speed up pandas calculation

Mark Lawrence breamoreboy at yahoo.co.uk
Thu Jul 31 01:29:56 CEST 2014


On 31/07/2014 00:04, Vincent Davis wrote:
> I know this is a general python list and I am asking about pandas but
> this question is probably not great for asking on stackoverflow.
> I have a list of files (~80 files, ~30,000 rows) I need to process with
> my current code it is take minutes for each file. Any suggestions of a
> fast way. I am try to stick with pandas for educational purposes. Any
> suggestions would be great. If you are curious the can find the data
> file I am using below here.
> http://www.nber.org/nhamcs/data/nhamcsopd2010.csv
>
> drugs_current = {'CITALOPRAM': 4332,
>           'ESCITALOPRAM': 4812,
>           'FLUOXETINE': 236,
>           'FLUVOXAMINE': 3804,
>           'PAROXETINE': 3157,
>           'SERTRALINE': 880,
>           'METHYLPHENIDATE': 900,
>           'DEXMETHYLPHENIDATE': 4777,
>           'AMPHETAMINE-DEXTROAMPHETAMINE': 4035,
>           'DEXTROAMPHETAMINE': 804,
>           'LISDEXAMFETAMINE': 6663,
>           'METHAMPHETAMINE': 805,
>           'ATOMOXETINE': 4827,
>           'CLONIDINE': 44,
>           'GUANFACINE': 717}
>
> drugs_98_05 = { 'SERTRALINE': 56635,
>                  'CITALOPRAM': 59829,
>                  'FLUOXETINE': 80006,
>                  'PAROXETINE_HCL': 57150,
>                  'FLUVOXAMINE': 57064,
>                  'ESCITALOPRAM': 70466,
>                  'DEXMETHYLPHENIDATE': 70427,
>                  'METHYLPHENIDATE': 70374,
>                  'METHAMPHETAMINE': 53485,
>                  'AMPHETAMINE1': 70257,
>                  'AMPHETAMINE2': 70258,
>                  'AMPHETAMINE3': 50265,
>                  'DEXTROAMPHETAMINE1': 70259,
>                  'DEXTROAMPHETAMINE2': 70260,
>                  'DEXTROAMPHETAMINE3': 51665,
>                  'COMBINATION_PRODUCT': 51380,
>                  'FIXED_COMBINATION': 51381,
>                  'ATOMOXETINE': 70687,
>                  'CLONIDINE1': 51275,
>                  'CLONIDINE2': 70357,
>                  'GUANFACINE': 52498
>                 }
>
> df = pd.read_csv('nhamcsopd2010.csv' , index_col='PATCODE',
> low_memory=False)
> col_init = list(df.columns.values)
> keep_col = ['PATCODE', 'PATWT', 'VDAY', 'VMONTH', 'VYEAR', 'MED1',
> 'MED2', 'MED3', 'MED4', 'MED5']
> for col in col_init:
>      if col not in keep_col:
>          del df[col]
> if f[-3:] == 'csv' and f[-6:-4] in ('93', '94', '95', '96', '97', '98',
> '99', '00', '91', '02', '03', '04', '05'):
>      drugs = drugs_98_05
> elif f[-3:]  == 'csv' and f[-6:-4] in ('06', '08', '09', '10'):
>      drugs = drugs_current
> for n in drugs:
>      df[n] =
> df[['MED1','MED2','MED3','MED4','MED5']].isin([drugs[n]]).any(1)
>
>
> Vincent Davis
> 720-301-3003
>
>

I suggest you ask here 
https://mail.python.org/mailman/listinfo/pandas-dev which I believe is 
also gmane.comp.python.pydata.


-- 
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.

Mark Lawrence




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