population-trend 3.0.0__py3-none-any.whl → 3.1.0__py3-none-any.whl

population_trend/__init__.py

@@ -1,6 +1,8 @@
 """A template Python module"""
 
-__version__ = "3.0.0"
+__version__ = "3.1.0"
 from .cli import *  # noqa
 from .filter_data import *  # noqa
 from .population_growth_model import *  # noqa
+from .calculate_growth_rates import *  # noqa
+from bootstrapping_tools import *  # noqa

population_trend/calculate_growth_rates.py

@@ -0,0 +1,206 @@
+from bootstrapping_tools import (
+    lambda_calculator,
+    power_law,
+    bootstrap_from_time_series,
+    get_bootstrap_deltas,
+    generate_latex_interval_string,
+    calculate_p_values,
+)
+from matplotlib.ticker import MaxNLocator
+
+import json
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+def do_nothing():
+    pass
+
+
+def fit_population_model(seasons_series, data_series):
+    parameters = lambda_calculator(seasons_series, data_series)
+    model = power_law(
+        seasons_series - seasons_series.iloc[0],
+        parameters[0],
+        parameters[1],
+    )
+    return model
+
+
+def calculate_porcentual_diff(x, y):
+    return 100 * (x - y) / y
+
+
+def generate_number_and_season_string(number, season):
+    return "{} ({})".format(
+        number,
+        season,
+    )
+
+
+def calculate_seasons_intervals(seasons):
+    years = []
+    first_index = 0
+    for index in np.where(np.diff(seasons) != 1)[0]:
+        if seasons[first_index] == seasons[index]:
+            years.append(f"{seasons[index]}")
+        else:
+            years.append(f"{seasons[first_index]}-{seasons[index]}")
+        first_index = index + 1
+    years.append(f"{seasons[first_index]}-{seasons[-1]}")
+    return years
+
+
+def calculate_interest_numbers(cantidad_nidos, model):
+    first_number = generate_number_and_season_string(
+        cantidad_nidos["Maxima_cantidad_nidos"].iloc[0],
+        cantidad_nidos["Temporada"].iloc[0],
+    )
+    first_number_calculated = generate_number_and_season_string(
+        model.iloc[0], cantidad_nidos["Temporada"].iloc[0]
+    )
+    last_number = "{{{:,.0f}}} ({})".format(
+        cantidad_nidos["Maxima_cantidad_nidos"].iloc[-1],
+        int(cantidad_nidos["Temporada"].iloc[-1]),
+    )
+    last_number_calculated = generate_number_and_season_string(
+        model.iloc[-1],
+        cantidad_nidos["Temporada"].iloc[-1],
+    )
+    return first_number, first_number_calculated, last_number, last_number_calculated
+
+
+def calculate_percent_diff_in_seasons(cantidad_nidos, model):
+    if cantidad_nidos["Maxima_cantidad_nidos"].iloc[0] == 0:
+        porcentaje_cambio = calculate_porcentual_diff(model.iloc[-1], model.iloc[0])
+    else:
+        porcentaje_cambio = calculate_porcentual_diff(
+            model.iloc[-1], cantidad_nidos["Maxima_cantidad_nidos"].iloc[0]
+        )
+    return porcentaje_cambio
+
+
+class Bootstrap_from_time_series_parameterizer:
+    def __init__(self, blocks_length=3, N=2000):
+        self.parameters = dict(
+            dataframe=None,
+            column_name="Maxima_cantidad_nidos",
+            N=N,
+            return_distribution=True,
+            blocks_length=blocks_length,
+        )
+
+    def set_data(self, data):
+        self.parameters["dataframe"] = data
+
+
+Bootstrap = dict(
+    default=Bootstrap_from_time_series_parameterizer(),
+    testing=Bootstrap_from_time_series_parameterizer(blocks_length=2, N=100),
+)
+
+
+class Bootstrap_from_time_series:
+    def __init__(self, bootstrap_parametrizer):
+        self.parameters = bootstrap_parametrizer.parameters
+        self.lambdas_distribution, self.intervals = self._calculate_distribution_and_interval()
+        self.season_series = self.parameters["dataframe"]["Temporada"]
+        self.data_series = self.parameters["dataframe"][self.parameters["column_name"]]
+        self.lambdas = [interval[0] for interval in self.intervals]
+
+    def get_distribution(self):
+        return self.lambdas_distribution
+
+    def _calculate_distribution_and_interval(self):
+        lambdas_distribution, intervals = bootstrap_from_time_series(**self.parameters)
+        return lambdas_distribution, intervals
+
+    def get_inferior_central_and_superior_limit(self):
+        inferior_limit, central, superior_limit = get_bootstrap_deltas(
+            self.lambdas, **{"decimals": 2}
+        )
+        return inferior_limit, central, superior_limit
+
+    def get_lambda_interval_latex_string(self):
+        lambda_latex_string = generate_latex_interval_string(self.lambdas, **{"decimals": 2})
+        return lambda_latex_string
+
+    def generate_season_interval(self):
+        return "({}-{})".format(
+            self.season_series.min(axis=0),
+            self.season_series.max(axis=0),
+        )
+
+    def get_monitored_seasons(self):
+        monitored_seasons = np.sort(self.season_series.astype(int).unique())
+        if len(monitored_seasons) == 1:
+            return f"{monitored_seasons[0]}"
+        else:
+            seasons_intervals = calculate_seasons_intervals(monitored_seasons)
+            return ",".join(seasons_intervals)
+
+    def xxfit_population_model(self):
+        parameters = lambda_calculator(self.season_series, self.data_series)
+        model = power_law(
+            self.season_series - self.season_series.iloc[0],
+            parameters[0],
+            parameters[1],
+        )
+        return model
+
+    def save_intervals(self, output_path):
+        json_dict = {
+            "intervals": list(self.intervals),
+            "lambda_latex_interval": self.get_lambda_interval_latex_string(),
+        }
+        with open(output_path, "w") as file:
+            json.dump(json_dict, file)
+
+
+def calculate_growth_rates_table(bootstrap: Bootstrap_from_time_series_parameterizer):
+    bootstraper = Bootstrap_from_time_series(bootstrap)
+    df = bootstrap.parameters["dataframe"]
+    model = bootstraper.xxfit_population_model()
+    inferior_limit, central, superior_limit = bootstraper.get_inferior_central_and_superior_limit()
+    lambda_latex_string = bootstraper.get_lambda_interval_latex_string()
+    bootstrap_distribution = bootstraper.get_distribution()
+    lambdas_distribution = [interval[0] for interval in bootstrap_distribution]
+    p_value_mayor, p_value_menor = calculate_p_values(lambdas_distribution)
+    intervalo = bootstraper.generate_season_interval()
+    monitored_seasons = bootstraper.get_monitored_seasons()
+    porcentaje_cambio = calculate_percent_diff_in_seasons(df, model)
+    (
+        first_number,
+        _,
+        last_number,
+        last_number_calculated,
+    ) = calculate_interest_numbers(df, model)
+    return [
+        intervalo,
+        first_number,
+        last_number,
+        last_number_calculated,
+        lambda_latex_string,
+        df["Latitud"].iloc[0],
+        central,
+        f"-{inferior_limit}",
+        f"+{superior_limit}",
+        f"{{{int(porcentaje_cambio):,}}}",
+        p_value_mayor,
+        p_value_menor,
+        monitored_seasons,
+    ]
+
+
+def set_axis_plot_config(ax):
+    ax.xaxis.set_major_locator(MaxNLocator(integer=True))
+    ax.spines["right"].set_visible(False)
+    ax.spines["top"].set_visible(False)
+    plt.yticks(rotation=90, size=20)
+    locs_x, labels_x = plt.xticks()
+    locs_y, labels_y = plt.yticks()
+    plt.xticks(locs_x[1:], size=20)
+    plt.xlim(locs_x[0], locs_x[-1])
+    plt.ylim(0, locs_y[-1])
+    plt.xlabel("Año", size=20, labelpad=10)
+    plt.ylabel("Cantidad de parejas reproductoras", size=20)

