I have 2 data frames pd and pd2:
pd
Name A B Mean
t1 1.0 2.0 1.5
t2 2.0 3.0 2.5
t3 9.4 3.3 6.35
pd2
Name A B Mean
t1 1.1 2.7 1.9
t2 3.7 3.0 3.35
t3 10.4 4.3 7.35
I would like to do the ttest calculation for columns 'A' on both dataframes and column B on both dataframes the result can be added to one of the dataframes or it can be added to a new data frame. The output should have the columns:
ttestA ttestB ttestC ...etc
Using for loop
from scipy import stats
l=[]
listofname=['A','B']
for x in listofname:
l.append(stats.ttest_ind(df[x],df2[x], equal_var=False))
Related
I have a three column of data as arranged below:
Input file:
>>>>>
1.0 2.0 3.0
2.0 2.0 4.0
3.0 4.5 8.0
>>>>>
1.0 2.5 6.8
2.0 3.5 6.8
3.0 1.2 1.9
>>>>>
1.0 1.2 1.3
2.0 2.7 1.8
3.0 4.5 8.5
In the above input file the first column values are repeated so I want to take only once that value and want to sum the third column values row wise and do not want to take any second column values.
I also want to append a third column with the fixed value 1.0
Finally want to save the result on another test file called output.txt.
Output:
1.0 11.1 1.0
2.0 12.6 1.0
3.0 18.4 1.0
In the output second column values resulted from is following:
3.0+6.8+1.3
4.0+6.8+1.8
8.0+1.9+8.5
I tried with numpy but getting error:
import numpy as np
import pandas as pd
import glob
data=np.loadtxt("input.txt")
You need to read your input file using pandas.read_csv, you need to set the delimiter to " ", specify no header and ">" as comment lines.
Then perform the groupby/sum operation, and export without header using pandas.to_csv
import pandas as pd
# input
df = pd.read_csv('filename.csv', delimiter=' ', header=None, comment='>')
# output
(df.groupby(0)[[2]].sum()
.assign(col=1.0)
.to_csv('output.txt', header=False, sep=' ', float_format='%.2f')
)
output.txt:
1.00 11.10 1.00
2.00 12.60 1.00
3.00 18.40 1.00
Try:
df[2].groupby(np.arange(len(df)) % 3).sum()
# or df.iloc[:, 2].groupby(np.arange(len(df)) % 3).sum()
0 11.1
1 12.6
2 18.4
Name: 2, dtype: float64
Use groupby with reset index
dfNew = df.groupby(0)[2].sum().reset_index()
dfNew.to_csv('output.txt', index= False)
I'm trying to reshape a multi-indexed data frame so that the values from the second level of the index are incorporated into the column names in the new data frame. In the data frame below, I want to move A and B from "source" into the columns so that I have s1_A, s1_B, s2_A, ..., s3_B.
I've tried creating the structure of the new data frame explicitly and populating it with a nested for loop to reassign the values, but it is excruciatingly slow. I've tried a number of functions from the pandas API, but without much luck. Any help would be much appreciated.
