Hurdle model in AdaSTEM¶

Yangkang Chen
Jan 12, 2024

This notebook is to discuss the pros and cons of two different AdaSTEM modeling framework: Hurdle in AdaSTEM and AdaSTEM in Hurdle.

To recap the content here (If you don't know what is hurdle model please read this), if the task is to predict abundance, there are two ways to leverage the hurdle model.

1. First, hurdle in AdaSTEM: one can use hurdle model in each AdaSTEM (regressor) stixel;

That is:

Model_Hurdle_in_Ada = AdaSTEMRegressor(
   base_model=Hurdle(
       classifier=XGBClassifier(...),
       regressor=XGBRegressor(...)
   ),  
   ...
)

2. Second, AdaSTEM in hurdle: one can use AdaSTEMClassifier as the classifier of the hurdle model, and AdaSTEMRegressor as the regressor of the hurdle model.

That is:

model_Ada_in_Hurdle = Hurdle_for_AdaSTEM(
   classifier=AdaSTEMClassifier(
       base_model=XGBClassifier(...),
       ...),
   regressor=AdaSTEMRegressor(
       base_model=XGBRegressor(...),
       ...)
)

In the first case, the classifier and regressor "talk" to each other in each separate stixel (hereafter, "hurdle in Ada"); In the second case, the classifiers and regressors form two "unions" separately, and these two unions only "talk" to each other at the final combination, instead of in each stixel (hereafter, "Ada in hurdle"). This is a common practice in most paper I've seen, including reference [1-3].

The conclusion goes first:
We recommend users to always use Hurdle model as base model of AdaSTEMRegressor (Hurdle in Ada)

In [2]:

import pandas as pd
import numpy as np
import random
from tqdm.auto import tqdm
import matplotlib.pyplot as plt
import matplotlib
import warnings
import pickle
import os

from stemflow.model.AdaSTEM import AdaSTEM, AdaSTEMClassifier, AdaSTEMRegressor
from xgboost import XGBClassifier, XGBRegressor # remember to install xgboost if you use it as base model
from stemflow.model.Hurdle import Hurdle_for_AdaSTEM, Hurdle
from stemflow.model_selection import ST_CV

# warnings.filterwarnings('ignore')
%matplotlib inline

import pandas as pd import numpy as np import random from tqdm.auto import tqdm import matplotlib.pyplot as plt import matplotlib import warnings import pickle import os from stemflow.model.AdaSTEM import AdaSTEM, AdaSTEMClassifier, AdaSTEMRegressor from xgboost import XGBClassifier, XGBRegressor # remember to install xgboost if you use it as base model from stemflow.model.Hurdle import Hurdle_for_AdaSTEM, Hurdle from stemflow.model_selection import ST_CV # warnings.filterwarnings('ignore') %matplotlib inline

In [3]:

%load_ext autoreload
%autoreload 2

%load_ext autoreload %autoreload 2

Download data¶

Please download the sample data from:

• Mallard: https://figshare.com/articles/dataset/Sample_data_Mallard_csv/24080745
  

Suppose now it's downloaded and saved as './Sample_data_Mallard.csv'

Alternatively, you can try other species like

• Alder Flycatcher: https://figshare.com/articles/dataset/Sample_data_Alder_Flycatcher_csv/24080751
  
• Short-eared Owl: https://figshare.com/articles/dataset/Sample_data_Short-eared_Owl_csv/24080742
  
• Eurasian Tree Sparrow: https://figshare.com/articles/dataset/Sample_data_Eurasian_Tree_Sparrow_csv/24080748
  

Caveat: These bird observation data are about 200MB each file.

