bdext 0.1.62__py3-none-any.whl → 0.1.64__py3-none-any.whl

bdeissct_dl/bdeissct_model.py

@@ -7,7 +7,6 @@ RHO = 'rho'
 INFECTIOUS_TIME = 'd_I'
 REPRODUCTIVE_NUMBER = 'R'
 INFECTION_DURATION = 'd'
-SAMPLING_FRACTION = 'p'
 
 F_E = 'f_E'
 MU = 'mu'
@@ -129,5 +128,5 @@ for model in (BDEISSCT, BDEISSCT1, BDEISSCT2, BDEISSCT2000):
 
 
 
-CT_EPI_COLUMNS = [REPRODUCTIVE_NUMBER, INFECTION_DURATION, SAMPLING_FRACTION, LA, F_E, F_S, X_S, UPSILON, X_C]
-CT_RATE_COLUMNS = [PSI, RHO]
+CT_EPI_COLUMNS = [REPRODUCTIVE_NUMBER, LA, F_E, F_S, X_S, UPSILON, X_C]
+CT_RATE_COLUMNS = [PSI]

bdeissct_dl/scaler_fitting.py

@@ -11,12 +11,11 @@ from bdeissct_dl.training import get_data_characteristics
 
 
 def fit_scalers(paths, x_indices, scaler_x=None):
-    # First pass: calculate mean and var
-    for path in paths:
+   for path in paths:
         df = pd.read_csv(path)
         if scaler_x:
             X = df.iloc[:, x_indices].to_numpy(dtype=float, na_value=0)
-            scaler_x.partial_fit(X)
+            scaler_x.fit(X)
 
 
 def main():

bdeissct_dl/train_ct.py

@@ -74,8 +74,8 @@ def main():
 
     os.makedirs(params.model_path, exist_ok=True)
 
-    # R,d,p,f_E,f_S,X_S,upsilon,X_C,kappa,la are given
-    # psi,rho are to be predicted
+    # R,f_E,f_S,X_S,upsilon,X_C,kappa,la are given
+    # psi is to be predicted
 
     feature_columns = CT_EPI_COLUMNS
     target_columns = CT_RATE_COLUMNS
@@ -87,8 +87,8 @@ def main():
 
 
     x_indices, y_col2index = get_data_characteristics(paths=params.train_data,
-                                                                 feature_columns=feature_columns,
-                                                                 target_columns=target_columns)
+                                                      feature_columns=feature_columns,
+                                                      target_columns=target_columns)
 
     scaler_x = StandardScaler()
     fit_scalers(paths=params.train_data, x_indices=x_indices, scaler_x=scaler_x)

{bdext-0.1.62.dist-info → bdext-0.1.64.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bdext
-Version: 0.1.62
+Version: 0.1.64
 Summary: Estimation of BDEISS-CT parameters from phylogenetic trees.
 Home-page: https://github.com/modpath/bdeissct
 Author: Anna Zhukova

{bdext-0.1.62.dist-info → bdext-0.1.64.dist-info}/RECORD

@@ -1,6 +1,6 @@
 README.md,sha256=Fk-VeZXo2zltZ9NXdFnnHS3ETwtiBPRiZ86ttUQUgTE,5894
 bdeissct_dl/__init__.py,sha256=glAW73vlD9Abbb_Fto-sKys078qVEn5iTcx2Mq3Z72s,361
-bdeissct_dl/bdeissct_model.py,sha256=--dnDxvvWcFb45bKIGv8-GUAcSnXA_x6p4D9MFsyXPk,3566
+bdeissct_dl/bdeissct_model.py,sha256=gbrP9IHtgqrpu48YLZqquqnjBSGqwr5VzxlePGk1L_M,3498
 bdeissct_dl/dl_model.py,sha256=q8RFbbd2n52Y0_HMKSEHdIgBouE4LbHL5CZO3M_3G3E,7364
 bdeissct_dl/estimator.py,sha256=UIQAy62I0_2HKagfck9WBGbbHU6l_WfRypP9CyeHrFE,7313
 bdeissct_dl/estimator_ct.py,sha256=P5Up-NnAYS2Nen5_KPEYP04VXr5hm1Dtjq5TuW5OHjM,2604
@@ -8,15 +8,15 @@ bdeissct_dl/main_covid.py,sha256=wCeJgc4XzEPjcVCaQt_-zGiVX0wdpQhFq2qh9xQzc7w,288
 bdeissct_dl/model_finder.py,sha256=TC6EcIE6rBO6PefaYfn2reEl6HPkORbIgTzQGsDoXcU,1763
 bdeissct_dl/model_serializer.py,sha256=Ojhy-fUElc4NClhJaF0EWnrAJGK0omk8e7cwwrBk3Yk,3768
 bdeissct_dl/pinball_loss.py,sha256=Xg2jFDlwPOt0AhBY574lWB0yRyuA0bQRiyOYHGL6P54,1602
-bdeissct_dl/scaler_fitting.py,sha256=SdU9DHj9JUAONfbcIfrvK5OYgzcwHlbVQP2rJknF8tQ,1975
+bdeissct_dl/scaler_fitting.py,sha256=ekaokmRFmZIInNylaCV5oQznpLKnRwNVAvaSyud3iSk,1925
 bdeissct_dl/sumstat_checker.py,sha256=BHMgoqjymHc3Ic-Sv7m-zuvCeLlCt4OCDVaKDltSII0,1867
-bdeissct_dl/train_ct.py,sha256=AYhotLFlb_OIoUQzir6SrvCmI1p0FhemjWkdNz0dkTQ,5392
+bdeissct_dl/train_ct.py,sha256=nog5l_VN1hUfMxma8U4faHcki4NdFYUXcbDxBvJVhOs,5361
 bdeissct_dl/training.py,sha256=QBjly8e_8yqvxDbHGPw0F4LeL8BbA6UQ8SANFc0NCYY,8990
 bdeissct_dl/tree_encoder.py,sha256=WrrSk_HXOF_rAKHpU7u9_i_gCmp5tz7Tk_Jvbwx0N_g,19193
 bdeissct_dl/tree_manager.py,sha256=UXxUVmEkxwUhKpJeACVgiXZ8Kp1o_hiv8Qb80b6qmVU,11814
-bdext-0.1.62.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-bdext-0.1.62.dist-info/METADATA,sha256=FclgIK27gkWC1nDGO2Pw-Ym-kCTGgMqVFtqZAu1iAlo,6834
-bdext-0.1.62.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
-bdext-0.1.62.dist-info/entry_points.txt,sha256=En4b5js0-eCuBp0Jiqye0fte6svXbXSLiSJOW_KdzV4,286
-bdext-0.1.62.dist-info/top_level.txt,sha256=z4dadFfcLghr4lwROy7QR3zEICpa-eCPT6mmcoHeEJY,12
-bdext-0.1.62.dist-info/RECORD,,
+bdext-0.1.64.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+bdext-0.1.64.dist-info/METADATA,sha256=9Wt_UFvFcgz8LiSiH-8vKFQdQl4TYpX_-9h7uYHcyCY,6834
+bdext-0.1.64.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+bdext-0.1.64.dist-info/entry_points.txt,sha256=En4b5js0-eCuBp0Jiqye0fte6svXbXSLiSJOW_KdzV4,286
+bdext-0.1.64.dist-info/top_level.txt,sha256=z4dadFfcLghr4lwROy7QR3zEICpa-eCPT6mmcoHeEJY,12
+bdext-0.1.64.dist-info/RECORD,,