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Speed up operations over Python Pandas dataframes

I would like to speed up a loop over a python Pandas Dataframe. Unfortunately, decades of using low-level languages mean I often struggle to find prepackaged solutions. Note: data is private, but I will see if I can fabricate something and add it into an edit if it helps.
The code has three pandas dataframes: drugUseDF, tempDF, which holds the data, and tempDrugUse, which stores what's been retrieved. I look over every row of tempDF (there will be several million rows), retrieving the prodcode identified from each row and then using that to retrieve the corresponding value from use1 column in the drugUseDF. I've added comments to help navigate.
This is the structure of the dataframes:
tempDF
patid eventdate consid prodcode issueseq
0 20001 21/04/2005 2728 85 0
1 25001 21/10/2000 3939 40 0
2 25001 21/02/2001 3950 37 0
drugUseDF
index prodcode ... use1 use2
0 171 479 ... diabetes NaN
1 172 9105 ... diabetes NaN
2 173 5174 ... diabetes NaN
tempDrugUse
use1
0 NaN
1 NaN
2 NaN
This is the code:
dfList = []
# if the drug dataframe contains the use1 column. Can this be improved?
if sum(drugUseDF.columns.isin(["use1"])) == 1:
#predine dataframe where we will store the results to be the same length as the main data dataframe.
tempDrugUse = DataFrame(data=None, index=range(len(tempDF.index)), dtype=np.str, columns=["use1"])
#go through each row of the main data dataframe.
for ind in range(len(tempDF)):
#retrieve the prodcode from the *ind* row of the main data dataframe
prodcodeStr = tempDF.iloc[ind]["prodcode"]
#get the corresponding value from the use1 column matching the prodcode column
useStr = drugUseDF[drugUseDF.loc[:, "prodcode"] == prodcodeStr]["use1"].values[0]
#update the storing dataframe
tempDrugUse.iloc[ind]["use1"] = useStr
print("[DEBUG] End of loop for use1")
dfList.append(tempDrugUse)
The order of the data matters. I can't retrieve multiple rows by matching the prodcode because each row has a date column. Retrieving multiple rows and adding them to the tempDrugUse dataframe could mean that the rows are no longer in chronological date order.

When trying to combine data in two dataframes you should use the merge (similar to JOIN in sql-like languages). Performance wise, you should never loop over the rows - you should use the pandas built-in methods whenever possible. Ordering can be achieved with the sort_values method.

If I understand you correctly, you want to map the prodcode from both tables. You can do this via pd.merge (please note the example in the code below differs from your data):
tempDF = pd.DataFrame({'patid': [20001, 25001, 25001],
'prodcode': [101,102,103]})
drugUseDF = pd.DataFrame({'prodcode': [101,102,103],
'use1': ['diabetes', 'hypertonia', 'gout']})
merged_df = pd.merge(tempDF, drugUseDF, on='prodcode', how='left')

Create dataframe column using another column for source variable suffix

Difficult to title, so apologies for that...
Here is some example data:
region FC_EA FC_EM FC_GL FC_XX FC_YY ...
GL 4 2 8 6 1 ...
YY 9 7 2 1 3 ...
There are many columns with a suffix, hence the ...
[edit] And there are many other columns. I want to keep all columns.
The aim is to create a column called FC that is the value according to the region column value.
So, for this data the resultant column would be:
FC
8
3
I have a couple of ways to achieve this at present - one way is minimal code (perhaps fine for a small dataset):
df['FC'] = df.apply(lambda x: x['FC_'+x.region], axis=1)
Another way is a stacked np.where query - faster for large datasets I am advised...:
df['FC'] = np.where(df.region=='EA', df.FC_EA,
np.where(df.region=='EM', df.FC_EM,
np.where(df.region=='GL', df.FC_GL, ...
I am wondering if anyone out there can suggest the best way to do this, if there is something better than these options?
That would be great.
Thanks!