Load data¶

In [4]:

data = pd.read_csv(f'./Sample_data_Mallard.csv')
data = data.drop('sampling_event_identifier', axis=1)

data = pd.read_csv(f'./Sample_data_Mallard.csv') data = data.drop('sampling_event_identifier', axis=1)

In [5]:

data.head()

data.head()

Out[5]:

	longitude	latitude	count	DOY	duration_minutes	Traveling	Stationary	Area	effort_distance_km	number_observers	obsvr_species_count	time_observation_started_minute_of_day	elevation_mean	slope_mean	eastness_mean	northness_mean	bio1	bio2	bio3	bio4	bio5	bio6	bio7	bio8	bio9	bio10	bio11	bio12	bio13	bio14	bio15	bio16	bio17	bio18	bio19	closed_shrublands	cropland_or_natural_vegetation_mosaics	croplands	deciduous_broadleaf_forests	deciduous_needleleaf_forests	evergreen_broadleaf_forests	evergreen_needleleaf_forests	grasslands	mixed_forests	non_vegetated_lands	open_shrublands	permanent_wetlands	savannas	urban_and_built_up_lands	water_bodies	woody_savannas	entropy
0	-83.472224	8.859308	0.0	22	300.0	1	0	0	4.828	5.0	34.0	476	7.555556	0.758156	0.036083	-0.021484	24.883502	5.174890	59.628088	93.482247	30.529131	21.850519	8.678612	24.302626	26.536822	26.213334	23.864924	0.720487	0.127594	0.003156	0.001451	0.332425	0.026401	0.044218	0.260672	0.0	0.000000	0.0	0.0	0.0	0.138889	0.000000	0.000000	0.000000	0.0	0.0	0.777778	0.000000	0.000000	0.083333	0.000000	0.676720
1	-2.687724	43.373323	9.0	290	90.0	1	0	0	0.570	2.0	151.0	1075	30.833336	3.376527	0.050544	-0.099299	14.107917	5.224109	31.174167	376.543853	23.219421	6.461607	16.757814	9.048385	19.092725	19.236082	9.287841	0.171423	0.035598	0.004512	0.000081	0.084657	0.018400	0.030210	0.065007	0.0	0.000000	0.0	0.0	0.0	0.333333	0.000000	0.000000	0.083333	0.0	0.0	0.000000	0.194444	0.027778	0.000000	0.361111	1.359063
2	-89.884770	35.087255	0.0	141	10.0	0	1	0	-1.000	2.0	678.0	575	91.777780	0.558100	-0.187924	-0.269078	17.396487	8.673912	28.688889	718.996078	32.948335	2.713938	30.234397	14.741099	13.759220	26.795849	7.747272	0.187089	0.031802	0.005878	0.000044	0.073328	0.026618	0.039616	0.059673	0.0	0.055556	0.0	0.0	0.0	0.000000	0.000000	0.305556	0.000000	0.0	0.0	0.000000	0.527778	0.000000	0.000000	0.111111	1.104278
3	-99.216873	31.218510	0.0	104	9.0	1	0	0	0.805	2.0	976.0	657	553.166700	0.856235	-0.347514	-0.342971	20.740836	10.665164	35.409121	666.796919	35.909941	5.790119	30.119822	18.444353	30.734456	29.546417	11.701038	0.084375	0.025289	0.000791	0.000052	0.052866	0.004096	0.006064	0.015965	0.0	0.000000	0.0	0.0	0.0	0.000000	0.000000	1.000000	0.000000	0.0	0.0	0.000000	0.000000	0.000000	0.000000	0.000000	-0.000000
4	-124.426730	43.065847	2.0	96	30.0	1	0	0	0.161	2.0	654.0	600	6.500000	0.491816	-0.347794	-0.007017	11.822340	6.766870	35.672897	396.157833	22.608788	3.639569	18.969219	8.184412	16.290802	17.258721	7.319234	0.144122	0.044062	0.000211	0.000147	0.089238	0.004435	0.004822	0.040621	0.0	0.000000	0.0	0.0	0.0	0.361111	0.166667	0.000000	0.472222	0.0	0.0	0.000000	0.000000	0.000000	0.000000	0.000000	1.020754

