Tools
Generic convenient tools.
biogeme.tools module
Implements some useful functions
- author:
Michel Bierlaire
- date:
Sun Apr 14 10:46:10 2019
- class biogeme.tools.LRTuple(message, statistic, threshold)[source]
Bases:
NamedTuple
Tuple for the likelihood ratio test
- Parameters:
message (str) –
statistic (float) –
threshold (float) –
-
message:
str
Alias for field number 0
-
statistic:
float
Alias for field number 1
-
threshold:
float
Alias for field number 2
- class biogeme.tools.ModelNames(prefix='Model')[source]
Bases:
object
Class generating model names from unique configuration string
- Parameters:
prefix (str) –
- class biogeme.tools.TemporaryFile[source]
Bases:
object
Class generating a temporary file, so that the user does not bother about its location, or even its name
Example:
with TemporaryFile() as filename: with open(filename, 'w') as f: print('stuff', file=f)
- biogeme.tools.calculate_prime_numbers(upper_bound)[source]
Calculate prime numbers
- Parameters:
upper_bound (
int
) – prime numbers up to this value will be computed- Return type:
list
[int
]- Returns:
array with prime numbers
- Raises:
BiogemeError – if the upper_bound is incorrectly defined (negative number, e.g.)
>>> tools.calculate_prime_numbers(10) [2, 3, 5, 7]
- biogeme.tools.checkDerivatives(the_function, x, names=None, logg=False)[source]
Verifies the analytical derivatives of a function by comparing them with finite difference approximations.
- Parameters:
the_function (
Callable
[[ndarray
],tuple
[float
,ndarray
,ndarray
]]) –A function object that takes a vector as an argument, and returns a tuple:
The first element of the tuple is the value of the function \(f\),
the second is the gradient of the function,
the third is the hessian.
x (
ndarray
) – arguments of the functionnames (
Optional
[list
[str
]]) – the names of the entries of x (for reporting).logg (
Optional
[bool
]) – if True, messages will be displayed.
- Return type:
tuple
[float
,ndarray
,ndarray
,ndarray
,ndarray
]- Returns:
tuple f, g, h, gdiff, hdiff where
f is the value of the function at x,
g is the analytical gradient,
h is the analytical hessian,
gdiff is the difference between the analytical gradient and the finite difference approximation
hdiff is the difference between the analytical hessian and the finite difference approximation
- biogeme.tools.countNumberOfGroups(df, column)[source]
This function counts the number of groups of same value in a column. For instance: 1,2,2,3,3,3,4,1,1 would give 5.
Example:
>>>df = pd.DataFrame({'ID': [1, 1, 2, 3, 3, 1, 2, 3], 'value':[1000, 2000, 3000, 4000, 5000, 5000, 10000, 20000]}) >>>tools.countNumberOfGroups(df,'ID') 6 >>>tools.countNumberOfGroups(df,'value') 7
- Return type:
int
- Parameters:
df (DataFrame) –
column (str) –
- biogeme.tools.findiff_H(the_function, x)[source]
Calculates the hessian of a function \(f\) using finite differences
- Parameters:
the_function (
Callable
[[ndarray
],tuple
[float
,ndarray
,Any
]]) – A function object that takes a vector as an argument, and returns a tuple. The first element of the tuple is the value of the function \(f\), and the second is the gradient of the function. The other elements are not used.x (
ndarray
) – argument of the function
- Return type:
ndarray
- Returns:
numpy matrix containing the hessian calculated by finite differences.
- biogeme.tools.findiff_g(the_function, x)[source]
Calculates the gradient of a function \(f\) using finite differences
- Parameters:
the_function (
Callable
[[ndarray
],tuple
[float
,...
]]) – A function object that takes a vector as an argument, and returns a tuple. The first element of the tuple is the value of the function \(f\). The other elements are not used.x (
ndarray
) – argument of the function
- Return type:
ndarray
- Returns:
numpy vector, same dimension as x, containing the gradient calculated by finite differences.
- biogeme.tools.flatten_database(df, merge_id, row_name=None, identical_columns=None)[source]
Combine several rows of a Pandas database into one. For instance, consider the following database:
ID Age Cost Name 0 1 23 34 Item3 1 1 23 45 Item4 2 1 23 12 Item7 3 2 45 65 Item3 4 2 45 34 Item7
If row_name is ‘Name’, the function generates the same data in the following format:
Age Item3_Cost Item4_Cost Item7_Cost ID 1 23 34 45.0 12 2 45 65 NaN 34
If row_name is None, the function generates the same data in the following format:
Age 1_Cost 1_Name 2_Cost 2_Name 3_Cost 3_Name ID 1 23 34 Item3 45 Item4 12.0 Item7 2 45 65 Item3 34 Item7 NaN NaN
- Parameters:
df (pandas.DataFrame) – initial data frame
merge_id (str) – name of the column that identifies rows that should be merged. In the above example: ‘ID’
row_name (str) – name of the columns that provides the name of the rows in the new dataframe. In the example above: ‘Name’. If None, the rows are numbered sequentially.
identical_columns (list(str)) – name of the columns that contain identical values across the rows of a group. In the example above: [‘Age’]. If None, these columns are automatically detected. On large database, there may be a performance issue.
- Returns:
reformatted database
- Return type:
pandas.DataFrame
- biogeme.tools.format_timedelta(td)[source]
Format a timedelta in a “human-readable” way
- Return type:
str
- Parameters:
td (timedelta) –
- biogeme.tools.generate_unique_ids(list_of_ids)[source]
If there are duplicates in the list, a new list is generated where there are renamed to obtain a list with unique IDs.
- Parameters:
list_of_ids (list[str]) – list of ids
- Returns:
a dict that maps the unique names with the original name
- biogeme.tools.get_prime_numbers(n)[source]
Get a given number of prime numbers
- Parameters:
n (
int
) – number of primes that are requested- Return type:
list
[int
]- Returns:
array with prime numbers
- Raises:
BiogemeError – if the requested number is non positive or a float
- biogeme.tools.likelihood_ratio_test(model1, model2, significance_level=0.05)[source]
This function performs a likelihood ratio test between a restricted and an unrestricted model.
- Parameters:
model1 (
tuple
[float
,int
]) – the final loglikelihood of one model, and the number of estimated parameters.model2 (
tuple
[float
,int
]) – the final loglikelihood of the other model, and the number of estimated parameters.significance_level (
float
) – level of significance of the test. Default: 0.05
- Return type:
- Returns:
a tuple containing:
a message with the outcome of the test
the statistic, that is minus two times the difference between the loglikelihood of the two models
the threshold of the chi square distribution.
- Raises:
BiogemeError – if the unrestricted model has a lower log likelihood than the restricted model.
- biogeme.tools.unique_product(*iterables, max_memory_mb=1024)[source]
Generate the Cartesian product of multiple iterables, keeping only the unique entries. Raises a MemoryError if memory usage exceeds the specified threshold.
- Parameters:
iterables (Iterable) – Variable number of iterables to compute the Cartesian product from.
max_memory_mb (int) – Maximum memory usage in megabytes (default: 1024MB).
- Returns:
Yields unique entries from the Cartesian product.
- Return type:
Iterator[tuple]