midx = pd.MultiIndex.from_product( [[1,2,3], ['A','B']], names=["sample","source"])
df = pd.DataFrame( index=midx, columns=['s1', 's2', 's3'], data=np.ndarray(shape=(6,3)) )
>>> df
s1 s2 s3
sample source
1 A 1.2 3.4 5.6
B 1.2 3.4 5.6
2 A 1.2 3.4 5.6
B 1.2 3.4 5.6
3 A 1.2 3.4 5.6
B 1.2 3.4 5.6
# Want to build a new data frame thatlooks like this:
>>> df_new
s1_A s1_B s2_A s2_B s3_A s3_B
sample
1 1.2 1.2 3.4 3.4 5.6 5.6
2 1.2 1.2 3.4 3.4 5.6 5.6
3 1.2 1.2 3.4 3.4 5.6 5.6
Here's how I'm currently doing it. It's extremely slow, and I know there must be a more idiomatic way to do this with pandas, but I'm still new to its API:
substances = df.columns.values
sources = ['A','B']
subst_and_src = sorted([ subst + "_" + src for src in sources for subst in substances ])
df_new = pd.DataFrame(index=df.index.unique(0), columns=subst_and_src)
# Runs forever
for (sample, source) in df.index:
for subst in df.columns:
df_new[sample, subst + "_" + source] = df.loc[(sample,source), subst]
df = df.unstack(level=1)
df.columns = ['_'.join(col).strip() for col in df.columns.values]
print(df)
Prints:
s1_A s1_B s2_A s2_B s3_A s3_B
sample
1 4.665045e-310 6.904071e-310 0.0 0.0 6.903913e-310 2.121996e-314
2 6.904071e-310 0.000000e+00 0.0 0.0 3.458460e-323 0.000000e+00
3 0.000000e+00 0.000000e+00 0.0 0.0 0.000000e+00 0.000000e+00
Unstack into a new dataframe and collapse multilevel index of resulting frmae using f string
df1= df.unstack()
df1.columns = df1.columns.map('{0[0]}_{0[1]}'.format)
s1_A s1_B s2_A s2_B s3_A s3_B
sample
1 1.2 1.2 3.4 3.4 5.6 5.6
2 1.2 1.2 3.4 3.4 5.6 5.6
3 1.2 1.2 3.4 3.4 5.6 5.6
I have two pd.dataframes:
df1:
Year Replaced Not_replaced
2015 1.5 0.1
2016 1.6 0.3
2017 2.1 0.1
2018 2.6 0.5
df2:
Year HI LO RF
2015 3.2 2.9 3.0
2016 3.0 2.8 2.9
2017 2.7 2.5 2.6
2018 2.6 2.2 2.3
I need to create a third df3 by using the following equation:
df3[column1]=df1['Replaced']-df1['Not_replaced]+df2['HI']
df3[column2]=df1['Replaced']-df1['Not_replaced]+df2['LO']
df3[column3]=df1['Replaced']-df1['Not_replaced]+df2['RF']
I can merge the two dataframes and manually create 3 new columns one by one, but I can't figure out how to use the loop function to create the results.
You can create an empty dataframe & fill it with values while looping
(Note: col_names & df3.columns must be of the same length)
df3 = pd.DataFrame(columns = ['column1','column2','column3'])
col_names = ["HI", "LO","RF"]
for incol,df3column in zip(col_names,df3.columns):
df3[df3column] = df1['Replaced']-df1['Not_replaced']+df2[incol]
print(df3)
output
column1 column2 column3
0 4.6 4.3 4.4
1 4.3 4.1 4.2
2 4.7 4.5 4.6
3 4.7 4.3 4.4
for the for loop, I would first merge df1 and df2 into to create a new df, called df3. Then, I would create a list of te names of the columns you want to iterate through:
col_names = ["HI", "LO","RF"]
for col in col_names:
df3[f"column_{col}]= df3['Replaced']-df3['Not_replaced]+df3[col]
This question already has answers here:
Reshape wide to long in pandas
(2 answers)
Closed 4 years ago.
I am manipulating a data frame using Pandas in Python to match a specific format.
I currently have a data frame with a row for each measurement location (A or B). Each row has a nominal target and multiple measured data points.
This is the format I currently have:
df=
Location Nominal Meas1 Meas2 Meas3
A 4.0 3.8 4.1 4.3
B 9.0 8.7 8.9 9.1
I need to manipulate this data so there is only one measured data point per row, and copy the Location and Nominal values from the source rows to the new rows. The measured data also needs to be put in the first column.
This is the format I need:
df =
Meas Location Nominal
3.8 A 4.0
4.1 A 4.0
4.3 A 4.0
8.7 B 9.0
8.9 B 9.0
9.1 B 9.0
I have tried concat and append functions with and without transpose() with no success.
This is the most similar example I was able to find, but it did not get me there:
for index, row in df.iterrows():
pd.concat([row]*3, ignore_index=True)
Thank you!