Get X and y¶

In [5]:

X = data.drop('count', axis=1)
y = data['count'].values

X = data.drop('count', axis=1) y = data['count'].values

First thing first: Spatio-temporal train test split¶

In [6]:

CV = 5
CV_generator = ST_CV(X, y, 
                    Spatio_blocks_count = 50, Temporal_blocks_count=50,
                    random_state=42, CV=CV)

CV = 5 CV_generator = ST_CV(X, y, Spatio_blocks_count = 50, Temporal_blocks_count=50, random_state=42, CV=CV)

For more discussion on parameters please see AdaSTEM demo.

Train Hurdle in AdaSTEM¶

Now, we use the recommended model structure: Hurdle model as base model of AdaSTEM framework:

In [8]:

model_hurdle_in_Ada = AdaSTEMRegressor(
    base_model=Hurdle(
        classifier=XGBClassifier(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1),
        regressor=XGBRegressor(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1)
    ),
    save_gridding_plot = True,
    ensemble_fold=10, 
    min_ensemble_required=7,
    grid_len_upper_threshold=25,
    grid_len_lower_threshold=5,
    points_lower_threshold=50,
    Spatio1='longitude',
    Spatio2 = 'latitude', 
    Temporal1 = 'DOY',
    use_temporal_to_train=True,
    n_jobs=4                       
)

model_hurdle_in_Ada = AdaSTEMRegressor( base_model=Hurdle( classifier=XGBClassifier(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1), regressor=XGBRegressor(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1) ), save_gridding_plot = True, ensemble_fold=10, min_ensemble_required=7, grid_len_upper_threshold=25, grid_len_lower_threshold=5, points_lower_threshold=50, Spatio1='longitude', Spatio2 = 'latitude', Temporal1 = 'DOY', use_temporal_to_train=True, n_jobs=4 )

For more discussion on parameters please see AdaSTEM demo and Optimizing stixel size.

We train and evaluate the model for each CV partition, and plot the charts:

In [9]:

metric_dict_list = []
for X_train, X_test, y_train, y_test in tqdm(CV_generator, total=CV):
    ## fit model
    model_hurdle_in_Ada.fit(X_train, y_train, verbosity=0)
    ## predict on test set
    pred_hurdle_in_Ada = model_hurdle_in_Ada.predict(X_test, verbosity=0)
    pred_hurdle_in_Ada = np.where(pred_hurdle_in_Ada<0, 0, pred_hurdle_in_Ada)
    ## calculate metrics
    metrics_hurdle_in_Ada= AdaSTEM.eval_STEM_res('hurdle', y_test.flatten(), pred_hurdle_in_Ada.flatten())
    metric_dict_list.append(metrics_hurdle_in_Ada)
    
    # plot
    a = pd.DataFrame({
        'y_true':y_test.flatten(),
        'y_pred':pred_hurdle_in_Ada.flatten()
    }).dropna()
    plt.scatter(np.log(a.y_true+1), np.log(a.y_pred+1), s=0.2)
    plt.plot([0,np.log(a.y_pred+1).max()],[0,np.log(a.y_pred+1).max()], c='red')
    plt.show()

metric_dict_list = [] for X_train, X_test, y_train, y_test in tqdm(CV_generator, total=CV): ## fit model model_hurdle_in_Ada.fit(X_train, y_train, verbosity=0) ## predict on test set pred_hurdle_in_Ada = model_hurdle_in_Ada.predict(X_test, verbosity=0) pred_hurdle_in_Ada = np.where(pred_hurdle_in_Ada<0, 0, pred_hurdle_in_Ada) ## calculate metrics metrics_hurdle_in_Ada= AdaSTEM.eval_STEM_res('hurdle', y_test.flatten(), pred_hurdle_in_Ada.flatten()) metric_dict_list.append(metrics_hurdle_in_Ada) # plot a = pd.DataFrame({ 'y_true':y_test.flatten(), 'y_pred':pred_hurdle_in_Ada.flatten() }).dropna() plt.scatter(np.log(a.y_true+1), np.log(a.y_pred+1), s=0.2) plt.plot([0,np.log(a.y_pred+1).max()],[0,np.log(a.y_pred+1).max()], c='red') plt.show()