You could use melt:
(df.melt(id_vars='region', value_name='FC')
.loc[lambda d: d['region'].eq(d['variable'].str[3:]), ['region', 'FC']]
)
or using apply (probably quite slower):
df['FC'] = (df.set_index('region')
.apply(lambda r: r.loc[f'FC_{r.name}'], axis=1)
.values
)
output:
region FC
4 GL 8
9 YY 3

Python, lambda function as argument for groupby

I'm trying to figure out what a piece of code is doing, but I'm getting kinda lost on it.
I have a pandas dataframe, which has been loaded by the following .csv file:
origin_census_block_group,date_range_start,date_range_end,device_count,distance_traveled_from_home,bucketed_distance_traveled,median_dwell_at_bucketed_distance_traveled,completely_home_device_count,median_home_dwell_time,bucketed_home_dwell_time,at_home_by_each_hour,part_time_work_behavior_devices,full_time_work_behavior_devices,destination_cbgs,delivery_behavior_devices,median_non_home_dwell_time,candidate_device_count,bucketed_away_from_home_time,median_percentage_time_home,bucketed_percentage_time_home,mean_home_dwell_time,mean_non_home_dwell_time,mean_distance_traveled_from_home
010539707003,2020-06-25T00:00:00-05:00,2020-06-26T00:00:00-05:00,49,626,"{""16001-50000"":5,""0"":11,"">50000"":4,""2001-8000"":3,""1-1000"":9,""1001-2000"":7,""8001-16000"":1}","{""16001-50000"":110,"">50000"":155,""<1000"":40,""2001-8000"":237,""1001-2000"":27,""8001-16000"":180}",12,627,"{""721-1080"":11,""361-720"":9,""61-360"":1,""<60"":11,"">1080"":12}","[32,32,28,30,30,31,27,23,20,20,20,17,19,19,15,14,17,20,20,21,25,22,24,23]",7,3,"{""120330012011"":1,""010030107031"":1,""010030114052"":2,""120330038001"":1,""010539701003"":1,""010030108001"":1,""010539707002"":14,""010539705003"":2,""120330015001"":1,""121130102003"":1,""010539701002"":1,""120330040001"":1,""370350101014"":2,""120330033081"":2,""010030106003"":1,""010539706001"":2,""010539707004"":3,""120330039001"":1,""010539699003"":1,""120330030003"":1,""010539707003"":41,""010970029003"":1,""010539705004"":1,""120330009002"":1,""010539705001"":3,""010539704003"":1,""120330028012"":1,""120330035081"":1,""120330036102"":1,""120330036142"":1,""010030114062"":1,""010539706004"":7,""010539706002"":1,""120330036082"":1,""010539707001"":7,""010030102001"":1,""120330028011"":1}",2,241,71,"{""21-45"":4,""481-540"":2,""541-600"":1,""721-840"":1,""1201-1320"":1,""301-360"":3,""<20"":13,""61-120"":3,""241-300"":3,""121-180"":1,""421-480"":3,""1321-1440"":4,""1081-1200"":1,""961-1080"":2,""601-660"":1,""181-240"":1,""661-720"":2,""361-420"":3}",72,"{""0-25"":13,""76-100"":21,""51-75"":6,""26-50"":3}",657,413,1936
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010890017002,2020-06-25T00:00:00-05:00,2020-06-26T00:00:00-05:00,78,1934,"{""16001-50000"":2,""0"":12,"">50000"":9,""2001-8000"":27,""1-1000"":12,""1001-2000"":8,""8001-16000"":8}","{""16001-50000"":49,"">50000"":99,""<1000"":111,""2001-8000"":37,""1001-2000"":24,""8001-16000"":28}",11,787,"{""721-1080"":17,""361-720"":11,""61-360"":11,""<60"":15,"">1080"":23}","[49,42,48,48,47,48,44,44,39,32,34,32,36,31,32,36,40,37,36,38,49,45,46,46]",5,1,"{""010890101002"":1,""010730108041"":1,""010890020003"":2,""010890010001"":2,""010890025011"":3,""010890026001"":4,""280819505003"":1,""281059504004"":1,""010890103022"":1,""120990056011"":1,""010890109012"":2,""010890019021"":6,""010890013021"":4,""010890015004"":3,""010890108003"":1,""010890014022"":6,""281059501003"":1,""281059503001"":1,""010890007022"":3,""010890017001"":3,""010890107023"":1,""010890021002"":1,""010890009011"":1,""010890109013"":1,""010730120022"":1,""010890031003"":15,""011170303151"":1,""010890019011"":9,""010890030002"":2,""010890110221"":1,""011170305021"":1,""010890026003"":2,""010890025012"":3,""010730117034"":1,""010830208022"":1,""010890031002"":2,""010890112002"":1,""010210602001"":1,""010890002022"":1,""010890017002"":65,""281059506021"":1,""010890010