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rename input arguments. fixes #11
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@tompollard
tompollard committed Aug 1, 2017
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103 changes: 53 additions & 50 deletions README.rst
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Expand Up @@ -31,24 +31,26 @@ Example
url="https://raw.githubusercontent.com/tompollard/data/master/primary-biliary-cirrhosis/pbc.csv"
data=pd.read_csv(url)

#. List of columns containing continuous variables::
#. List of columns to be included in Table 1::

convars = ['time','age','bili','chol','albumin','copper',
'alk.phos','ast','trig','platelet','protime']
columns = ['time','age','bili','chol','albumin','copper',
'alk.phos','ast','trig','platelet','protime',
'status', 'ascites', 'hepato', 'spiders', 'edema',
'stage', 'sex', 'trt']

#. List of columns containing categorical variables::

catvars = ['status', 'ascites', 'hepato', 'spiders', 'edema',
categorical = ['status', 'ascites', 'hepato', 'spiders', 'edema',
'stage', 'sex']

#. Optionally, a categorical variable for stratification and a list of non-normal variables::

strat = 'trt'
groupby = 'trt'
nonnormal = ['bili']

#. Create an instance of TableOne with the input arguments::

mytable = TableOne(data, convars, catvars, strat, nonnormal)
mytable = TableOne(data, columns, categorical, groupby, nonnormal)

#. Type the name of the instance in an interpreter::

Expand All @@ -57,95 +59,96 @@ Example
#. ...which prints the following table to screen::

Stratified by trt
1.0 2.0
--------------------- ----------------- -----------------
n 158 154
time (mean (std)) 2015.62 (1094.12) 1996.86 (1155.93)
age (mean (std)) 51.42 (11.01) 48.58 (9.96)
bili (median [IQR]) 1.40 [0.80,3.20] 1.30 [0.72,3.60]
chol (mean (std)) 365.01 (209.54) 373.88 (252.48)
albumin (mean (std)) 3.52 (0.44) 3.52 (0.40)
copper (mean (std)) 97.64 (90.59) 97.65 (80.49)
alk.phos (mean (std)) 2021.30 (2183.44) 1943.01 (2101.69)
ast (mean (std)) 120.21 (54.52) 124.97 (58.93)
trig (mean (std)) 124.14 (71.54) 125.25 (58.52)
platelet (mean (std)) 258.75 (100.32) 265.20 (90.73)
protime (mean (std)) 10.65 (0.85) 10.80 (1.14)
status (n (%))
1.0 2.0 isnull
--------------------- ----------------- ----------------- --------
n 158 154 106
time (mean (std)) 2015.62 (1094.12) 1996.86 (1155.93) 0
age (mean (std)) 51.42 (11.01) 48.58 (9.96) 0
bili (median [IQR]) 1.40 [0.80,3.20] 1.30 [0.72,3.60] 0
chol (mean (std)) 365.01 (209.54) 373.88 (252.48) 134
albumin (mean (std)) 3.52 (0.44) 3.52 (0.40) 0
copper (mean (std)) 97.64 (90.59) 97.65 (80.49) 108
alk.phos (mean (std)) 2021.30 (2183.44) 1943.01 (2101.69) 106
ast (mean (std)) 120.21 (54.52) 124.97 (58.93) 106
trig (mean (std)) 124.14 (71.54) 125.25 (58.52) 136
platelet (mean (std)) 258.75 (100.32) 265.20 (90.73) 11
protime (mean (std)) 10.65 (0.85) 10.80 (1.14) 2
status (n (%)) 0
0 83 (52.53) 85 (55.19)
1 10 (6.33) 9 (5.84)
2 65 (41.14) 60 (38.96)
ascites (n (%))
ascites (n (%)) 106
0.0 144 (91.14) 144 (93.51)
1.0 14 (8.86) 10 (6.49)
hepato (n (%))
hepato (n (%)) 106
0.0 85 (53.80) 67 (43.51)
1.0 73 (46.20) 87 (56.49)
spiders (n (%))
spiders (n (%)) 106
0.0 113 (71.52) 109 (70.78)
1.0 45 (28.48) 45 (29.22)
edema (n (%))
edema (n (%)) 0
0.0 132 (83.54) 131 (85.06)
0.5 16 (10.13) 13 (8.44)
1.0 10 (6.33) 10 (6.49)
stage (n (%))
stage (n (%)) 6
1.0 12 (7.59) 4 (2.60)
2.0 35 (22.15) 32 (20.78)
3.0 56 (35.44) 64 (41.56)
4.0 55 (34.81) 54 (35.06)
sex (n (%))
sex (n (%)) 0
f 137 (86.71) 139 (90.26)
m 21 (13.29) 15 (9.74)
m 21 (13.29) 15 (9.74)


