missing data visualization and imputation
To provide an easy to use yet thorough assessment of missing values in one's dataset:
- in addition to the blackholes plot bellow,
- show the variable-to-variable, subject-to-subject co-missingness, and
- quantify the TYPE of missingness etc
To easily manage your data with missing values etc, I strongly recommend you to move away from CSV files and start managing your data in self-contained flexible data structures like pyradigm, as your data, as well your needs, will only get bigger & more complicated e.g. with mixed-types, missing values and large number of groups.
These would be great contributions if you have time.
- visualization
- imputation (coming!)
- other handling
- Software is beta and under dev
- Contributions most welcome.
pip install -U missingdata
Let's say you have all the data in a pandas DataFrame, where subject IDs are in a 'sub_ids'
column
and variable names are in a 'var_names'
column, and they belong to groups identified by sub_class
and var_group
,
you can use the following code produce the blackholes
plot:
from missingdata import blackholes
blackholes(data_frame,
label_rows_with='sub_ids', label_cols_with='var_names',
group_rows_by=sub_class, group_cols_by=var_group)
If you were interested in seeing subjects/variables with least amount of missing data, you can control miss perc window
with filter_spec_samples
and/or filter_spec_variables
by passing a tuple of two floats e.g. (0, 0.1) which
will filter away those with more than 10% of missing data.
from missingdata import blackholes
blackholes(data_frame,
label_rows_with='sub_ids', label_cols_with='var_names',
filter_spec_samples=(0, 0.1))
The other parameters for the function are self-explanatory.
Please open an issue if you find something confusing, or have feedback to improve, or identify a bug. Thanks.
If you find this package useful, I'd greatly appreciate if cite this package via:
Pradeep Reddy Raamana, (2019), "missingdata python library" (Version v0.1). Zenodo. http://doi.org/10.5281/zenodo.3352336 DOI: 10.5281/zenodo.3352336