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hotfix for batch var
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jvivian committed Jun 10, 2024
1 parent 3592467 commit 386cd72
Showing 2 changed files with 78 additions and 6 deletions.
73 changes: 73 additions & 0 deletions covid19_drdfm/data/processed/test_input_2state.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
Time,Pandemic_10,Pandemic_9,Pandemic_1,Pandemic_7,State
1/1/2020,0,0,0,0,AK
2/1/2020,0,0,0,0,AK
3/1/2020,0.0058740602,0.0397350993,0.0042229655,0.0609357998,AK
4/1/2020,0.0693139098,0.0198675497,0.0024131231,0.0282916213,AK
5/1/2020,0.1379229323,0.0264900662,0.0025728151,0.0304678999,AK
6/1/2020,0.1734022556,0.0264900662,0.0108767976,0.0631120783,AK
7/1/2020,0.4814379699,0.1059602649,0.040277864,0.1828073993,AK
8/1/2020,0.313674812,0.1258278146,0.0370130504,0.204570185,AK
9/1/2020,0.1459116541,0.1125827815,0.0532484009,0.1566920566,AK
10/1/2020,0.0773026316,0.3112582781,0.1582192571,0.4243743199,AK
11/1/2020,0.155075188,0.5894039735,0.3026162868,0.752992383,AK
12/1/2020,0.5227913534,0.5033112583,0.1744191205,0.5571273123,AK
1/1/2021,1,0.178807947,0.0982904087,0.2176278564,AK
2/1/2021,0.6719924812,0.0993377483,0.0558034724,0.1523394995,AK
3/1/2021,0.2319078947,0.1125827815,0.072748565,0.2241566921,AK
4/1/2021,0.0838815789,0.0066225166,0.0778320928,0.289445049,AK
5/1/2021,0.0714285714,0.1390728477,0.0299511165,0.1284004353,AK
6/1/2021,0.0723684211,0.0529801325,0.0149666865,0.0957562568,AK
7/1/2021,0.0728383459,0.0794701987,0.0817711614,0.39390642,AK
8/1/2021,0.1268796992,0.3245033113,0.26157545,0.8019586507,AK
9/1/2021,0.2814849624,0.8278145695,0.4060079669,1,AK
10/1/2021,0.274906015,0.9470198675,0.3689594294,0.8335146899,AK
11/1/2021,0.2709116541,1,0.1806914662,0.4494015234,AK
12/1/2021,0.4515977444,0.1059602649,0.1362261238,0.2655059848,AK
1/1/2022,0.4642857143,0.2847682119,1,0.478781284,AK
2/1/2022,0.4090695489,0.5165562914,0.2854316563,0.2491838955,AK
3/1/2022,0.3106203008,0.4304635762,0.1077388504,0.1284004353,AK
4/1/2022,0.1604793233,0.1589403974,0.0940142126,0.0718171926,AK
5/1/2022,0.0817669173,0.2185430464,0.1257574279,0.1099020675,AK
6/1/2022,0.0507518797,0,0.1572433617,0.1077257889,AK
7/1/2022,0.0594454887,0.1523178808,0.1569505931,0.1088139282,AK
8/1/2022,0.0812969925,0.1920529801,0.0951143128,0.112078346,AK
9/1/2022,0.0601503759,0.1655629139,0.0211769298,0.0402611534,AK
10/1/2022,0,0,0.0135738176,0.0293797606,AK
11/1/2022,0,0,0.0134850999,0.0054406964,AK
12/1/2022,0,0,0.0121365899,0.0087051143,AK
1/1/2020,0,0,0,0,CA
2/1/2020,0,0,0,0,CA
3/1/2020,0.0058740602,0.0397350993,0.0042229655,0.0609357998,CA
4/1/2020,0.0693139098,0.0198675497,0.0024131231,0.0282916213,CA
5/1/2020,0.1379229323,0.0264900662,0.0025728151,0.0304678999,CA
6/1/2020,0.1734022556,0.0264900662,0.0108767976,0.0631120783,CA
7/1/2020,0.4814379699,0.1059602649,0.040277864,0.1828073993,CA
8/1/2020,0.313674812,0.1258278146,0.0370130504,0.204570185,CA