003"":2,""010890106222"":1,""120990059182"":1,""010890110222"":1,""010890020001"":1,""010890101003"":1,""010890018013"":1,""010890021001"":1,""010890109021"":1,""010890108001"":1,""010770106005"":1,""281059506011"":1,""010030114032"":2,""010830209001"":1,""010890027222"":1,""010730128023"":1,""010890009021"":1,""010030114051"":1,""010030109031"":1,""010030103003"":1,""010890031001"":1,""010890021003"":1,""010030114062"":4,""010890106241"":1,""281059504003"":1,""010890018011"":10,""010890019031"":5,""010890027012"":1,""010730108054"":1,""010890106223"":2,""010890111001"":1,""010210603002"":1,""010890109011"":1,""010890019012"":2,""010890113001"":1,""010890028013"":3}",1,229,99,"{""481-540"":3,""541-600"":2,""46-60"":1,""721-840"":1,""1201-1320"":7,""301-360"":6,""<20"":18,""61-120"":10,""241-300"":5,""121-180"":2,""1321-1440"":2,""841-960"":1,""1081-1200"":1,""961-1080"":3,""601-660"":3,""181-240"":2,""661-720"":3}",78,"{""0-25"":16,""76-100"":44,""51-75"":11,""26-50"":7}",708,353,14328
010950308022,2020-06-25T00:00:00-05:00,2020-06-26T00:00:00-05:00,100,2481,"{""16001-50000"":11,""0"":19,"">50000"":11,""2001-8000"":40,""1-1000"":6,""1001-2000"":3,""8001-16000"":4}","{""16001-50000"":150,"">50000"":23,""<1000"":739,""2001-8000"":23,""1001-2000"":12,""8001-16000"":208}",17,703,"{""721-1080"":21,""361-720"":19,""61-360"":10,""<60"":24,"">1080"":26}","[62,64,64,63,65,67,54,48,37,37,34,33,30,34,32,33,35,43,50,56,58,56,56,57]",8,6,"{""010950306004"":1,""010950302023"":1,""011030054051"":1,""010950311002"":1,""010950309023"":1,""010499606003"":1,""121319506023"":2,""010950308022"":86,""121319506016"":2,""010950304013"":1,""010950307024"":1,""010950309041"":1,""010890019021"":2,""010950312001"":5,""010499607002"":1,""011150402013"":1,""010550102003"":1,""120050027043"":3,""010719509003"":1,""010950302022"":1,""010950308023"":2,""120050027051"":2,""471079701022"":1,""010890106221"":1,""010950306001"":1,""010950302011"":2,""011150405013"":1,""011150402041"":2,""010950312002"":16,""011030054042"":1,""010950301002"":2,""130459105011"":1,""010730001001"":1,""130459102001"":1,""010890109013"":2,""010950308013"":14,""010719508004"":1,""120050027041"":3,""010550110021"":3,""010730049022"":1,""010950308024"":1,""010950312004"":6,""010950312003"":1,""010550104012"":2,""010550110013"":1,""120860004111"":1,""010890027222"":1,""010950306002"":2,""010950304015"":1,""011030054041"":1,""010950309031"":8,""010950308021"":1,""010950302024"":1,""010950307011"":5,""010550110012"":2,""011150404013"":1,""130459103003"":1,""120050027032"":3,""010950307012"":5,""010950309022"":2,""010950307023"":1,""010719508003"":1,""010499608001"":2,""010950310003"":1,""011150402043"":1,""120860099063"":1,""010950309021"":4,""010950309043"":2,""010950308011"":1,""010950306003"":3,""120050027042"":1,""010950308025"":5,""010950309032"":6,""010499607001"":1}",1,199,132,"{""21-45"":8,""481-540"":6,""541-600"":4,""46-60"":3,""721-840"":3,""1201-1320"":4,""301-360"":3,""<20"":20,""61-120"":10,""241-300"":2,""121-180"":4,""421-480"":3,""1321-1440"":1,""841-960"":3,""961-1080"":2,""601-660"":1,""181-240"":3,""661-720"":1,""361-420"":2}",74,"{""0-25"":20,""76-100"":48,""51-75"":23,""26-50"":4}",661,350,5044
df = pd.read_csv(csv_file,
usecols=[
'origin_census_block_group',
'date_range_start',
'date_range_end',
'device_count',
'distance_traveled_from_home',
'completely_home_device_count',
'median_home_dwell_time',
'part_time_work_behavior_devices',
'full_time_work_behavior_devices'
],
dtype={'origin_census_block_group': str},
).set_index('origin_census_block_group')
and, later in the code, the dataframe is modified by:
df = df.groupby(lambda cbg: cbg[:5]).sum()
I don't quite understand what this line is doing precisely.
Groupby generally groups a dataframe by column, so...is it grouping the dataframe using multiple columns (0 to 5)? What is the effect of .sum() at the end?

