population-trend 0.1.0__py3-none-any.whl → 2.0.0__py3-none-any.whl

population_trend/__init__.py

@@ -1,4 +1,6 @@
 """A template Python module"""
 
-__version__ = "0.1.0"
+__version__ = "2.0.0"
+from .cli import *  # noqa
+from .filter_data import *  # noqa
 from .population_growth_model import *  # noqa

population_trend/cli.py

@@ -0,0 +1,51 @@
+from population_trend.filter_data import filter_by_species_and_island
+from population_trend.population_growth_model import (
+    Population_Trend_Model,
+    Plotter_Population_Trend_Model,
+)
+import pandas as pd
+import typer
+import json
+
+app = typer.Typer(help="Write filtered burrows data by species and island")
+
+
+@app.command(help="Write csv with ouput-path")
+def write_burrows_by_species_and_island(
+    data_path: str = "data/processed/subset_burrows_data.csv",
+    species: str = "Guadalupe Murrelet",
+    island: str = "Guadalupe",
+    output_path: str = "data/processed/gumu_guadalupe_burrows.csv",
+):
+    data = pd.read_csv(data_path)
+    filtered = filter_by_species_and_island(data, species, island)
+    filtered.to_csv(output_path, index=False)
+
+
+@app.command(help="Plot population trend")
+def plot_population_trend(
+    data_path: str = "",
+    intervals_path: str = "",
+    island: str = "Guadalupe",
+    variable_of_interest: str = "Maxima_cantidad_nidos",
+    output_path=None,
+):
+    fit_data = pd.read_csv(data_path)
+    with open(intervals_path, "r") as read_file:
+        intervals_json = json.load(read_file)
+    intervals = intervals_json["intervals"]
+    lambda_latex = intervals_json["lambda_latex_interval"]
+
+    Modelo_Tendencia_Poblacional = Population_Trend_Model(fit_data, intervals, variable_of_interest)
+    Graficador = Plotter_Population_Trend_Model()
+    Graficador.plot_smooth(Modelo_Tendencia_Poblacional)
+    Graficador.plot_model(Modelo_Tendencia_Poblacional)
+    Graficador.plot_data(Modelo_Tendencia_Poblacional, fit_data[variable_of_interest])
+    legend_mpl_object = Graficador.set_legend_location(island)
+    Graficador.set_x_lim(Modelo_Tendencia_Poblacional)
+    Graficador.set_y_lim(fit_data[variable_of_interest])
+    Graficador.set_labels()
+    Graficador.set_ticks(Modelo_Tendencia_Poblacional)
+    Graficador.draw()
+    Graficador.plot_growth_rate_interval(legend_mpl_object, lambda_latex)
+    Graficador.savefig(island, output_path)

population_trend/filter_data.py

@@ -0,0 +1,14 @@
+import pandas as pd
+
+
+def filter_by_species_and_island(data: pd.DataFrame, species: str, island: str):
+    filtered_by_species = filter_by_species(data, species)
+    return filter_data_by_islet(filtered_by_species, island)
+
+
+def filter_by_species(data: pd.DataFrame, species: str):
+    return data[data.Nombre_en_ingles == species]
+
+
+def filter_data_by_islet(df, islet):
+    return df[df.Isla == islet]

population_trend/population_growth_model.py

@@ -1,13 +1,9 @@
 import numpy as np
 from geci_plots import geci_plot, roundup, ticks_positions_array, order_magnitude
-from bootstrapping_tools import lambda_calculator, power_law
+from bootstrapping_tools import power_law
 import matplotlib.pyplot as plt
 
 
-def filter_data_by_islet(df, islet):
-    return df[df.Isla == islet]
-
-
 def resample_seasons(df):
     first_season = int(df.Temporada.min())
     last_season = int(df.Temporada.max())
@@ -31,19 +27,19 @@ class Population_Trend_Model:
         self.time_to_model = np.linspace(
             self.ticks_positions.min(), self.ticks_positions.max(), 100
         )
-        self.parameters = lambda_calculator(fit_data["Temporada"], fit_data[interest_variable])[1]
+        self.initial_population = fit_data[interest_variable].iloc[0]
 
