pyabc.storage
Data store
Purpose of the data store
The most important class here is the History class. The History class is the interface to the database in which pyABC stores and logs information during the ABC-SMC run, but also the interface which allows you to query that information later on.
Initializing the database interface from a file
For querying, you initialize a History object with a valid SQLAlchemy database identifier. For example, if your ABC-SMC data is stored in a file “data.db”, you initialize the History with:
history = History("sqlite:///data.db")
Don’t mind the three slashes. This is SQLAlchemy syntax.
If more than one ABC-SMC run is stored in your database file, these runs will have ids. The first run has id=1, the second run id=2, and so on. Per default, the first run found in the database is automatically selected. To select a specific run n (e.g. n=3), do
history.id = n
Querying the database
The History class has a number of methods which are relevant for querying the stored data. The most important ones are:
History.get_distribution
to retrieve information on the parameter posteriors,History.get_model_probabilities
to retrieve information on the model probabilities in case you’re doing model selection,History.get_all_populations
, to retrieve information on the evolution of the acceptance threshold and the number of sample attempts per population,History.get_nr_particles_per_population
, to retrieve the number of particles per population (this number os not necessariliy constant),History.get_weighted_distances
, to retrieve the distances the parameter samples achieved,History.n_populations
to get the total number of populations, andHistory.total_nr_simulations
to get the total number of simulations, i.e. sample attempts.
Use get_distribution
to retrieve your posterior particle population. For
example,
df, w = history.get_distribution(m)
will return a DataFrame df of parameters and an array w of weights of the particles of model m in the last available population. If you’re interested in intermediate populations, add the optional t parameter, which indicates the population number (the first population is t=0)
df, w = history.get_distribution(m, t)
What can be stored as summary statistics
Currently, integers, floats, strings, and in general everything that can be converted to a numpy array, can be stored. In addition, it is also possible to store pandas DataFrames.
Warning
Storage of pandas DataFrames is considered experimental at this point.
- class pyabc.storage.History(db: str, stores_sum_stats: bool = True, _id: int = None, create: bool = True)[source]
Bases:
object
History for ABCSMC.
This class records the evolution of the populations and stores the ABCSMC results.
- db
SQLalchemy database identifier. For a relative path use the template “sqlite:///file.db”, for an absolute path “sqlite:////path/to/file.db”, and for an in-memory database “sqlite://”.
- Type:
- stores_sum_stats
Whether to store summary statistics to the database. Note: this is True by default, and should be set to False only for testing purposes (i.e. to speed up the writing to the file system), as it can not be guaranteed that all methods of pyabc work correctly if the summary statistics are not stored.
- Type:
bool, optional (default = True)
- id
The id of the ABCSMC analysis that is currently in use. If there are analyses in the database already, this defaults to the latest id. Manually set if another run is wanted.
- Type:
- __init__(db: str, stores_sum_stats: bool = True, _id: int = None, create: bool = True)[source]
Initialize history object.
- Parameters:
create – If False, an error is thrown if the database does not exist.
- alive_models(t: int = None) List [source]
Get the models which are still alive at time t.
- Parameters:
t (int, optional (default = self.max_t)) – Population index.
- Returns:
alive – A list which contains the indices of those models which are still alive.
- Return type:
List
- append_population(t: int, current_epsilon: float, population: Population, nr_simulations: int, model_names)[source]
Append population to database.
- Parameters:
t (int) – Population number.
current_epsilon (float) – Current epsilon value.
population (Population) – List of sampled particles.
nr_simulations (int) – The number of model evaluations for this population.
model_names (list) – The model names.
Note. This function is called by the
pyabc.ABCSMC
class internally. You should most likely not find it necessary to call this method under normal circumstances.
- done(end_time: datetime = None)[source]
Close database sessions and store end time of the analysis.
- Parameters:
end_time – End time of the analysis.
Note. This function is called by the
pyabc.ABCSMC
class internally. You should most likely not find it necessary to call this method under normal circumstances.
- get_all_populations()[source]
Returns a pandas DataFrame with columns
t: Population number
population_end_time: The end time of the population
- samples: The number of sample attempts performed
for a population
epsilon: The acceptance threshold for the population.
- Returns:
all_populations – DataFrame with population info
- Return type:
pd.DataFrame
- get_distribution(m: int = 0, t: int = None) Tuple[DataFrame, ndarray] [source]
Returns the weighted population sample for model m and timepoint t as a tuple.
- Parameters:
- Returns:
df, w –
df: a DataFrame of parameters
w: are the weights associated with each parameter
- Return type:
pandas.DataFrame, np.ndarray
- get_ground_truth_parameter() Parameter [source]
Create a pyabc.Parameter object from the ground truth parameters saved in the database, if existent.
- Return type:
A PyParameter dictionary.
- get_model_probabilities(t: int | None = None) DataFrame [source]
Model probabilities.
- Parameters:
t (int or None (default = None)) – Population index. If None, all populations of indices >= 0 are considered.
- Returns:
probabilities – Model probabilities.
- Return type:
np.ndarray
- get_nr_particles_per_population() Series [source]
Get the number of particles per population.
- Returns:
nr_particles_per_population – A pandas DataFrame containing the number of particles for each population.
