def subset(self,
country,
province=None,
start_date=None,
end_date=None,
population=None):
"""
Return the subset of dataset with Recovered > 0.
Args:
country (str): country name or ISO3 code
province (str or None): province name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
population (int or None): population value
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pd.Timestamp): Observation date
- Confirmed (int): the number of confirmed cases
- Infected (int): the number of currently infected cases
- Fatal (int): the number of fatal cases
- Recovered (int): the number of recovered cases (> 0)
- Susceptible (int): the number of susceptible cases, if calculated
Note:
If @population (high priority) is not None or population values are registered in subset,
the number of susceptible cases will be calculated.
"""
country_alias = self.ensure_country_name(country)
# Subset with area, start/end date
subset_df = self._subset(country=country,
province=province,
start_date=start_date,
end_date=end_date)
if subset_df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date)
# Calculate Susceptible
df = self._calculate_susceptible(subset_df, population)
# Select records where Recovered > 0
df = df.loc[df[self.R] > 0, :].reset_index(drop=True)
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date,
message="with 'Recovered > 0'") from None
return df
def _subset_by_area(self, country, province=None):
"""
Return subset for the country/province.
Args:
country (str): country name
province (str or None): province name or None (country level data)
Returns:
pandas.DataFrame: subset for the country/province, columns are not changed
Raises:
SubsetNotFoundError: no records were found for the condition
"""
# Country level
if province is None or province == self.UNKNOWN:
df = self.layer(country=None)
country_alias = self.ensure_country_name(country)
df = df.loc[df[self.COUNTRY] == country_alias]
return df.reset_index(drop=True)
# Province level
df = self.layer(country=country)
df = df.loc[df[self.PROVINCE] == province]
if df.empty:
raise SubsetNotFoundError(country=country)
return df.reset_index(drop=True)
def subset(self, country, **kwargs):
"""
Create a subset for a country.
Args:
country (str): country name or ISO 3166-1 alpha-3, like JPN
kwargs: the other arguments will be ignored in the latest version.
Raises:
covsirphy.SubsetNotFoundError: no records were found
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pd.Timestamp): Observation date
- other column names are defined by OxCGRTData.COL_DICT
"""
country_arg = country
country = self.ensure_country_name(country)
try:
df = super().subset(country=country)
except SubsetNotFoundError:
raise SubsetNotFoundError(country=country_arg,
country_alias=country) from None
df = df.groupby(self.DATE).last().reset_index()
return df.loc[:, self.OXCGRT_COLS_WITHOUT_COUNTRY]
def value(self, country, province=None, date=None):
"""
Return the value of population in the place.
Args:
country (str): country name or ISO3 code
province (str): province name
date (str or None): observation date, like 01Jun2020
Returns:
int: population in the place
Note:
If @date is None, the created date of the instancewill be used
"""
country_alias = self.ensure_country_name(country)
try:
df = self.subset(country=country,
province=province,
start_date=date,
end_date=date)
except KeyError:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
date=date)
df = df.sort_values(self.DATE)
return int(df.loc[df.index[-1], [self.N]].values[0])
def ensure_country_name(self, country):
"""
Ensure that the country name is correct.
If not, the correct country name will be found.
Args:
country (str): country name
Returns:
str: country name
"""
df = self._ensure_dataframe(self._cleaned_df,
name="the cleaned dataset",
columns=[self.COUNTRY])
selectable_set = set(df[self.COUNTRY].unique())
# return country name as-is if selectable
if country in selectable_set:
return country
# Convert country name
converted = coco.convert(country, to="name_short", not_found=None)
# Additional abbr
abbr_dict = {
"Congo Republic": "Republic of the Congo",
"DR Congo": "Democratic Republic of the Congo",
"UK": "United Kingdom",
"Vatican": "Holy See",
}
name = abbr_dict.get(converted, converted)
# Return the name if registered in the dataset
if name in selectable_set:
return name
raise SubsetNotFoundError(country=country, country_alias=name)
def retrieve(self, country):
"""
Retrieve the dataset of the country from the local file or the server.