#. Compute p values by setting the ``pval`` argument to True. The name of the test that was used is also displayed::

mytable = TableOne(data, convars, catvars, strat, nonnormal, pval=True)
mytable = TableOne(data, columns, categorical, groupby, nonnormal, pval=True)

#. ...which prints::

Stratified by trt
1.0 2.0 pval testname
--------------------- ----------------- ----------------- ------ --------------
n 158 154
time (mean (std)) 2015.62 (1094.12) 1996.86 (1155.93) 0.883 One_way_ANOVA
age (mean (std)) 51.42 (11.01) 48.58 (9.96) 0.018 One_way_ANOVA
bili (median [IQR]) 1.40 [0.80,3.20] 1.30 [0.72,3.60] 0.842 Kruskal-Wallis
chol (mean (std)) 365.01 (209.54) 373.88 (252.48) 0.748 One_way_ANOVA
albumin (mean (std)) 3.52 (0.44) 3.52 (0.40) 0.874 One_way_ANOVA
copper (mean (std)) 97.64 (90.59) 97.65 (80.49) 0.999 One_way_ANOVA
alk.phos (mean (std)) 2021.30 (2183.44) 1943.01 (2101.69) 0.747 One_way_ANOVA
ast (mean (std)) 120.21 (54.52) 124.97 (58.93) 0.460 One_way_ANOVA
trig (mean (std)) 124.14 (71.54) 125.25 (58.52) 0.886 One_way_ANOVA
platelet (mean (std)) 258.75 (100.32) 265.20 (90.73) 0.555 One_way_ANOVA
protime (mean (std)) 10.65 (0.85) 10.80 (1.14) 0.197 One_way_ANOVA
status (n (%)) 0.894 Chi-squared
1.0 2.0 isnull pval testname
--------------------- ----------------- ----------------- -------- ------ --------------
n 158 154 106
time (mean (std)) 2015.62 (1094.12) 1996.86 (1155.93) 0 0.883 One_way_ANOVA
age (mean (std)) 51.42 (11.01) 48.58 (9.96) 0 0.018 One_way_ANOVA
bili (median [IQR]) 1.40 [0.80,3.20] 1.30 [0.72,3.60] 0 0.842 Kruskal-Wallis
chol (mean (std)) 365.01 (209.54) 373.88 (252.48) 134 0.748 One_way_ANOVA
albumin (mean (std)) 3.52 (0.44) 3.52 (0.40) 0 0.874 One_way_ANOVA
copper (mean (std)) 97.64 (90.59) 97.65 (80.49) 108 0.999 One_way_ANOVA
alk.phos (mean (std)) 2021.30 (2183.44) 1943.01 (2101.69) 106 0.747 One_way_ANOVA
ast (mean (std)) 120.21 (54.52) 124.97 (58.93) 106 0.460 One_way_ANOVA
trig (mean (std)) 124.14 (71.54) 125.25 (58.52) 136 0.886 One_way_ANOVA
platelet (mean (std)) 258.75 (100.32) 265.20 (90.73) 11 0.555 One_way_ANOVA
protime (mean (std)) 10.65 (0.85) 10.80 (1.14) 2 0.197 One_way_ANOVA
status (n (%)) 0 0.894 Chi-squared
0 83 (52.53) 85 (55.19)
1 10 (6.33) 9 (5.84)
2 65 (41.14) 60 (38.96)
ascites (n (%)) 0.567 Chi-squared
ascites (n (%)) 106 0.567 Chi-squared
0.0 144 (91.14) 144 (93.51)
1.0 14 (8.86) 10 (6.49)
hepato (n (%)) 0.088 Chi-squared
hepato (n (%)) 106 0.088 Chi-squared
0.0 85 (53.80) 67 (43.51)
1.0 73 (46.20) 87 (56.49)
spiders (n (%)) 0.985 Chi-squared
spiders (n (%)) 106 0.985 Chi-squared
0.0 113 (71.52) 109 (70.78)
1.0 45 (28.48) 45 (29.22)
edema (n (%)) 0.877 Chi-squared
edema (n (%)) 0 0.877 Chi-squared
0.0 132 (83.54) 131 (85.06)
0.5 16 (10.13) 13 (8.44)
1.0 10 (6.33) 10 (6.49)
stage (n (%)) 0.201 Chi-squared
stage (n (%)) 6 nan Not tested
1.0 12 (7.59) 4 (2.60)
2.0 35 (22.15) 32 (20.78)
3.0 56 (35.44) 64 (41.56)
4.0 55 (34.81) 54 (35.06)
sex (n (%)) 0.421 Chi-squared
sex (n (%)) 0 0.421 Chi-squared
f 137 (86.71) 139 (90.26)
m 21 (13.29) 15 (9.74)



#. Tables can be exported to file in various formats, including LaTeX, Markdown, CSV, and HTML. Files are exported by calling the ``to_format`` methods. For example, mytable can be exported to a CSV named 'mytable.csv' with the following command::

mytable.to_csv('mytable.csv')
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