.3; Result 2 0.9, 95%-CI: 0.6, 1.2.

 

A Create a scatter plot on a logscale for odds ratios with confipic1dence intervals:

  1. Create a scatterplot with x values 0.5 and 1 for the two odds Ratios. Add Error bars (Chart tools/layout/more error bar options)  custom and use CI-upper minus OR as positive, OR minus CI-lower as negative value.
  2. Now change the Y-axis to a log scale. Change the horizontal axis cross to 1.0 and minimum and maximum to fixed values of your liking/how it fits your data. Remember there is no 0 on a log-scale. pic2Unfortunately there is no way to get ticks at smaller values. So we need to use a trick as next step
  3. Add a dataseries on set of values with x-value 0 and y-values that cover the ticks you would like on the y-axis.pic3c
  4. Format that Data series: Marker Built – small minus/size 5; Marker fill – solid fill / black;  Marker Line Color – no line. Add data labels on the left  (see chart tools/ Layout). To smooth the 1 – you might want to delete the marker here.
  5. Finally format the x-axis – Axis labels – low.

pic4

 

B Create a bar chart on a logscale for odds ratios with confidence intervals:pic5c

  1. Follow steps 1-5 as above. Now click on OR data series and Change chart type to bar chart.
  2. Change dataset for OR series, change horizontal axis label to Result 1 and Result 2.
  3. Change Axis Options for x-axis. Change Position Axis to on tick marks.
  4. Since now the bars are not fully visible you need to include a phantom OR. Add nother data point to the OR series with an OR of value 0 (yes an error message comes up but that doesnt matter.
  5. Now you have two options to finish the barchart.
    1) change the the y-axis value to 0.1 and increase your Axis tick set to include the other values.
    pic8
    Or 2) Format y-axis.
    Horizental axis cross- Axis value 1.0.pic9

 

I hope this is helpful. Please comment if you have any further questions.

 

Day 2 – 5 days 5 meals – how to stay healthy while busy

 


Mint pea soup

Time needed: 17 minutes
Ingredients:

Frozen green peasIMG_20161120_171523.jpg
Fresh or dried mint leaves
Vegetable stock cubes/powder
water

Place green peas (amount about two bowls) in pot, add mint, vegetable stock and fill up water, that the peas are not fully covered -cook until peas start to look wrinkly. Now blend soup with a hand-held blender, add hot water if you like it more watery. – Done! The soup can also be reheated in a microwave for lunch the next day. – Enjoy!

Day 1 – 5 days 5 meals – how to stay healthy while busy

Keeping up healthy behaviours while in stress is a major hurdle – but as a nutrition scientist, I can’t stress enough that a healthy diet will make you feel much better inside and out.  >>> That’s why I am going to post a 5 great suggestions to make a fast dinner under 20minutes for each weekday!


 

 

 

Fresh pasta saladIMG_20161118_203422.jpg

Time needed: 18 minutes
Ingredients:
Wholemeal pasta
1 Avocado

1 Handful tomatoes
2 Tablespoons Nuts/Seeds
Rocket or curled Kale (if in season)
Salt, Pepper, Balsamic Vinegar, Olive oil

Start by preparing water for cooking the noodles, I prefer wholegrain noodles. While cooking the water and the noodles – cut the avocado and tomatoes  and put them in a bowl now add the fresh rocket or kale.  To get ripe avocados faster fold them in newspaper or store them in a bag or bowl of apples.IMG_20161118_202735.jpg
Add nuts or seeds, salt, pepper, balsamic vinegar and olive oil and mix well.
When the noodles are ready drain them and add them to the salad mixture. If you want to save some for lunch for the next day mix in the salad last, so
 you can just add it the next day and it won’t soak too much.

How to keep up with the literature

One major issue in research is to keep up with the literature. Therefore I’d like to share a few ways how to keep up:

  1. Social media – facebook: Depending on your research topic it’s a great way to follow research. Follow the main research societies in your area and some of the main research journals. I for example follow the Obesity Society which is very active on facebook, this is a great way to get links to current papers! (Probably twitter works in the same way. I personally find it less easy to overview but if you’re into twitter I am sure it can be used in a similar way.)
  2. Researchgate: Researchgate is a great way to keep track with the major researchers in your field. Follow the researchers that publish the most in your area or the ones that you found published interesting findings. Via researchgate you get notified if they published new research!
  3. etalia notifications for Mendeley and Zotero users: this is a tip of a friend of mine. Etalia sends out suggestions for new publications based on your saved literature.
  4. Furthermore on many journal websites you can order a mailservice when a certain paper gets cited. This can be very helpful if you want to keep track on a certain question that has only been addressed few times before. Finally search services like scopus and pubmed can send you updates on your searches.

Please post your own tips in the comments.

PhD/ Scientific writing resources

As a non-native English speaker I’ve been very afraid of writing from the start. Even though you read loads it gets really tricky as soon as you sit in front of your computer and plan – “I am going to write XY now..”.

From the start I had an amazing book at hand English for Writing Research Papers from Adrian Wallwork – in it’s penultimate chapter you can find a list of examples and synonyms for writing different sections which is such a gift! On top of it Adrian Wallwork’s approach is really helpful and before I write a section I would often reread the sectionspecific chapter to make sure I got everything covered. Please correct me if I am wrong but I felt it also covered at least some different areas of research which is probably really useful if you are actually a student in Public health.

Another great source for example sentences and finding the right wording for scientific writing is the Academic Phrasebank from the University of Manchester . Here you can find all synonymes you need to write a good text without repeating your vocabulary constantly!

My final recommendation for now is another book of Adrian Wallwork. – Maybe you know this feeling when you have to write a quite straight forward email, but you feel you just don’t know what’s the best way to phrase it?- English for Academic Correspondence and Socialising from Adrian Wallwork is the perfect tool to find the right words for that, knowing that you’re polite and won’t embarrass yourself. Furthermore it has great advice on writing and responding to peer reviews!

Adrian Wallwork has also a number of other good resources on his page – so I would encourage to have a look at his blog!