Args:
country (str): country name
Returns:
pandas.DataFrame: retrieved data
Index
reset index
Columns
- Country (pandas.Category): country name
- Year (int): year
- Sex (str): Female/Male
- Age (int): age
- Population (int): population value
"""
if not self._raw.empty and country in self._raw[self.COUNTRY].unique():
df = self._raw.copy()
df = df.loc[df[self.COUNTRY] == country, :].reset_index(drop=True)
else:
# Retrieve from World Bank Open Data
try:
df = self._retrieve_from_server(country)
except SubsetNotFoundError:
raise SubsetNotFoundError(country=country) from None
# Add to raw dataset
self._raw = pd.concat([self._raw, df], ignore_index=True, axis=0)
self._raw.to_csv(self._filename, index=False)
# Data types
cat_cols, int_cols = [self.COUNTRY, self.SEX], [self.AGE, self.N]
df[cat_cols] = df[cat_cols].astype("category")
df[int_cols] = df[int_cols].astype(np.int64)
return df
def _colored_map_country(self, country, variable, title, date, **kwargs):
"""
Create country-specific colored map to show the values at province level.
Args:
country (str): country name
variable (str): variable name to show
title (str): title of the figure
date (str or None): date of the records or None (the last value)
kwargs: arguments of covsirphy.ColoredMap() and covsirphy.ColoredMap.plot()
"""
df = self._cleaned_df.copy()
country_alias = self.ensure_country_name(country)
# Check variable name
if variable not in df.columns:
candidates = [col for col in df.columns if col not in self.AREA_ABBR_COLS]
raise UnExpectedValueError(name="variable", value=variable, candidates=candidates)
# Select country-specific data
self._ensure_dataframe(df, name="cleaned dataset", columns=[self.COUNTRY, self.PROVINCE])
df = df.loc[df[self.COUNTRY] == country_alias]
df = df.loc[df[self.PROVINCE] != self.UNKNOWN]
if df.empty:
raise SubsetNotFoundError(
country=country, country_alias=country_alias, message="at province level")
# Select date
if date is not None:
self._ensure_dataframe(df, name="cleaned dataset", columns=[self.DATE])
df = df.loc[df[self.DATE] == pd.to_datetime(date)]
df = df.groupby(self.PROVINCE).last().reset_index()
# Plotting
df[self.COUNTRY] = country_alias
df.rename(columns={variable: "Value"}, inplace=True)
self._colored_map(title=title, data=df, level=self.PROVINCE, **kwargs)
def subset(self, country, province=None, start_date=None, end_date=None):
"""
Return subset with country/province name and start/end date.
Args:
country (str): country name or ISO3 code
province (str or None): province name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
Returns:
pandas.DataFrame
Index
reset index
Columns
without ISO3, Country, Province column
Raises:
SubsetNotFoundError: no records were found for the condition
"""
country_alias = self.ensure_country_name(country, errors="coerce")
try:
df = self._subset_by_area(country=country, province=province)
except SubsetNotFoundError:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province) from None
df = df.drop([self.COUNTRY, self.ISO3, self.PROVINCE],
axis=1,
errors="ignore")
# Subset with Start/end date
if start_date is None and end_date is None:
return df.reset_index(drop=True)
df = self._ensure_dataframe(df,
name="the cleaned dataset",
columns=[self.DATE])
series = df[self.DATE].copy()
start_obj = self.date_obj(date_str=start_date, default=series.min())
end_obj = self.date_obj(date_str=end_date, default=series.max())
df = df.loc[(start_obj <= series) & (series <= end_obj), :]
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date) from None
return df.reset_index(drop=True)
def _retrieve_from_server(self, country):
"""
Retrieve the dataset of the country from the server.
Args:
country (str): country name
Returns:
pandas.DataFrame: retrieved data
Index
reset index
Columns
- Country (object): country name
- Year (int): year
- Sex (object): Female/Male
- Age (object): age
- Population (object): population value
"""
if self.verbose:
print(
f"Retrieving population pyramid dataset ({country}) from https://data.worldbank.org/"
)
# Retrieve from World Bank Open Data
iso3_code = coco.convert(country, to="ISO3", not_found=None)
try:
df = wbdata.get_dataframe(self.INDICATOR_DICT,
country=iso3_code,
convert_date=True)
except RuntimeError:
raise SubsetNotFoundError(country=country) from None
# Preprocessing (-> Country, Population, Min, Max, Sex, Year)
df = df.stack().reset_index()
df.insert(0, self.COUNTRY, country)
df.columns = [self.COUNTRY, "Date", "Attribute", self.N]
df2 = df["Attribute"].str.split("-", expand=True)
df2.columns = ["Min", "Max", self.SEX]
df = pd.concat([df.drop("Attribute", axis=1), df2], axis=1)
df["Max"] = df["Max"].replace("UP", self.ELDEST)
for col in [self.N, "Min", "Max"]:
df[col] = pd.to_numeric(df[col], downcast="integer")
df[self.SEX].replace({"FE": "Female", "MA": "Male"}, inplace=True)
df[self.YEAR] = df["Date"].dt.year
df = df.drop("Date", axis=1)
# Preprocessing (-> Country, Year, Sex, Age, Population)
df[self.AGE] = df[["Min",
"Max"]].apply(lambda x: range(x[0], x[1] + 1),
axis=1)
df[self.N] = df[["Min", "Max", self.N]].apply(lambda x: x[2] /
(x[1] - x[0] + 1),
axis=1)
df = df.explode(self.AGE).reset_index(drop=True)
df[self.N] = df[self.N].astype(np.int64)
return df.loc[:, self.PYRAMID_COLS]
def records(self,
country,
province=None,
start_date=None,
end_date=None,
auto_complement=True,
**kwargs):
"""
Return the subset. If necessary, complemention will be performed.