If you run your code exactly as you wrote it (both the creation of df and the groupby) you can see the result. I print first couple of columns of the output of groupby
device_count distance_traveled_from_home
----- -------------- -----------------------------
01053 49 626
01073 139 2211
01089 78 1934
01095 100 2481
What happens here is the function lambda cbg: cbg[:5] is applied to each of the index values (strings that look like numbers in column origin_census_block_group). As a side, note the statement
...
dtype={'origin_census_block_group': str},
when creating the df, so somebody went into trouble to make sure they are actually str
So the function is applied to string like '010539707003' and returns a substring which is the first 5 characters of that string:
'010539707003'[:5]
produces
'01053'
so I assume there are multiple keys that share the first 5 characters (in the actual file -- the snippet has them all unique so not very interesting) and all these rows are grouped together
Then .sum() is applied to each numerical column of each group and returns, well, the column sum per each groupby key. This is what you see in my output in column 'device_count' and so on.
Hope this is clear now

Pandas' read_csv() will render a csv-formatted file a Pandas Dataframe.
I recommend having a ready at the Pandas' documentation, as it's very exhaustive -> https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html
usecols=[
'origin_census_block_group',
'date_range_start',
'date_range_end',
'device_count',
'distance_traveled_from_home',
'completely_home_device_count',
'median_home_dwell_time',
'part_time_work_behavior_devices',
'full_time_work_behavior_devices'
],
The usecols parameter will take as input an array of desired columns and will only load the specified columns into the dataframe.
dtype={'origin_census_block_group': str}
The dtype parameter will take a dict as input and is to specify the data type of the values, like {'column' : datatype}
.set_index('origin_census_block_group')
.set_index() will set the specificed column as the index column (ie: the first column). The usual index of Pandas' Dataframe is the row's index number, which appears as the first column of the dataframe. By setting the index, the first column now becomes the specified column. See: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.set_index.html
Panda's .groupby() function will take a dataframe a regroup it basing on the occurrences of he values from the specified column.
That is to say, if we a dataframe such as df =
Fruit Name Quality Count
Apple Marco High 4
Pear Lucia Medium 10
Apple Francesco Low 3
Banana Carlo Medium 6
Pear Timmy Low 7
Apple Roberto High 8
Banana Joe High 21
Banana Jack Low 3
Pear Rob Medium 5
Apple Louis Medium 6
Pear Jennifer Low 7
Pear Laura High 8
Performing a groupby operations, such as:
df = df.groupby(lambda x: x[:2]).sum()
Will take all the elements in the index, slice them from index 0 through index 2 and return the sum of all the corresponding values, ie:
Ap 21
Ba 30
Pe 37
Now, you might be wondering about that final .sum() method. If you try to print the dataframe without applying it, you'll likely get something like this:
<bound method GroupBy.sum of <pandas.core.groupby.generic.DataFrameGroupBy object at 0x109d260a0>>
This is because Pandas has created a groubpy object and does not yet now how to display it to you. Do you want to have it displayed by the number of the occurrences in the index? You'd do this:
df = df.groupby(lambda x: x[:2]).size()
And that would output:
Ap 4
Ba 3
Pe 5
Or maybe the sum of their respective summable values? (Which is what is done in the example)
df = df.groupby(lambda x: x[:2]).sum()
Which again, will output:
Ap 21
Ba 30
Pe 37
Notice it has taken the first two letters of the string in the index. Had it been x[:3], it would have taken the first three letters, of course.
Summing it up:
-> .groupby() takes the elements in the index, i.e. the first column of the dataframe and organises the dataframe in groups relating to the index
-> The input you have given to groubpy is an anonymous function, i.e. lambda function, slicing from index 0 through 5 of its mapped input
-> You may choose how to have the results of groubpy by appending the methos .sum() or .size() to a groubpy object
I also recommend reading about Python's lambda functions:
https://docs.python.org/3/reference/expressions.html