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Save the metrics for later plotting:

In [10]:

hurdle_in_Ada_metrics = pd.DataFrame(metric_dict_list)
hurdle_in_Ada_metrics

hurdle_in_Ada_metrics = pd.DataFrame(metric_dict_list) hurdle_in_Ada_metrics

Out[10]:

	AUC	kappa	f1	precision	recall	average_precision	Spearman_r	Pearson_r	R2	MAE	MSE	poisson_deviance_explained
0	0.776556	0.399602	0.533535	0.402644	0.790514	0.353562	0.486733	0.228122	0.004291	4.060732	1547.538014	0.163586
1	0.763234	0.378516	0.519680	0.390772	0.775506	0.341389	0.466746	0.200849	-0.006095	4.367535	1690.584790	0.166015
2	0.766110	0.384527	0.528265	0.397766	0.786202	0.350321	0.476049	0.212550	-0.686252	4.488267	1561.115758	0.188853
3	0.766000	0.386848	0.525204	0.397605	0.773404	0.346218	0.469835	0.158039	-0.091035	4.305906	1755.312096	0.173555
4	0.766309	0.381845	0.526306	0.394553	0.790164	0.348524	0.474678	0.107553	0.010033	4.417231	9685.441546	0.161657

In [11]:

hurdle_in_Ada_metrics.to_csv('./hurdle_in_Ada_metrics.csv', index=False)

hurdle_in_Ada_metrics.to_csv('./hurdle_in_Ada_metrics.csv', index=False)

Train AdaSTEM in Hurdle¶

Likewise, we also train models that using AdaSTEM as regressor and classifier for a single hurdle model:

In [8]:

model_Ada_in_Hurdle = Hurdle_for_AdaSTEM(
    classifier=AdaSTEMClassifier(base_model=XGBClassifier(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1),
                                save_gridding_plot = True,
                                ensemble_fold=10, 
                                min_ensemble_required=7,
                                grid_len_upper_threshold=25,
                                grid_len_lower_threshold=5,
                                points_lower_threshold=50,
                                Spatio1='longitude',
                                Spatio2 = 'latitude', 
                                Temporal1 = 'DOY',
                                use_temporal_to_train=True,
                                n_jobs=4),
    regressor=AdaSTEMRegressor(base_model=XGBRegressor(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1),
                                save_gridding_plot = True,
                                ensemble_fold=10, 
                                min_ensemble_required=7,
                                grid_len_upper_threshold=25,
                                grid_len_lower_threshold=5,
                                points_lower_threshold=50,
                                Spatio1='longitude',
                                Spatio2 = 'latitude', 
                                Temporal1 = 'DOY',
                                use_temporal_to_train=True,
                                n_jobs=4)
)

model_Ada_in_Hurdle = Hurdle_for_AdaSTEM( classifier=AdaSTEMClassifier(base_model=XGBClassifier(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1), save_gridding_plot = True, ensemble_fold=10, min_ensemble_required=7, grid_len_upper_threshold=25, grid_len_lower_threshold=5, points_lower_threshold=50, Spatio1='longitude', Spatio2 = 'latitude', Temporal1 = 'DOY', use_temporal_to_train=True, n_jobs=4), regressor=AdaSTEMRegressor(base_model=XGBRegressor(tree_method='hist',random_state=42, verbosity = 0, n_jobs=1), save_gridding_plot = True, ensemble_fold=10, min_ensemble_required=7, grid_len_upper_threshold=25, grid_len_lower_threshold=5, points_lower_threshold=50, Spatio1='longitude', Spatio2 = 'latitude', Temporal1 = 'DOY', use_temporal_to_train=True, n_jobs=4) )