Args:
country (str): country name or ISO3 code
province (str or None): province name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
auto_complement (bool): if True and necessary, the number of cases will be complemented
kwargs: the other arguments of complement
Returns:
pandas.DataFrame
Index
reset index
Columns
without ISO3, Country, Province column
"""
country_alias = self.ensure_country_name(country)
subset_arg_dict = {
"country": country,
"province": province,
"start_date": start_date,
"end_date": end_date
}
if auto_complement:
try:
df, is_complemented = self.subset_complement(
**subset_arg_dict, **kwargs)
if not df.empty:
return (df, is_complemented)
except NotImplementedError:
pass
try:
return (self.subset(**subset_arg_dict), False)
except SubsetNotFoundError:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date) from None
def subset(self, country, product=None, start_date=None, end_date=None):
"""
Return subset of the country/province and start/end date.
Args:
country (str or None): country name or ISO3 code
product (str or None): product name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pandas.TimeStamp): observation date
- Vaccinations (int): the number of vaccinations
"""
df = self._cleaned_df.copy()
# Subset by country
country_alias = self.ensure_country_name(country)
df = df.loc[df[self.COUNTRY] == country_alias]
# Subset by product name
if product is not None:
df = df.loc[df[self.PRODUCT] == product]
# Subset with start date
if start_date is not None:
df = df.loc[df[self.DATE] >= self.date_obj(start_date)]
# Subset with end date
if end_date is not None:
df = df.loc[df[self.DATE] <= self.date_obj(end_date)]
# Resampling
df = df.set_index(self.DATE).resample("D").sum().reset_index()
# Fill in the blanks
df[self.VAC] = df[self.VAC].replace(0, None)
df[self.VAC] = df[self.VAC].fillna(method="ffill").fillna(0)
# Check records were found
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=product,
start_date=start_date,
end_date=end_date)
return df
def subset(self,
country,
province=None,
start_date=None,
end_date=None,
dataset="COVID-19 Data Hub"):
"""
Return subset of the country/province and start/end date.
Args:
country (str): country name or ISO3 code
province (str or None): province name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
dataset (str): 'COVID-19 Data Hub' or 'Our World In Data'
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pd.TimeStamp): Observation date
- Tests (int): the number of total tests performed
- Confirmed (int): the number of confirmed cases
"""
country_alias = self.ensure_country_name(country)
df = self._subset_by_area(country=country_alias,
province=province,
dataset=dataset)
df = df.drop([self.COUNTRY, self.ISO3, self.PROVINCE], axis=1)
# Subset with Start/end date
if start_date is None and end_date is None:
return df.reset_index(drop=True)
series = df[self.DATE].copy()
start_obj = self.date_obj(date_str=start_date, default=series.min())
end_obj = self.date_obj(date_str=end_date, default=series.max())
df = df.loc[(start_obj <= series) & (series <= end_obj), :]
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date)
return df.reset_index(drop=True)
def layer(self, country=None):
"""
Return the cleaned data at the selected layer.
Args:
country (str or None): country name or None (country level data or country-specific dataset)
Returns:
pandas.DataFrame:
Index
reset index
Columns
- Country (str): country names
- Province (str): province names (or removed when country level data)
- any other columns of the cleaned data
Raises:
SubsetNotFoundError: no records were found for the country (when @country is not None)
KeyError: @country was None, but country names were not registered in the dataset
Note:
When @country is None, country level data will be returned.