Assign value to dataframe from another dataframe based on two conditions

I am trying to assign values from a column in df2['values'] to a column df1['values']. However values should only be assigned if:
df2['category'] is equal to the df1['category'] (rows are part of the same category)
df1['date'] is in df2['date_range'] (date is in a certain range for a specific category)
So far I have this code, which works, but is far from efficient, since it takes me two days to process the two dfs (df1 has ca. 700k rows).
for i in df1.category.unique():
for j in df2.category.unique():
if i == j: # matching categories
for ia, ra in df1.loc[df1['category'] == i].iterrows():
for ib, rb in df2.loc[df2['category'] == j].iterrows():
if df1['date'][ia] in df2['date_range'][ib]:
df1.loc[ia, 'values'] = rb['values']
break
I read that I should try to avoid using for-loops when working with dataframes. List comprehensions are great, however since I do not have a lot of experience yet, I struggle formulating more complicated code.
How can I iterate over this problem more efficient? What essential key aspect should I think about when iterating over dataframes with conditions?
The code above tends to skip some rows or assigns them wrongly, so I need to do a cleanup afterwards. And the biggest problem, that it is really slow.
Thank you.
Some df1 insight:
df1.head()
date category
0 2015-01-07 f2
1 2015-01-26 f2
2 2015-01-26 f2
3 2015-04-08 f2
4 2015-04-10 f2
Some df2 insight:
df2.date_range[0]
DatetimeIndex(['2011-11-02', '2011-11-03', '2011-11-04', '2011-11-05',
'2011-11-06', '2011-11-07', '2011-11-08', '2011-11-09',
'2011-11-10', '2011-11-11', '2011-11-12', '2011-11-13',
'2011-11-14', '2011-11-15', '2011-11-16', '2011-11-17',
'2011-11-18'],
dtype='datetime64[ns]', freq='D')
df2 other two columns:
df2[['values','category']].head()
values category
0 01 f1
1 02 f1
2 2.1 f1
3 2.2 f1
4 03 f1

Edit: Corrected erroneous code and added OP input from a comment
Alright so if you want to join the dataframes on similar categories, you can merge them :
import pandas as pd
df3 = df1.merge(df2, on = "category")
Next, since date is a timestamp and the "date_range" is actually generated from two columns, per OP's comment, we rather use :
mask = (df3["startdate"] <= df3["date"]) & (df3["date"] <= df3["enddate"])
subset = df3.loc[mask]
Now we get back to df1 and merge on the common dates while keeping all the values from df1. This will create NaN for the subset values where they didn't match with df1 in the earlier merge.
As such, we set df1["values"] where the entries in common are not NaN and we leave them be otherwise.
common_dates = df1.merge(subset, on = "date", how= "left") # keeping df1 values
df1["values"] = np.where(common_dates["values_y"].notna(),
common_dates["values_y"], df1["values"])
N.B : If more than one df1["date"] matches with the date range, you'll have to drop some values otherwise duplicates mess up the explanation.

You could accomplish the first point:
1. df2['category'] is equal to the df1['category']
with the use of a join.
You could then use a for loop for filtering the data poings from df1[date] inside the merged dataframe that are not contemplated in the df2[date_range]. Unfortunately I need more information about the content of df1[date] and df2[date_range] to write the code here that would exactly do that.

How do I groupby a dataframe based on values that are common to multiple columns?

I am trying to aggregate a dataframe based on values that are found in two columns. I am trying to aggregate the dataframe such that the rows that have some value X in either column A or column B are aggregated together.
More concretely, I am trying to do something like this. Let's say I have a dataframe gameStats:
awayTeam homeTeam awayGoals homeGoals
Chelsea Barca 1 2
R. Madrid Barca 2 5
Barca Valencia 2 2
Barca Sevilla 1 0
... and so on
I want to construct a dataframe such that among my rows I would have something like:
team goalsFor goalsAgainst
Barca 10 5
One obvious solution, since the set of unique elements is small, is something like this:
for team in teamList:
aggregateDf = gameStats[(gameStats['homeTeam'] == team) | (gameStats['awayTeam'] == team)]
# do other manipulations of the data then append it to a final dataframe
However, going through a loop seems less elegant. And since I have had this problem before with many unique identifiers, I was wondering if there was a way to do this without using a loop as that seems very inefficient to me.

The solution is 2 folds, first compute goals for each team when they are home and away, then combine them. Something like:
goals_when_away = gameStats.groupby(['awayTeam'])['awayGoals', 'homeGoals'].agg('sum').reset_index().sort_values('awayTeam')
goals_when_home = gameStats.groupby(['homeTeam'])['homeGoals', 'awayGoals'].agg('sum').reset_index().sort_values('homeTeam')
then combine them
np_result = goals_when_away.iloc[:, 1:].values + goals_when_home.iloc[:, 1:].values
pd_result = pd.DataFrame(np_result, columns=['goal_for', 'goal_against'])
result = pd.concat([goals_when_away.iloc[:, :1], pd_result], axis=1, ignore_index=True)
Note .values when summing to get result in numpy array, and ignore_index=True when concat, these are to avoid pandas trap when it sums by column and index names.