     @property
     def model_min(self):
-        return power_law(self.time_to_model, self.intervals[0], self.parameters)
+        return power_law(self.time_to_model, self.intervals[0], self.initial_population)
 
     @property
     def model_med(self):
-        return power_law(self.time_to_model, self.intervals[1], self.parameters)
+        return power_law(self.time_to_model, self.intervals[1], self.initial_population)
 
     @property
     def model_max(self):
-        return power_law(self.time_to_model, self.intervals[2], self.parameters)
+        return power_law(self.time_to_model, self.intervals[2], self.initial_population)
 
 
 class Plotter_Population_Trend_Model:
@@ -117,11 +113,19 @@ class Plotter_Population_Trend_Model:
         plt.gcf().subplots_adjust(bottom=0.2)
         plt.draw()
 
-    def savefig(self, islet):
-        plt.savefig(
-            "reports/figures/cormorant_population_trend_{}".format(islet.replace(" ", "_").lower()),
-            dpi=300,
-        )
+    def savefig(self, islet, output_path=None):
+        if output_path is None:
+            plt.savefig(
+                "reports/figures/cormorant_population_trend_{}".format(
+                    islet.replace(" ", "_").lower()
+                ),
+                dpi=300,
+            )
+        else:
+            plt.savefig(
+                output_path,
+                dpi=300,
+            )
 
     def set_legend_location(self, islet):
         legend_mpl_object = plt.legend(loc="best")

{population_trend-0.1.0.dist-info → population_trend-2.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: population_trend
-Version: 0.1.0
+Version: 2.0.0
 Summary: A template Python module
 Home-page: https://github.com/IslasGECI/population_trend
 Author: Ciencia de Datos • GECI
@@ -10,6 +10,7 @@ Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Requires-Dist: bootstrapping-tools==0.5.7
 Requires-Dist: geci-plots
+Requires-Dist: typer
 
 <a href="https://www.islas.org.mx/"><img src="https://www.islas.org.mx/img/logo.svg" align="right" width="256" /></a>
 # Dummy Transformations

population_trend-2.0.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+population_trend/__init__.py,sha256=6rhCXlely23zShU26Ujo3WBjM3rSwXX5bQQhSECEtn8,163
+population_trend/cli.py,sha256=8QdnQqvozFZDXHumyaib1KC0GhAzO1n71Zwl70v9MFw,1982
+population_trend/filter_data.py,sha256=D0Y1vztcbbo98af9q7wRhlHfH__bNFI8tnVOdJY6hu0,403
+population_trend/population_growth_model.py,sha256=fNniRWuWtznAMglfKu2Yo6cpUG9lBmVhpx4RK4S0k2k,4238
+population_trend-2.0.0.dist-info/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+population_trend-2.0.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+population_trend-2.0.0.dist-info/METADATA,sha256=7gc6DZwPN1lip3IECUIRiSUyw_b71EZ0nGjf3D-T9H0,1504
+population_trend-2.0.0.dist-info/RECORD,,

population_trend-0.1.0.dist-info/RECORD

@@ -1,6 +0,0 @@
-population_trend/__init__.py,sha256=ZYSrjN0CEDVKrqHNVXUEiIR47N6st8otSCpe5ZkOv74,101
-population_trend/population_growth_model.py,sha256=u3aZus5w5xwjYBn0vRFIOTJ_P7hNJuskfUfQNt-JNOg,4122
-population_trend-0.1.0.dist-info/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-population_trend-0.1.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-population_trend-0.1.0.dist-info/METADATA,sha256=PNhfZC8zmAYzIx8OjVbXhLA9HukZuFnmupErXWkfNJE,1483
-population_trend-0.1.0.dist-info/RECORD,,