When @country is a country name, province level data in the selected country will be returned.
"""
df = self._cleaned_df.copy()
self._ensure_dataframe(df,
name="the cleaned dataset",
columns=[self.COUNTRY])
if self.PROVINCE not in df:
df[self.PROVINCE] = self.UNKNOWN
df[self.AREA_COLUMNS] = df[self.AREA_COLUMNS].astype(str)
# Country level data
if country is None:
df = df.loc[df[self.PROVINCE] == self.UNKNOWN]
return df.drop(self.PROVINCE, axis=1).reset_index(drop=True)
# Province level data at the selected country
country_alias = self.ensure_country_name(country, errors="coerce")
df = df.loc[df[self.COUNTRY] == country_alias]
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias) from None
df = df.loc[df[self.PROVINCE] != self.UNKNOWN]
return df.reset_index(drop=True)
def specialized(self, model=None, country=None, province=None):
"""
Return dimensional records with model variables.
Args:
model (cs.ModelBase or None): the first ODE model
country (str or None): country name
province (str or None): province name
Note:
If country is None, the name of the model will be used.
If province is None, '-' will be used.
"""
country, province = self._model_to_area(
model=model, country=country, province=province)
try:
return self._specialized_dict[country][province]
except KeyError:
raise SubsetNotFoundError(country=country, province=province)
def non_dim(self, model=None, country=None, province=None):
"""
Return non-dimensional data.
Args:
model (cs.ModelBase or None): the first ODE model
country (str or None): country name
province (str or None): province name
Note:
If country is None, the name of the model will be used.
If province is None, '-' will be used.
"""
country, province = self._model_to_area(
model=model, country=country, province=province)
try:
return self.nondim_dict[country][province]
except KeyError:
raise SubsetNotFoundError(country=country, province=province)
def subset(self, country, province=None, start_date=None, end_date=None):
"""
Return subset of the country/province and start/end date.
Args:
country (str): country name or ISO3 code
province (str or None): province name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pd.Timestamp): Observation date
- Tests (int): the number of total tests performed
- Tests_diff (int): daily number of tests on date
- Confirmed (int): the number of confirmed cases
"""
country_alias = self.ensure_country_name(country)
df = self._subset_select(country=country_alias,
province=province or self.UNKNOWN)
# Calculate Tests_diff
df[self.T_DIFF] = df[self.TESTS].diff().fillna(0)
df.loc[df[self.T_DIFF] < 0, self.T_DIFF] = 0
df[self.T_DIFF] = df[self.T_DIFF].astype(np.int64)
df = df.loc[:, [self.DATE, self.TESTS, self.T_DIFF, self.C]]
# Subset with Start/end date
if start_date is None and end_date is None:
return df.reset_index(drop=True)
series = df[self.DATE].copy()
start_obj = self._ensure_date(start_date, default=series.min())
end_obj = self._ensure_date(end_date, default=series.max())
df = df.loc[(start_obj <= series) & (series <= end_obj), :]
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date)
return df.reset_index(drop=True)
def subset(self, country, product=None, start_date=None, end_date=None):
"""
Return subset of the country/province and start/end date.
Args:
country (str or None): country name or ISO3 code
product (str or None): product name
start_date (str or None): start date, like 22Jan2020
end_date (str or None): end date, like 01Feb2020
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pandas.TimeStamp): observation date
- Vaccinations (int): the number of vaccinations
- Vaccinated_once (int): cumulative number of people who received at least one vaccine dose
- Vaccinated_full (int): cumulative number of people who received all doses prescrived by the protocol
"""
df = self._cleaned_df.copy()
# Subset by country
country_alias = self.ensure_country_name(country)
df = df.loc[df[self.COUNTRY] == country_alias]
# Subset by product name
if product is not None:
df = df.loc[df[self.PRODUCT] == product]
# Subset with start date
if start_date is not None:
df = df.loc[df[self.DATE] >= self._ensure_date(start_date)]
# Subset with end date
if end_date is not None:
df = df.loc[df[self.DATE] <= self._ensure_date(end_date)]
# Check records were found
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=product,
start_date=start_date,
end_date=end_date)
return df.loc[:, self.VAC_SUBSET_COLS].reset_index(drop=True)
def subset(self, country, province=None):
"""
Return subset of the country/province.
