python调用r语言函数_在python中调用R的pwr功效函数

已封装为函数，

文件名 - PyPower.py

# 推荐使用conda管理环境

# conda create --name test python=3.6

# source activate test

# conda install rpy2 # should add conda-forge channel

# reference link: ,

def pyPower_ttest(n='NULL', d='NULL', sig_level=0.05, power='NULL', type="two.sample", alternative='two.sided'):

'''

Compute power of tests or determine parameters to obtain target power. Exactly one of the parameters 'd','n','power' and 'sig_level' must be passed as 'NULL'. Results returned as a dictory.

This is an API function calling pwr.t.test function of R in Python using rpy2, pwr package (R environment) must be pre-installed.

Arguments:

n

Number of observations (per sample)

d

Effect size (Cohen's d) - difference between the means divided by the pooled standard deviation

sig_level

Significance level (Type I error probability)

power

Power of test (1 minus Type II error probability)

type

Type of t test : one- two- or paired-samples

alternative

a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less"

Example:

from PyPower import pyPower_ttest

pyPower_ttest(d=0.2,n=60,sig_level=0.10,type="one.sample",alternative="two.sided")

pyPower_ttest(d=2/2.8,n=30,sig_level=0.05,type="two.sample",alternative="two.sided")

pyPower_ttest(d=0.3,power=0.75,sig_level=0.05,type="two.sample",alternative="greater")

Note:

More information please run ?pwr::pwr.t.test in R console

'''

# 载入r对象

from rpy2 import robjects

# 载入导入包函数

from rpy2.robjects.packages import importr

# 将pwr包导入为模块，记得提前在（test环境下）R中安装好pwr包

pwr = importr('pwr')

# When one wants to create a vector from Python, either the class Vector or the convenience classes IntVector, FloatVector, BoolVector, StrVector can be used.

# 将参数中的.替换为_，解决不兼容问题， 来自rpy2文档函数部分

# rpy2默认支持该转换，可以删除该部分以简化代码

def iamfeelinglucky(func):

def f(*args, **kwargs):

d = {}

for k, v in kwargs.items():

d[k.replace('_', '.')] = v

return func(**d)

return f

# 矫正参数名

power_ttest = iamfeelinglucky(pwr.pwr_t_test)

# 重命名r中的as.null函数，用于将字符'NULL'转换为NULL对象

as_null = robjects.r['as.null']

# 转换

args_list = [n, d, sig_level, power]

for i,v in enumerate(args_list):

if v == "NULL":

args_list[i] = as_null(v)

# 调用函数

pwr_res = power_ttest(n=args_list[0], d=args_list[1], sig_level=args_list[2], power=args_list[3], type=type, alternative=alternative)

# 输出分析结果

print(pwr_res)

res = list(pwr_res)

# 返回结果中需要的值构建字典

res = {'n':res[0], 'd':res[1], 'sig_level':res[2], 'power':res[3], 'alternative':res[4], 'method':res[6]}

# 返回的是robject对象，再转换为标准的python对象

res['n'] = list(res['n'])[0]

res['d'] = list(res['d'])[0]

res['sig_level'] = list(res['sig_level'])[0]

res['power'] = list(res['power'])[0]

res['alternative'] = list(res['alternative'])[0]

res['method'] = list(res['method'])[0]

return(res)