将 R 函数输出读取为列 [英] Read R function output as columns

问题描述

我正在想办法解决我昨天问的这个问题:

rpy2 无法导入 'rgl' R 包

我的目标是从 python 中检查某些软件包是否安装在 R 中.

遵循 Dirk Eddelbuettel 在对 他的回答，我正在使用 R 中的 installed.packages() 函数来列出所有可用的包.

这是我目前得到的:

from rpy2.rinterface import RRuntimeError从 rpy2.robjects.packages 导入导入器utils = importr('utils')def importr_tryhard(packname, contriburl):尝试:rpack = utils.installed_pa​​ckages()除了 RRuntimeError:rpack = []返回 rpackcontriburl = 'http://cran.stat.ucla.edu/'rpack = importr_tryhard(packname, contriburl)打印包

返回一个相当大的表单输出:

 包 LibPath 版本ks "ks" "/usr/local/lib/R/site-library" "1.8.13"misc3d "misc3d" "/usr/local/lib/R/site-library" "0.8-4"mvtnorm "mvtnorm" "/usr/local/lib/R/site-library" "0.9-9996"rgl "rgl" "/usr/local/lib/R/site-library" "0.93.986"基基"/usr/lib/R/library"3.0.1"引导引导"/usr/lib/R/library"1.3-9"类类"/usr/lib/R/library"7.3-9"集群集群"/usr/lib/R/library"1.14.4"codetools "codetools" "/usr/lib/R/library" "0.2-8"编译器编译器"/usr/lib/R/library"3.0.1"数据集数据集"/usr/lib/R/library"3.0.1"外国外国"/usr/lib/R/library"0.8-49"图形图形"/usr/lib/R/library"3.0.1"grDevices "grDevices" "/usr/lib/R/library" "3.0.1"网格网格"/usr/lib/R/library"3.0.1"KernSmooth "KernSmooth" "/usr/lib/R/library" "2.23-10"格子格子"/usr/lib/R/library"0.20-23"MASS "MASS" "/usr/lib/R/library" "7.3-29"矩阵矩阵"/usr/lib/R/library"1.0-14"方法方法"/usr/lib/R/library"3.0.1"mgcv "mgcv" "/usr/lib/R/library" "1.7-26"nlme "nlme" "/usr/lib/R/library" "3.1-111"nnet "nnet" "/usr/lib/R/library" "7.3-7"并行并行"/usr/lib/R/library"3.0.1"rpart "rpart" "/usr/lib/R/library" "4.1-3"空间空间"/usr/lib/R/library"7.3-6"样条样条"/usr/lib/R/library"3.0.1"统计统计"/usr/lib/R/library"3.0.1"stats4 "stats4" "/usr/lib/R/library" "3.0.1"生存生存"/usr/lib/R/library"2.37-4"tcltk "tcltk" "/usr/lib/R/library" "3.0.1"工具工具"/usr/lib/R/library"3.0.1"utils "utils" "/usr/lib/R/library" "3.0.1"优先事项不适用杂项3d NAmvtnorm NArgl NA基地基地"引导推荐"推荐"类集群推荐"...

我只需要提取安装包的名称，所以第一列或第二列对我来说就足够了.

我尝试使用 np.loadtxt()、np.genfromtxt() 和 with open(rpack) as csvfile:，但没有人能够返回一个列表/数组，其中列或行被正确分隔(它们实际上都因不同的错误而失败).

我怎么能以列的形式读取这个输出，或者更准确地说，在列表/数组中提取已安装包的名称?

解决方案

rpack 在你的情况下是一个 rpy2.robjects.vectors.Matrix 对象.因此，您可以简单地使用 rpy2 类方法 .rx() 来提取列:

mylist = list(rpack.rx(True, 1))

试试看.

I'm trying to come up with a way to solve this question I asked yesterday:

rpy2 fails to import 'rgl' R package

My goal is to check if certain packages are installed inside R from within python.

Following the recommendation by Dirk Eddelbuettel given in a comment on his answer, I'm using the installed.packages() function from R to list all the available packages.