Args:
country (str): country name or ISO3 code
province (str or None): province name
Returns:
pandas.DataFrame
Index
reset index
Columns
- Hospitalized_date (pandas.TimeStamp or NT)
- Confirmation_date (pandas.TimeStamp or NT)
- Outcome_date (pandas.TimeStamp or NT)
- Confirmed (bool)
- Infected (bool)
- Recovered (bool)
- Fatal (bool)
- Symtoms (str)
- Chronic_disease (str)
- Age (int or None)
- Sex (str)
"""
df = self._cleaned_df.copy()
# Subset by country name
country = self.ensure_country_name(country)
df = df.loc[df[self.COUNTRY] == country]
# Subset by province name
if province not in (None, self.UNKNOWN):
df = df.loc[df[self.PROVINCE] == province]
# Check records are registered
country_alias = self.ensure_country_name(country)
if df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province)
df = df.drop([self.COUNTRY, self.PROVINCE], axis=1)
return df.reset_index(drop=True)
def ensure_country_name(self, country, errors="raise"):
"""
Ensure that the country name is correct.
If not, the correct country name will be found.
Args:
country (str): country name
errors (str): 'raise' or 'coerce'
Returns:
str: country name
Raises:
SubsetNotFoundError: no records were found for the country and @errors is 'raise'
"""
df = self._cleaned_df.copy()
self._ensure_dataframe(df,
name="the cleaned dataset",
columns=[self.COUNTRY])
selectable_set = set(df[self.COUNTRY].unique())
# return country name as-is if selectable
if country in selectable_set:
return country
# Convert country name
warnings.simplefilter("ignore", FutureWarning)
converted = coco.convert(country, to="name_short", not_found=None)
# Additional abbr
abbr_dict = {
"Congo Republic": "Republic of the Congo",
"DR Congo": "Democratic Republic of the Congo",
"UK": "United Kingdom",
"Vatican": "Holy See",
}
name = abbr_dict.get(converted, converted)
# Return the name if registered in the dataset
if name in selectable_set:
return name
if errors == "raise":
raise SubsetNotFoundError(country=country, country_alias=name)
def subset(self, country, **kwargs):
"""
Create a subset for a country.
Args:
country (str): country name or ISO 3166-1 alpha-3, like JPN
kwargs: the other arguments will be ignored in the latest version.
Raises:
covsirphy.SubsetNotFoundError: no records were found
Returns:
pandas.DataFrame
Index
reset index
Columns
- Date (pandas.Timestamp): Observation date
- School_closing
- Workplace_closing
- Cancel_events
- Gatherings_restrictions
- Transport_closing
- Stay_home_restrictions
- Internal_movement_restrictions
- International_movement_restrictions
- Information_campaigns
- Testing_policy
- Contact_tracing
- Stringency_index
"""
country_arg = country
country = self.ensure_country_name(country)
try:
df = super().subset(country=country)
except SubsetNotFoundError:
raise SubsetNotFoundError(country=country_arg,
country_alias=country) from None
df = df.groupby(self.DATE).last().reset_index()
return df.loc[:, self.SUBSET_COLS]
def records(self,
country,
province=None,
start_date=None,
end_date=None,
population=None,
auto_complement=True,
**kwargs):
"""
JHU-style dataset for the area from the start date to the end date.
Records with Recovered > 0 will be selected.
Args:
country(str): country name or ISO3 code
province(str or None): province name
start_date(str or None): start date, like 22Jan2020
end_date(str or None): end date, like 01Feb2020
population(int or None): population value
auto_complement (bool): if True and necessary, the number of cases will be complemented
kwargs: the other arguments of JHUData.subset_complement()
Returns:
tuple(pandas.DataFrame, bool):
pandas.DataFrame:
Index
reset index
Columns
- Date(pd.TimeStamp): Observation date
- Confirmed(int): the number of confirmed cases
- Infected(int): the number of currently infected cases
- Fatal(int): the number of fatal cases
- Recovered (int): the number of recovered cases ( > 0)
- Susceptible(int): the number of susceptible cases, if calculated
str or bool: kind of complement or False
Note:
- If @ population is not None, the number of susceptible cases will be calculated.
- If necessary and @auto_complement is True, complement recovered data.
"""
country_alias = self.ensure_country_name(country)
subset_arg_dict = {
"country": country,
"province": province,
"start_date": start_date,
"end_date": end_date,
"population": population,
}
if auto_complement:
df, is_complemented = self.subset_complement(
**subset_arg_dict, **kwargs)
if not df.empty:
return (df, is_complemented)
try:
return (self.subset(**subset_arg_dict), False)
except ValueError:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date,
message="with 'Recovered > 0'") from None
def subset_complement(self,
country,
province=None,
start_date=None,
end_date=None,
population=None,
**kwargs):
"""
Return the subset of dataset and complement recovered data, if necessary.
