Pythonhealthdatascience.com

Preface — Python for health data science.

WEBHealth service analysts (particularly in the UK’s NHS) who are looking to boost their python skills to be a more rounded data scientist. The book aims to support these groups …

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Analysing real data sets — Python for health data science.

WEBAnalysing real data sets. #. Let’s take a look at some of the analysis and visualisation functionality built into pandas. We will work with a real dataset. The dataset describes …

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numpy debug — Python for health data science.

WEBDescription of the code. The model is a simplification of a stroke treatment pathway at a hospital. Patients must be treated within 180 minutes of the onset of their symptoms. …

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Array slicing and indexing — Python for health data science.

WEBArray slicing and indexing#. Slicing and indexing are powerful ways to select and access elements within an array. The complexity of what you can achieve with numpy using …

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Local python packages — Python for health data science.

WEBA framework for simulation based ranking and selection. A toolkit for pre-processing high frequency vital sign observations from critically ill children. Sometimes a local package …

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Coding scientific functions — Python for health data science.

WEBNote that the solutions to these exercises are in standard Python. If you have knowledge of scientific python libraries such as numpy or scipy and are confident in using them to …

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Install python and an IDE — Python for health data science.

WEBMy personal preferences. Alternatively (and my preference) you can install substantially smaller Miniconda and install the packages you need using the provided …

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Random variables and simulation — Python for health data science.

WEBTo create a Generator use the default_rng() function. rng = np.random.default_rng() Consider a project where you are modelling a simple two stage patient pathway. In the …

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Conditionals and Loops — Python for health data science.

WEBA better way to do this in code is to use a LOOP. Do the following 3 steps, 3 times: Put a slice of bread in the toaster. Push lever down to turn on the toaster. Remove the toasted …

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Version control — Python for health data science.

WEBIn my experience this sort of structure turns up surprisingly often, for all sorts of data science and non-data science projects. It is certainly more common than a cleanly …

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Python Basics — Python for health data science.

WEBVariables Names#. Variables names can only contain letters, numbers, and underscores ( _ ).. Underscores are used instead of spaces. For example, use student_name instead of …

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PyPi — Python for health data science.

WEBThis is the important file for pip. setup.py controls the installation of your package. I’ve included a template in the repo. We need to use the setuptools PyPI package to do the …

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Basic Python — Python for health data science.

WEBOne of the most useful functions in Python is the print() function. It is used to display information to the user. It can be used to present the result of computations, …

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Computing prime numbers — Python for health data science.

WEBIt works as follows: Consider the primes up to 10. First write out a list of number 2 to 10. Here we’ll represent this as a python list called candidates. As we work out which …

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Conditionals and Loops — Python for health data science.

WEBLoops example 3: A guessing game using a while loop #. We generally use while if we do not know the number of iterations in advance. A classic use of a while loop is a main …

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Managing time series — Python for health data science.

WEBManaging time series#. Time series data (and time series data science problems) involve the observation of one or more variables over time. Time series data are highly …

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Coding Standards — Python for health data science.

WEBLine length #. In python we usually keep line length to 79 or 80 characters. That is a line that exceeds this length breaks PEP8 coding standards. More concretely - it becomes …

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Case study: Basic use of Git — Python for health data science.

WEBStep 2: Initialise the Git repository #. Navigate to the directory on your machine where you want to store your code. If you need to create a new directory for example …

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Case study: Combining multiple sources — Python for health data …

WEBThis case study will work with data taken from NHS England’s open diagnostic imaging dataset from 2019/20. We will use three datasets. Diagnostic imaging report times by …

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