The evaluation is also conducted for each CV partition:

In [10]:

CV_generator = ST_CV(X, y, 
                    Spatio_blocks_count = 50, Temporal_blocks_count=50,
                    random_state=42, CV=CV)


metric_dict_list = []
for X_train, X_test, y_train, y_test in tqdm(CV_generator, total=CV):
    ## fit model
    model_Ada_in_Hurdle.fit(X_train, y_train, verbosity=0)
    ## predict on test set
    pred_Ada_in_Hurdle = model_Ada_in_Hurdle.predict(X_test, verbosity=0)
    pred_Ada_in_Hurdle = np.where(pred_Ada_in_Hurdle<0, 0, pred_Ada_in_Hurdle)
    
    ## calculate metrics
    metrics_Ada_in_Hurdle= AdaSTEM.eval_STEM_res('hurdle', y_test.flatten(), pred_Ada_in_Hurdle.flatten())
    metric_dict_list.append(metrics_Ada_in_Hurdle)
    
    # plot
    a = pd.DataFrame({
        'y_true':y_test.flatten(),
        'y_pred':pred_Ada_in_Hurdle.flatten()
    }).dropna()
    plt.scatter(np.log(a.y_true+1), np.log(a.y_pred+1), s=0.2)
    plt.plot([0,np.log(a.y_pred+1).max()],[0,np.log(a.y_pred+1).max()], c='red')
    plt.show()

CV_generator = ST_CV(X, y, Spatio_blocks_count = 50, Temporal_blocks_count=50, random_state=42, CV=CV) metric_dict_list = [] for X_train, X_test, y_train, y_test in tqdm(CV_generator, total=CV): ## fit model model_Ada_in_Hurdle.fit(X_train, y_train, verbosity=0) ## predict on test set pred_Ada_in_Hurdle = model_Ada_in_Hurdle.predict(X_test, verbosity=0) pred_Ada_in_Hurdle = np.where(pred_Ada_in_Hurdle<0, 0, pred_Ada_in_Hurdle) ## calculate metrics metrics_Ada_in_Hurdle= AdaSTEM.eval_STEM_res('hurdle', y_test.flatten(), pred_Ada_in_Hurdle.flatten()) metric_dict_list.append(metrics_Ada_in_Hurdle) # plot a = pd.DataFrame({ 'y_true':y_test.flatten(), 'y_pred':pred_Ada_in_Hurdle.flatten() }).dropna() plt.scatter(np.log(a.y_true+1), np.log(a.y_pred+1), s=0.2) plt.plot([0,np.log(a.y_pred+1).max()],[0,np.log(a.y_pred+1).max()], c='red') plt.show()

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In [11]:

Ada_in_hurdle_metrics = pd.DataFrame(metric_dict_list)
Ada_in_hurdle_metrics

Ada_in_hurdle_metrics = pd.DataFrame(metric_dict_list) Ada_in_hurdle_metrics

Out[11]:

	AUC	kappa	f1	precision	recall	average_precision	Spearman_r	Pearson_r	R2	MAE	MSE	poisson_deviance_explained
0	0.697080	0.441068	0.519759	0.613785	0.450714	0.367964	0.458361	0.141498	-0.061558	3.993602	1541.766283	0.142712
1	0.680297	0.412394	0.493349	0.607135	0.415482	0.351356	0.432512	0.138424	-0.138857	4.550810	1919.024133	0.121617
2	0.690239	0.426277	0.510518	0.606079	0.440988	0.364719	0.444202	0.266970	-0.431011	4.352729	1226.860455	0.228450
3	0.684105	0.418367	0.499448	0.607101	0.424224	0.355112	0.435636	0.114824	-0.209990	4.320640	1940.877595	0.157750
4	0.688389	0.424938	0.507825	0.609872	0.435032	0.363110	0.444321	0.097006	0.004345	4.393659	9567.505443	0.252556