Records with Recovered > 0 will be selected.
Args:
country(str): country name or ISO3 code
province(str or None): province name
start_date(str or None): start date, like 22Jan2020
end_date(str or None): end date, like 01Feb2020
population(int or None): population value
kwargs: keyword arguments of JHUDataComplementHandler(), control factors of complement
Returns:
tuple(pandas.DataFrame, str or bool):
pandas.DataFrame:
Index
reset index
Columns
- Date(pd.TimeStamp): Observation date
- Confirmed(int): the number of confirmed cases
- Infected(int): the number of currently infected cases
- Fatal(int): the number of fatal cases
- Recovered (int): the number of recovered cases ( > 0)
- Susceptible(int): the number of susceptible cases, if calculated
str or bool: kind of complement or False
Note:
If @population is not None, the number of susceptible cases will be calculated.
"""
# Subset with area, start/end date and calculate Susceptible
country_alias = self.ensure_country_name(country)
subset_df = self._subset(country=country,
province=province,
start_date=start_date,
end_date=end_date)
if subset_df.empty:
raise SubsetNotFoundError(country=country,
country_alias=country_alias,
province=province,
start_date=start_date,
end_date=end_date) from None
# Complement, if necessary
self._recovery_period = self._recovery_period or self.calculate_recovery_period(
)
handler = JHUDataComplementHandler(
recovery_period=self._recovery_period, **kwargs)
df, status, _ = handler.run(subset_df)
# Calculate Susceptible
df = self._calculate_susceptible(df, population)
# Kind of complement or False
is_complemented = status or False
# Select records where Recovered > 0
df = df.loc[df[self.R] > 0, :].reset_index(drop=True)
return (df, is_complemented)
def show_complement(self,
country=None,
province=None,
start_date=None,
end_date=None,
**kwargs):
"""
To monitor effectivity and safety of complement on JHU subset,
we need to know what kind of complement was done for JHU subset
for each country (if country/countries specified) or for all countries.
Args:
country (str or list[str] or None): country/countries name or None (all countries)
province(str or None): province name
start_date(str or None): start date, like 22Jan2020
end_date(str or None): end date, like 01Feb2020
kwargs: keyword arguments of JHUDataComplementHandler(), control factors of complement
Raises:
ValueError: @province was specified when @country is not a string
covsirphy.SubsetNotFoundError: No records were registered for the area/dates
Returns:
pandas.DataFrame
Index
reset index
Columns
- country (str): country name
- province (str): province name
- Monotonic_confirmed (bool): True if applied for confirmed cases or False otherwise
- Monotonic_fatal (bool): True if applied for fatal cases or False otherwise
- Monotonic_recovered (bool): True if applied for recovered or False otherwise
- Full_recovered (bool): True if applied for recovered or False otherwise
- Partial_recovered (bool): True if applied for recovered or False otherwise
"""
self._recovery_period = self._recovery_period or self.calculate_recovery_period(
)
# Area name
if country is None:
country = [
c for c in self._cleaned_df[self.COUNTRY].unique()
if c != "Others"
]
province = province or self.UNKNOWN
if not isinstance(country, str) and province != self.UNKNOWN:
raise ValueError(
"@province cannot be specified when @country is not a string.")
if not isinstance(country, list):
country = [country]
# Create complement handler
handler = JHUDataComplementHandler(
recovery_period=self._recovery_period, **kwargs)
# Check each country
complement_df = pd.DataFrame(columns=[
self.COUNTRY, self.PROVINCE,
*JHUDataComplementHandler.SHOW_COMPLEMENT_FULL_COLS
])
complement_df.set_index(self.COUNTRY, inplace=True)
for cur_country in country:
subset_df = self._subset(country=cur_country,
province=province,
start_date=start_date,
end_date=end_date)
if subset_df.empty:
raise SubsetNotFoundError(country=cur_country,
province=province,
start_date=start_date,
end_date=end_date)
*_, complement_dict = handler.run(subset_df)
complement_dict_values = pd.Series(complement_dict.values(),
dtype=bool).values
complement_df.loc[cur_country] = [
province, *complement_dict_values
]
return complement_df.reset_index()
