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Demographics and Comorbidity of Behavior Problems in Dogs

License: MIT License

Python 8.78% Jupyter Notebook 89.31% TeX 1.91%

canine veterinary research pet dogs research-paper journal-article article analysis

pdbs-study-1's Introduction

pdbs-study-1

Analysis repository for the paper titled Demographics and Comorbidity of Behavior Problems in Dogs.

Project Organization

├── LICENSE
├── README.md          <- Repository overview.
├── data
│   ├── processed      <- The final, canonical data sets for modeling.
│   └── raw            <- The original, immutable data dump.
│
├── docs               <- Data dictionaries, manuals, and all other explanatory materials.
│
├── figures            <- Generated figures to be used in reporting (PDF).
│
├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
│                         the creator's initials, and a short `-` delimited description.
│
├── requirements.txt   <- The requirements file for reproducing the analysis environment, e.g.
│                         generated with `pip freeze > requirements.txt`
│
├── src                <- Source code for use in this project.
│   ├── __init__.py    <- Makes src a Python module
│   │
│   ├── data           <- Scripts to download or generate data.
│   │   └── make_dataset.py
│   │
│   └── utilities      <- Analysis utilities.
│       └── build_features.py
│
└── tables             <- Generated tables to be used in reporting (PDF and LaTeX).

pdbs-study-1's People

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pdbs-study-1's Issues

Quick newsletter stats for PDBS

Number of users who completed Phase I
Number of dogs for whom Phase I was completed
Number of dogs invited to participate in Phase II

Resolve identical numerical result bug in table 5.2

Add behavior problem prevalence by breed

Filter the raw data

Remove incompletes, duplicates, and any test data

First Investigation

Investigate the relationship between separation anxiety, noise phobia, and storm phobia.

Create high resolution output of heatmaps

Add intro jupyter page

Add unit tests for dataset forming scripts

Calculate total incidence

Second Investigation

Investigate the relationship between anxiety disorders and compulsive disorders.

Move to sql database

Third Investigation

Investigate relationship between fear-based conditions and owner-directed aggression.

Add matrix of chi2

Repeat execution of dataset script increases number of records

Run python src/data/make_dataset.py and examine the metrics report at reports/metrics.txt to see the "increasing" number or responses after each run.

Update database, do not overwrite it

Correct participant motivation order

Display in descending order

Use LaTex to represent chi-squared results

Calculate phase 1 geostats

Dataset script is attempting to populate the database without creating tables

Run python src/data/make_dataset.py to get error for missing users' table.

Add ipython notebook section for impact of gender and neutered status

Marking failed

Branching logic failed to execute for a survey response specifically tailored for marking.

Clean up notebook after last discussion

Remove small bar graphs
Determine/add missing behavior type breakdown (might be jumping)
Correct fields for feces consumption
Fix spelling errors
Revert field labels to those used in the study

Fix the denominator for prevalence calculations.

The current denominator is the total dogs in the study, but it should be (total dogs after filter).

Switch overall incidence from participants to dogs

Per recent discussion

Remove interim data from readme

Excess welcome text for pdbs phase 2 surveys

Only the pdbs phase 2 welcome survey should have a welcome text. The welcome text should be discarded for phase 2a, 2b, 2c, 2d, 2e.

Take this chance to review the remaining welcome text on the phase 2 welcome survey as well.

Update data fetching script to save the raw data in the data directory

Currently the raw data saves in the home directory

Move "with/without" headers to separate pages

The change for phase_2a has already been made. Repeat this change for phase_2b, 2c, 2d, and 2e.

Clean up dataset creation metrics

Add three-color heatmap for levels of significance

white = insignificant (p >= 0.05)
blue = significant (0.01 <= p < 0.05)
red = extremely significant (p < 0.01)

Add jupyter notebooks

Split results by dog instead of user

Remove irrelevant docs/folders from cookiecutter template

Add calculations for the prevalence of each behavior problem.

Use a table to effectively display the calculations.

JSON raw data is too large, switch to csv

Refactor IPython notebook to remove redundant code

Remove unused hash script

Independent has script has been replaced by fetch_raw_data.py. Remove the unused script.

Migrate contingency tables to venn diagrams

It has been reported that contingency tables are hard to read for some not familiar to the format.

Fix disorganized source directory

Add prevalence of subtypes

Remove aois from this repository

Update data fetching script to hash out user emails

We want to protect user privacy

Improve used of logger module

Review pdbs question branching logic for phase 2

Question branching logic needs to be updated and reviewed for each section of pdbs phase 2.

Include your name in the python notebook so that it has some sort of attribution

Update readme to be more informative of the project

Review pdbs phase transition branching logic

Breakdown of subtypes

Migrate to cookiecutter-data-science format

Add final raw dataset

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