In [12]:

Ada_in_hurdle_metrics.to_csv('./Ada_in_hurdle_metrics.csv', index=False)

Ada_in_hurdle_metrics.to_csv('./Ada_in_hurdle_metrics.csv', index=False)

Compare the two model structures¶

We have collected evaluation metrics for both Hurdle in Ada and Ada in Hurdle framework. We will now plot them:

In [13]:

hurdle_in_Ada_metrics = pd.read_csv('./hurdle_in_Ada_metrics.csv')
Ada_in_hurdle_metrics = pd.read_csv('./Ada_in_hurdle_metrics.csv')

hurdle_in_Ada_metrics = pd.read_csv('./hurdle_in_Ada_metrics.csv') Ada_in_hurdle_metrics = pd.read_csv('./Ada_in_hurdle_metrics.csv')

In [49]:

import seaborn as sns
hurdle_in_Ada_metrics['model'] = 'hurdle_in_Ada'
Ada_in_hurdle_metrics['model'] = 'Ada_in_hurdle'
new_dat = pd.concat([hurdle_in_Ada_metrics, Ada_in_hurdle_metrics], axis=0)
dat_for_plot = []
for index,row in new_dat.iterrows():
    for metric_name in ['AUC', 'kappa', 'f1', 'precision', 'recall', 'average_precision',
                        'Spearman_r', 'Pearson_r', 'R2', 'MAE', 'MSE', 'poisson_deviance_explained']:
        dat_for_plot.append({
            'model':row['model'],
            'metric_name':metric_name,
            'value':row[metric_name]
        })
        
dat_for_plot = pd.DataFrame(dat_for_plot)

# plot
fig, ax = plt.subplots(1, 4, figsize=(20,6), gridspec_kw={'width_ratios': [3, 3, 1, 1]})

### classification
plt.sca(ax[0])
sns.barplot(data=dat_for_plot[
        dat_for_plot.metric_name.isin(['AUC', 'kappa', 'f1', 'precision', 'recall', 'average_precision'])
    ], ci=95, 
            x="metric_name", y="value", hue="model")
plt.title('Model performance Classification')

## reg
plt.sca(ax[1])
sns.barplot(data=dat_for_plot[
        dat_for_plot.metric_name.isin(['Spearman_r', 'Pearson_r', 'R2', 'poisson_deviance_explained'])
    ], ci=95, 
            x="metric_name", y="value", hue="model")
plt.title('Model performance Regression')

## reg
plt.sca(ax[2])
sns.barplot(data=dat_for_plot[
        dat_for_plot.metric_name.isin(['MAE'])
    ], ci=95, 
            x="metric_name", y="value", hue="model")
plt.title('Model performance Regression')


## reg
plt.sca(ax[3])
sns.barplot(data=dat_for_plot[
        dat_for_plot.metric_name.isin(['MSE'])
    ], ci=95, 
            x="metric_name", y="value", hue="model")
plt.title('Model performance Regression')
# plt.legend(bbox_to_anchor=(1,1))

plt.tight_layout()
plt.show()