{population_trend-3.0.0.dist-info → population_trend-3.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: population_trend
-Version: 3.0.0
+Version: 3.1.0
 Summary: A template Python module
 Home-page: https://github.com/IslasGECI/population_trend
 Author: Ciencia de Datos • GECI
@@ -8,7 +8,7 @@ Author-email: ciencia.datos@islas.org.mx
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Requires-Dist: bootstrapping-tools==1.1.1
+Requires-Dist: bootstrapping-tools==2.0.0
 Requires-Dist: geci-plots
 Requires-Dist: typer
 

population_trend-3.1.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+population_trend/__init__.py,sha256=mr5F6CLyrEM5ITNVsP0YgFZff-b2E7GRbunCPuELGiA,251
+population_trend/calculate_growth_rates.py,sha256=SQobh1f2xKFKu7MO7To7avxU2Cym1ebu2tKfpbLTpbo,6901
+population_trend/cli.py,sha256=CkzXmfjekIV4RplUyJo1Af-GI22zovB4u5alt8BNYIo,1894
+population_trend/filter_data.py,sha256=D0Y1vztcbbo98af9q7wRhlHfH__bNFI8tnVOdJY6hu0,403
+population_trend/population_growth_model.py,sha256=fSUKg8UH-pdN1tNYskGcMmmiqqAy9Ciz0E4X-IeP9WM,4361
+population_trend-3.1.0.dist-info/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+population_trend-3.1.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+population_trend-3.1.0.dist-info/METADATA,sha256=e5YM8iZ6yCz3b9uRIrFOa2AeXa6uIPQ4bW77D0NAPno,1504
+population_trend-3.1.0.dist-info/RECORD,,

population_trend-3.0.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-population_trend/__init__.py,sha256=FT9rFbM8pRxixs5itfeXniGnSsbiZtuZ7bu_Ar8LEpI,163
-population_trend/cli.py,sha256=CkzXmfjekIV4RplUyJo1Af-GI22zovB4u5alt8BNYIo,1894
-population_trend/filter_data.py,sha256=D0Y1vztcbbo98af9q7wRhlHfH__bNFI8tnVOdJY6hu0,403
-population_trend/population_growth_model.py,sha256=fSUKg8UH-pdN1tNYskGcMmmiqqAy9Ciz0E4X-IeP9WM,4361
-population_trend-3.0.0.dist-info/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-population_trend-3.0.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-population_trend-3.0.0.dist-info/METADATA,sha256=9DcQkh2bjrLU5e03CBPSBo970FgoSn9Na26OATSlKYk,1504
-population_trend-3.0.0.dist-info/RECORD,,