- Return type:
pd.DataFrame
- get_population(t: int = None)[source]
Create a pyabc.Population object containing all particles, as far as those can be recreated from the database. In particular, rejected particles are currently not stored.
- Parameters:
t (int, optional (default = self.max_t)) – The population index.
- get_population_extended(*, m: int | None = None, t: int | str = 'last', tidy: bool = True) DataFrame [source]
Get extended population information, including parameters, distances, summary statistics, weights and more.
- Parameters:
m (int or None, optional (default = None)) – The model to query. If omitted, all models are returned.
t (int or str, optional (default = "last")) – Can be “last” or “all”, or a population index (i.e. an int). In case of “all”, all populations are returned. If “last”, only the last population is returned, for an int value only the corresponding population at that time index.
tidy (bool, optional) – If True, try to return a tidy DataFrame, where the individual parameters and summary statistics are pivoted. Setting tidy to true will only work for a single model and a single population.
- Returns:
full_population
- Return type:
DataFrame
- get_population_strategy()[source]
Get information on the population size strategy.
- Returns:
The population strategy.
- Return type:
population_strategy
- get_weighted_distances(t: int = None) DataFrame [source]
Population’s weighted distances to the measured sample. These weights do not necessarily sum up to 1.
- Parameters:
t (int, optional (default = self.max_t)) – Population index. If t is None, the last population is selected.
- Returns:
df_weighted – Weighted distances. The dataframe has column “w” for the weights and column “distance” for the distances.
- Return type:
pd.DataFrame
- get_weighted_sum_stats(t: int = None) Tuple[List[float], List[dict]] [source]
Population’s weighted summary statistics. These weights do not necessarily sum up to 1.
- Parameters:
t (int, optional (default = self.max_t)) – Population index. If t is None, the latest population is selected.
- Returns:
In the same order in the first array the weights (multiplied by the model probabilities), and tin the second array the summary statistics.
- Return type:
weights, sum_stats
- get_weighted_sum_stats_for_model(m: int = 0, t: int = None) Tuple[ndarray, List] [source]
Summary statistics for model m. The weights sum to 1, unless there were multiple acceptances per particle.
- property max_t
The population number of the last populations. This is equivalent to
n_populations - 1
.
- property n_populations
Number of populations stored in the database. This is equivalent to
max_t + 1
.
- nr_of_models_alive(t: int = None) int [source]
Number of models still alive.
- Parameters:
t (int, optional (default = self.max_t)) – Population index.
- Returns:
nr_alive – Number of models still alive. None is for the last population
- Return type:
int >= 0 or None
- observed_sum_stat()[source]
Get the observed summary statistics.
- Returns:
sum_stats_dct – The observed summary statistics.
- Return type:
- store_initial_data(ground_truth_model: int, options: dict, observed_summary_statistics: dict, ground_truth_parameter: dict, model_names: List[str], distance_function_json_str: str, eps_function_json_str: str, population_strategy_json_str: str, start_time: datetime = None) None [source]
Store the initial configuration data.
- Parameters:
ground_truth_model – Index of the ground truth model.
options – Of ABC metadata.
observed_summary_statistics – The measured summary statistics.
ground_truth_parameter – The ground truth parameters.
model_names – A list of model names.
distance_function_json_str – The distance function represented as json string.
eps_function_json_str – The epsilon represented as json string.
population_strategy_json_str – The population strategy represented as json string.
start_time – Start time of the analysis.
Note. This function is called by the
pyabc.ABCSMC
class internally. You should most likely not find it necessary to call this method under normal circumstances.
- store_pre_population(ground_truth_model: int, observed_summary_statistics: dict, ground_truth_parameter: dict, model_names: List[str])[source]
Store a dummy pre-population containing some configuration data and in particular some ground truth values.
For the parameters, see store_initial_data.
Note. This function is called by the
pyabc.ABCSMC
class internally. You should most likely not find it necessary to call this method under normal circumstances.
- property total_nr_simulations: int
Number of sample attempts for the ABC run.
- Returns:
nr_sim – Total nr of sample attempts for the ABC run.
- Return type:
- update_after_calibration(nr_samples: int, end_time: datetime)[source]
Update after the calibration iteration. In particular set time and number of samples. Update the number of samples used in iteration t.
- Parameters:
nr_samples – Number of samples reported.
end_time – End time of the calibration iteration.
Note. This function is called by the
pyabc.ABCSMC
class internally. You should most likely not find it necessary to call this method under normal circumstances.
- pyabc.storage.create_sqlite_db_id(dir_: str = None, file_: str = 'pyabc_test.db')[source]
Convenience function to create an sqlite database identifier which can be understood by sqlalchemy.
- Parameters:
dir – The base folder name. Optional, defaults to the system’s temporary directory, i.e. “/tmp/” on Linux. While this makes sense for testing purposes, for productive use a non-temporary location should be used.
file – The database file name. Optional, defaults to “pyabc_test.db”.
- pyabc.storage.load_dict_from_json(file_: str, key_type: type = <class 'int'>)[source]
Read in json file. Convert keys to key_type’. Inverse to `save_dict_to_json.
- Parameters:
file – Name of the file to read in.
key_type – Type to convert the keys into.
- Returns:
dct
- Return type:
The json file contents.