#!/usr/bin/env python
# coding: utf-8

# In[1]:


get_ipython().run_line_magic('matplotlib', 'inline')
get_ipython().run_line_magic('config', "InlineBackend.figure_format = 'retina'")

import numpy as np
import matplotlib
from matplotlib import pyplot as plt
import pandas as pd
from datetime import date, datetime
from lifelines import KaplanMeierFitter, CoxPHFitter, NelsonAalenFitter

matplotlib.rcParams['figure.figsize'] = (12.0, 6.0)
plt.style.use('seaborn-deep')


# ## Definition of censoring and death
# 
# Quitting is death, all else is censoring. This is different than the [original article](https://fivethirtyeight.com/features/two-years-in-turnover-in-trumps-cabinet-is-still-historically-high/)'s author's rules, who stated that switching roles _within_ a cabinet is an "event". 

# In[2]:


raw_df = pd.read_csv("https://raw.githubusercontent.com/fivethirtyeight/data/master/cabinet-turnover/cabinet-turnover.csv",
                    na_values=['Still in office', '#VALUE!']
                    )
TODAY = datetime.today().date()

INAUG_DATES = {
    'Trump': date(2017, 1, 20),
    'Obama': date(2009, 1, 20),
    'Bush 43': date(2001, 1, 20),
    'Clinton': date(1993, 1, 20),
    'Bush 41': date(1989, 1, 20),
    'Reagan': date(1981, 1, 20),
    'Carter': date(1977, 1, 20)
}

presidential_terms = pd.DataFrame(list(INAUG_DATES.items()))
presidential_terms.columns = ['president', 'president_start_date']
presidential_terms['president_end_date'] = presidential_terms['president_start_date'].shift(1).fillna(TODAY)
presidential_terms


# In[3]:


def fill_end(series):
    end, president = series
    if pd.notnull(end) and end.endswith('admin'):
        next_pres ,_ = end.split(' ')
        if next_pres == 'Bush':
            next_pres = next_pres + ' 43' if president == 'Clinton' else next_pres + ' 41'
        return INAUG_DATES[next_pres].strftime('%m/%d/%y')
    else:
        return end
    
def fill_start(series):
    end, president = series
    if pd.notnull(end) and end.endswith('admin'):
        prev_pres ,_ = end.split(' ')
        if prev_pres == 'Bush':
            prev_pres = prev_pres + ' 43' if president == 'Obama' else prev_pres + ' 41'
        return INAUG_DATES[president].strftime('%m/%d/%y')
    else:
        return end
    
    
raw_df['end'] = raw_df[['end', 'president']].apply(fill_end, axis=1)
raw_df['start'] = raw_df[['start', 'president']].apply(fill_start, axis=1)

raw_df['end'] = pd.to_datetime(raw_df['end']).dt.date
raw_df['end'] = raw_df['end'].fillna(TODAY)
raw_df['start'] = pd.to_datetime(raw_df['start']).dt.date


# In[4]:


raw_df = raw_df.merge(presidential_terms, left_on='president', right_on='president')
raw_df['event'] = (raw_df['end'] < raw_df['president_end_date']) & pd.notnull(raw_df['end'])


# In[5]:


# we need to "collapse" individuals into rows, because they may change positions, but that's not quitting...
def collapse(df):
    return df.groupby('appointee', as_index=False).aggregate({
        'start': 'min', 'end': 'max', 'event': 'all', 'president': 'last', 'president_end_date': 'last'
    })

raw_df = raw_df.groupby('president', as_index=False).apply(collapse).reset_index(drop=True)
raw_df['T'] = (raw_df['end'] - raw_df['start']).dt.days


# In[6]:


raw_df.tail(20)


# In[7]:


naf = NelsonAalenFitter()
ax = naf.fit(raw_df['T'],raw_df['event']).plot()

from lifelines import PiecewiseExponentialFitter
pf = PiecewiseExponentialFitter(breakpoints=[1440, 1500])
pf.fit(raw_df['T'], raw_df['event'])
pf.plot(ax=ax)
pf.print_summary(4)


# In[8]:


kmf = KaplanMeierFitter()

ax = plt.subplot()

for name, df_ in raw_df[['president','event', 'T']].groupby('president'):
    kmf.fit(df_['T'], df_['event'], label=name)
    ax = kmf.plot(ax=ax, ci_show=False)


# In[9]:


ax = plt.subplot()

for name, df_ in raw_df[['president','event', 'T']].groupby('president'):
    kmf.fit(df_['T'], df_['event'], label=name)
    if name == 'Trump':
        ax = kmf.plot(ax=ax, color='r')
    else:
        ax = kmf.plot(ax=ax, color='grey', alpha=0.5, ci_show=False)


# In[10]:


raw_df[['president','event', 'T']]

naf = NelsonAalenFitter()

ax = plt.subplot()

for name, df_ in raw_df[['president','event', 'T']].groupby('president'):
    if name in ['Trump', 'Carter']:
        naf.fit(df_['T'], df_['event'], label=name)
        ax = naf.plot(ax=ax)


# In[11]:


raw_df['year'] = raw_df['start'].apply(lambda d: int(d.year))

regression_df = raw_df[['president', 'T', 'event', 'year']]


# In[15]:


cph = CoxPHFitter()
cph.fit(regression_df, 'T', 'event', formula="president + bs(year, df=3)")
cph.print_summary(3)


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cph.check_assumptions(regression_df)


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cph.plot_covariate_groups("year", values=np.linspace(1977, 2016, 5), y="cumulative_hazard")


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# In[15]:


from lifelines import *

wf = WeibullAFTFitter(penalizer=0.0)
wf.fit(regression_df, 'T', 'event')
wf.print_summary(3)


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lnf = LogNormalAFTFitter(penalizer=0.0000)
lnf.fit(regression_df, 'T', 'event')
lnf.print_summary(3)


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llf = LogLogisticAFTFitter(penalizer=0.000)
llf.fit(regression_df, 'T', 'event')
llf.print_summary(3)


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