This is what I've got so far:

from rpy2.rinterface import RRuntimeError
from rpy2.robjects.packages import importr
utils = importr('utils')

def importr_tryhard(packname, contriburl):
    try:
        rpack = utils.installed_packages()
    except RRuntimeError:
        rpack = []
    return rpack

contriburl = 'http://cran.stat.ucla.edu/'
rpack = importr_tryhard(packname, contriburl)
print rpack

Which returns a quite large output of the form:

           Package      LibPath                         Version   
ks         "ks"         "/usr/local/lib/R/site-library" "1.8.13"  
misc3d     "misc3d"     "/usr/local/lib/R/site-library" "0.8-4"   
mvtnorm    "mvtnorm"    "/usr/local/lib/R/site-library" "0.9-9996"
rgl        "rgl"        "/usr/local/lib/R/site-library" "0.93.986"
base       "base"       "/usr/lib/R/library"            "3.0.1"   
boot       "boot"       "/usr/lib/R/library"            "1.3-9"   
class      "class"      "/usr/lib/R/library"            "7.3-9"   
cluster    "cluster"    "/usr/lib/R/library"            "1.14.4"  
codetools  "codetools"  "/usr/lib/R/library"            "0.2-8"   
compiler   "compiler"   "/usr/lib/R/library"            "3.0.1"   
datasets   "datasets"   "/usr/lib/R/library"            "3.0.1"   
foreign    "foreign"    "/usr/lib/R/library"            "0.8-49"  
graphics   "graphics"   "/usr/lib/R/library"            "3.0.1"   
grDevices  "grDevices"  "/usr/lib/R/library"            "3.0.1"   
grid       "grid"       "/usr/lib/R/library"            "3.0.1"   
KernSmooth "KernSmooth" "/usr/lib/R/library"            "2.23-10" 
lattice    "lattice"    "/usr/lib/R/library"            "0.20-23" 
MASS       "MASS"       "/usr/lib/R/library"            "7.3-29"  
Matrix     "Matrix"     "/usr/lib/R/library"            "1.0-14"  
methods    "methods"    "/usr/lib/R/library"            "3.0.1"   
mgcv       "mgcv"       "/usr/lib/R/library"            "1.7-26"  
nlme       "nlme"       "/usr/lib/R/library"            "3.1-111" 
nnet       "nnet"       "/usr/lib/R/library"            "7.3-7"   
parallel   "parallel"   "/usr/lib/R/library"            "3.0.1"   
rpart      "rpart"      "/usr/lib/R/library"            "4.1-3"   
spatial    "spatial"    "/usr/lib/R/library"            "7.3-6"   
splines    "splines"    "/usr/lib/R/library"            "3.0.1"   
stats      "stats"      "/usr/lib/R/library"            "3.0.1"   
stats4     "stats4"     "/usr/lib/R/library"            "3.0.1"   
survival   "survival"   "/usr/lib/R/library"            "2.37-4"  
tcltk      "tcltk"      "/usr/lib/R/library"            "3.0.1"   
tools      "tools"      "/usr/lib/R/library"            "3.0.1"   
utils      "utils"      "/usr/lib/R/library"            "3.0.1"   
           Priority     
ks         NA           
misc3d     NA           
mvtnorm    NA           
rgl        NA           
base       "base"       
boot       "recommended"
class      "recommended"
cluster    "recommended"
...

I need to extract just the names of the packages installed, so either the first or the second columns would be enough for me.

I've tried using np.loadtxt(), np.genfromtxt() and with open(rpack) as csvfile:, but none was able to give back a list/array where either the columns or the rows was correctly separated (they all failed with different errors actually).

How could I read this output in column form, or more to the point, extract the names of the installed packages in a list/array?

解决方案

rpack in your case is an rpy2.robjects.vectors.Matrix object. Therefore you can simply use rpy2 class method .rx() to extract the column:

mylist = list(rpack.rx(True, 1))

Have a try.

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