Its' a wide to long problem
pd.wide_to_long(df,'Meas',i=['Location','Nominal'],j='drop').reset_index().drop('drop',1)
Out[637]:
Location Nominal Meas
0 A 4.0 3.8
1 A 4.0 4.1
2 A 4.0 4.3
3 B 9.0 8.7
4 B 9.0 8.9
5 B 9.0 9.1
Another solution, using melt:
new_df = (df.melt(['Location','Nominal'],
['Meas1', 'Meas2', 'Meas3'],
value_name = 'Meas')
.drop('variable', axis=1)
.sort_values('Location'))
>>> new_df
Location Nominal Meas
0 A 4.0 3.8
2 A 4.0 4.1
4 A 4.0 4.3
1 B 9.0 8.7
3 B 9.0 8.9
5 B 9.0 9.1
I'm reading a csv file with Pandas. The format is:
Date Time x1 x2 x3 x4 x5
3/7/2012 11:09:22 13.5 2.3 0.4 7.3 6.4
12.6 3.4 9.0 3.0 7.0
3.6 4.4 8.0 6.0 5.0
10.6 3.5 1.0 3.0 8.0
...
3/7/2012 11:09:23 10.5 23.2 0.3 7.8 4.4
11.6 13.4 19.0 13.0 17.0
...
As you can see, not every row has a timestamp. Every row without a timestamp is from the same 1-second interval as the closest row above it that does have a timestamp.
I am trying to do 3 things:
1. combine the Date and Time columns to get a single timestamp column.
2. convert that column to have units of seconds.
3. fill empty cells to have the appropriate timestamp.
The desired end result is an array with the timestamp, in seconds, at each row.
I am not sure how to quickly convert the timestamps into units of seconds, other then to do a slow for loop and use the Python builtin time.mktime method.
Then when I fill in missing timestamp values, the problem is that the cells in the Date and Time columns which did not have a timestamp each get a "nan" value and when merged give a cell with the value "nan nan". Then when I use the fillna() method, it doesn't interpret "nan nan" as being a nan.
I am using the following code to get the problem result (not including the part of trying to convert to seconds):
import pandas as pd
df = pd.read_csv('file.csv', delimiter=',', parse_dates={'CorrectTime':[0,1]}, usecols=[0,1,2,4,6], names=['Date','Time','x1','x3','x5'])
df.fillna(method='ffill', axis=0, inplace=True)
Thanks for your help.
Assuming you want seconds since Jan 1, 1900...
import pandas
from io import StringIO
import datetime
data = StringIO("""\
Date,Time,x1,x2,x3,x4,x5
3/7/2012,11:09:22,13.5,2.3,0.4,7.3,6.4
,,12.6,3.4,9.0,3.0,7.0
,,3.6,4.4,8.0,6.0,5.0
,,10.6,3.5,1.0,3.0,8.0
3/7/2012,11:09:23,10.5,23.2,0.3,7.8,4.4
,,11.6,13.4,19.0,13.0,17.0
""")
df = pandas.read_csv(data, parse_dates=['Date']).fillna(method='ffill')
def dealwithdates(row):
datestring = row['Date'].strftime('%Y-%m-%d')
dtstring = '{} {}'.format(datestring, row['Time'])
date = datetime.datetime.strptime(dtstring, '%Y-%m-%d %H:%M:%S')
refdate = datetime.datetime(1900, 1, 1)
return (date - refdate).total_seconds()
df['ordinal'] = df.apply(dealwithdates, axis=1)
print(df)
Date Time x1 x2 x3 x4 x5 ordinal
0 2012-03-07 11:09:22 13.5 2.3 0.4 7.3 6.4 3540107362
1 2012-03-07 11:09:22 12.6 3.4 9.0 3.0 7.0 3540107362
2 2012-03-07 11:09:22 3.6 4.4 8.0 6.0 5.0 3540107362
3 2012-03-07 11:09:22 10.6 3.5 1.0 3.0 8.0 3540107362
4 2012-03-07 11:09:23 10.5 23.2 0.3 7.8 4.4 3540107363
5 2012-03-07 11:09:23 11.6 13.4 19.0 13.0 17.0 3540107363