9/1/2020,0.1459116541,0.1125827815,0.0532484009,0.1566920566,CA
10/1/2020,0.0773026316,0.3112582781,0.1582192571,0.4243743199,CA
11/1/2020,0.155075188,0.5894039735,0.3026162868,0.752992383,CA
12/1/2020,0.5227913534,0.5033112583,0.1744191205,0.5571273123,CA
1/1/2021,1,0.178807947,0.0982904087,0.2176278564,CA
2/1/2021,0.6719924812,0.0993377483,0.0558034724,0.1523394995,CA
3/1/2021,0.2319078947,0.1125827815,0.072748565,0.2241566921,CA
4/1/2021,0.0838815789,0.0066225166,0.0778320928,0.289445049,CA
5/1/2021,0.0714285714,0.1390728477,0.0299511165,0.1284004353,CA
6/1/2021,0.0723684211,0.0529801325,0.0149666865,0.0957562568,CA
7/1/2021,0.0728383459,0.0794701987,0.0817711614,0.39390642,CA
8/1/2021,0.1268796992,0.3245033113,0.26157545,0.8019586507,CA
9/1/2021,0.2814849624,0.8278145695,0.4060079669,1,CA
10/1/2021,0.274906015,0.9470198675,0.3689594294,0.8335146899,CA
11/1/2021,0.2709116541,1,0.1806914662,0.4494015234,CA
12/1/2021,0.4515977444,0.1059602649,0.1362261238,0.2655059848,CA
1/1/2022,0.4642857143,0.2847682119,1,0.478781284,CA
2/1/2022,0.4090695489,0.5165562914,0.2854316563,0.2491838955,CA
3/1/2022,0.3106203008,0.4304635762,0.1077388504,0.1284004353,CA
4/1/2022,0.1604793233,0.1589403974,0.0940142126,0.0718171926,CA
5/1/2022,0.0817669173,0.2185430464,0.1257574279,0.1099020675,CA
6/1/2022,0.0507518797,0,0.1572433617,0.1077257889,CA
7/1/2022,0.0594454887,0.1523178808,0.1569505931,0.1088139282,CA
8/1/2022,0.0812969925,0.1920529801,0.0951143128,0.112078346,CA
9/1/2022,0.0601503759,0.1655629139,0.0211769298,0.0402611534,CA
10/1/2022,0,0,0.0135738176,0.0293797606,CA
11/1/2022,0,0,0.0134850999,0.0054406964,CA
12/1/2022,0,0,0.0121365899,0.0087051143,CA
11 changes: 5 additions & 6 deletions covid19_drdfm/streamlit/pages/0_Dynamic_Factor_Model.py
Original file line number Diff line number Diff line change
@@ -51,10 +51,10 @@ def file_uploader(self) -> "DataHandler":
if self.df is None:
st.error("DataFrame is empty! Check input data")
st.stop()
batch_col = st.sidebar.selectbox("Select a batch column (optional):", ["None", *list(self.df.columns)])
if batch_col == "None":
self.batch_col = st.sidebar.selectbox("Select a batch column (optional):", ["None", *list(self.df.columns)])
if self.batch_col == "None":
self.batch_col = None
self.non_batch_cols = [col for col in self.df.columns if col != batch_col]
self.non_batch_cols = [col for col in self.df.columns if col != self.batch_col]
return self

@staticmethod
@@ -137,12 +137,11 @@ def create_anndata(self) -> ann.AnnData:
An AnnData object with additional metadata.
"""
if self.batch_col and self.batch_col in self.df.columns:
ad = ann.AnnData(self.df.drop(columns=self.batch_col))
ad = ann.AnnData(self.df.drop(columns=[self.batch_col]))
ad.obs[self.batch_col] = self.df[self.batch_col]
else:
ad = ann.AnnData(self.df)

ad.var["factor"] = [self.factor_mappings[x] for x in ad.var.index]
ad.var["factor"] = [self.factor_mappings[x] for x in self.non_batch_cols]
self.ad = ad
return ad

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