import seaborn as sns hurdle_in_Ada_metrics['model'] = 'hurdle_in_Ada' Ada_in_hurdle_metrics['model'] = 'Ada_in_hurdle' new_dat = pd.concat([hurdle_in_Ada_metrics, Ada_in_hurdle_metrics], axis=0) dat_for_plot = [] for index,row in new_dat.iterrows(): for metric_name in ['AUC', 'kappa', 'f1', 'precision', 'recall', 'average_precision', 'Spearman_r', 'Pearson_r', 'R2', 'MAE', 'MSE', 'poisson_deviance_explained']: dat_for_plot.append({ 'model':row['model'], 'metric_name':metric_name, 'value':row[metric_name] }) dat_for_plot = pd.DataFrame(dat_for_plot) # plot fig, ax = plt.subplots(1, 4, figsize=(20,6), gridspec_kw={'width_ratios': [3, 3, 1, 1]}) ### classification plt.sca(ax[0]) sns.barplot(data=dat_for_plot[ dat_for_plot.metric_name.isin(['AUC', 'kappa', 'f1', 'precision', 'recall', 'average_precision']) ], ci=95, x="metric_name", y="value", hue="model") plt.title('Model performance Classification') ## reg plt.sca(ax[1]) sns.barplot(data=dat_for_plot[ dat_for_plot.metric_name.isin(['Spearman_r', 'Pearson_r', 'R2', 'poisson_deviance_explained']) ], ci=95, x="metric_name", y="value", hue="model") plt.title('Model performance Regression') ## reg plt.sca(ax[2]) sns.barplot(data=dat_for_plot[ dat_for_plot.metric_name.isin(['MAE']) ], ci=95, x="metric_name", y="value", hue="model") plt.title('Model performance Regression') ## reg plt.sca(ax[3]) sns.barplot(data=dat_for_plot[ dat_for_plot.metric_name.isin(['MSE']) ], ci=95, x="metric_name", y="value", hue="model") plt.title('Model performance Regression') # plt.legend(bbox_to_anchor=(1,1)) plt.tight_layout() plt.show()

We show that:

1. For classification, "Hurdle in Ada" (the one in Johnston, 2015) shows better performance than "Ada in Hurdle" in terms of AUC, F1, and recall, while worse in kappa, precision, and average precision. This shold indicate that hurdle in ada is the choice if you care about occurence in SDM. Recall is more important than precision for the nature of species distribution modeling is to find suitable habitat, and for the fact that imperfect detections are common in observational data.

2. For regression (actually measuring a combination of regression and classification), there is no significant differences for these two modeling methods, except for that "Hurdle in Ada" shows higher spearman's r value.

Inconclusion, using hurdle model as AdaSTEM base model should be the choice for abundance modeling.

In [50]:

from watermark import watermark
print(watermark())
print(watermark(packages="stemflow,numpy,scipy,pandas,xgboost,tqdm,matplotlib,h3pandas,geopandas,scikit-learn"))

from watermark import watermark print(watermark()) print(watermark(packages="stemflow,numpy,scipy,pandas,xgboost,tqdm,matplotlib,h3pandas,geopandas,scikit-learn"))

Last updated: 2023-09-19T13:28:59.670936+08:00

Python implementation: CPython
Python version       : 3.9.7
IPython version      : 8.14.0

Compiler    : Clang 11.1.0 
OS          : Darwin
Release     : 21.6.0
Machine     : arm64
Processor   : arm
CPU cores   : 8
Architecture: 64bit

stemflow    : 0.0.24
numpy       : 1.24.3
scipy       : 1.10.1
pandas      : 2.0.3
xgboost     : 1.7.6
tqdm        : 4.65.0
matplotlib  : 3.7.1
h3pandas    : 0.2.4
geopandas   : 0.11.1
scikit-learn: 0.0

References:

1. Fink, D., Damoulas, T., & Dave, J. (2013, June). Adaptive Spatio-Temporal Exploratory Models: Hemisphere-wide species distributions from massively crowdsourced eBird data. In Proceedings of the AAAI Conference on Artificial Intelligence (Vol. 27, No. 1, pp. 1284-1290).

2. Fink, D., Auer, T., Johnston, A., Ruiz‐Gutierrez, V., Hochachka, W. M., & Kelling, S. (2020). Modeling avian full annual cycle distribution and population trends with citizen science data. Ecological Applications, 30(3), e02056.

3. Johnston, A., Fink, D., Reynolds, M. D., Hochachka, W. M., Sullivan, B. L., Bruns, N. E., ... & Kelling, S. (2015). Abundance models improve spatial and temporal prioritization of conservation resources. Ecological Applications, 25(7), 1749-1756.

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