I m working with rpy2 on Ubuntu 1104. I m following the COX file. The steps given in file are in R. I have to do same steps in python using rpy2. I didn't get any tutorial with rpy2. I managed to write following,
我在Ubuntu 1104上与rpy2合作。我在跟踪考克斯文件。文件中给出的步骤在r中，我必须使用rpy2在python中执行相同的步骤。我没有得到任何关于rpy2的教程。我设法写了如下，
from rpy2.robjects.packages import importr
from rpy2.robjects import IntVector, Formula
import rpy2.robjects as ro
cox = importr("survival")
csv = ro.vectors.DataFrame.from_csvfile('Rossi.txt', header=True, sep=' ')
fmla = Formula('Surv(week, arrest) ~ fin + age + race + wexp + mar + paro + prio')
mod_aalison = cox.coxph (fmla, data=csv)
But I'm getting following error,
但我有以下错误，
>>> mod_aalison = cox.coxph (fmla, data=csv)
Error in function (formula, data, weights, subset, na.action, init, control, :
No (non-missing) observations
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/rpy2/robjects/functions.py", line 83, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/rpy2/robjects/functions.py", line 35, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in function (formula, data, weights, subset, na.action, init, control, :
No (non-missing) observations
Am I missing any thing? I have no prior experience on R. I'm not sure the if data in function coxph has to be in dataframe format. Any help is appreciated.
我漏掉什么了吗?我没有以前的经验，我不确定是否函数coxph中的数据必须以dataframe格式。任何帮助都是感激。
This is link to Rossi.txt
这是链接到Rossi.txt。
1 个解决方案
#1
2
You read the data using read.csv with sep set to a single space, while the file has two spaces. This makes R interpret this as an existence of empty columns, which then mess with column names and finally create error in coxph.
您可以使用read读取数据。带有sep的csv设置为一个空格，而文件有两个空格。这使得R将其解释为空列的存在，然后将列名称弄乱，最后在coxph中创建错误。
Read the data with read.table, and it should be ok.
读取数据并读取。桌子，应该没问题。
#1
2
You read the data using read.csv with sep set to a single space, while the file has two spaces. This makes R interpret this as an existence of empty columns, which then mess with column names and finally create error in coxph.
您可以使用read读取数据。带有sep的csv设置为一个空格，而文件有两个空格。这使得R将其解释为空列的存在，然后将列名称弄乱，最后在coxph中创建错误。
Read the data with read.table, and it should be ok.
读取数据并读取。桌子，应该没问题。