Question

我试图通过limmbo R包使用py模块reticulate（https://github.com/HannahVMeyer/limmbo）和R.我已经使用Anaconda2成功安装了limmbo。我现在正在尝试使用函数limmbo$core$vdbootstrap$LiMMBo$runBootstrapCovarianceEstimation，如下面的代码所示。当我运行下面的代码时，我得到一个关于将float64转换为integer64的错误。

```{r}
library(reticulate)
import("limmbo") -> limmbo
```

然后我运行python代码：

```{python}
import numpy
from numpy.random import RandomState
from numpy.linalg import cholesky as chol
from limmbo.core.vdsimple import vd_reml
from limmbo.io.input import InputData
random = RandomState(15)
N = 100
S = 1000
P = 3
snps = (random.rand(N, S) < 0.2).astype(float)
kinship = numpy.dot(snps, snps.T) / float(10)
y  = random.randn(N, P)
pheno = numpy.dot(chol(kinship), y)
pheno_ID = [ 'PID{}'.format(x+1) for x in range(P)]
samples = [ 'SID{}'.format(x+1) for x in range(N)]
datainput = InputData()
datainput.addPhenotypes(phenotypes = pheno,
phenotype_ID = pheno_ID, pheno_samples = samples)
datainput.addRelatedness(relatedness = kinship,
relatedness_samples = samples)
```

当我尝试运行R函数limmbo$core$vdbootstrap$LiMMBo$runBootstrapCovarianceEstimation：

时出现问题

```{r}
(limmbo$core$vdbootstrap$LiMMBo(py$datainput, timing = TRUE, iterations = 100, S = 2) -> foo)
limmbo$core$vdbootstrap$LiMMBo$runBootstrapCovarianceEstimation(foo, cpus = 1, seed = 12345)
```



Error in py_call_impl(callable, dots$args, dots$keywords) : 
  TypeError: Cannot cast array from dtype('float64') to dtype('int64') according to the rule 'safe'

Detailed traceback: 
  File "/Users/frederickboehm/anaconda2/lib/python2.7/site-packages/limmbo/core/vdbootstrap.py", line 96, in runBootstrapCovarianceEstimation
    minCooccurrence=minCooccurrence)
  File "/Users/frederickboehm/anaconda2/lib/python2.7/site-packages/limmbo/core/vdbootstrap.py", line 353, in __generateBootstrapMatrix
    rand_state = np.random.RandomState(seed)
  File "mtrand.pyx", line 644, in mtrand.RandomState.__init__
  File "mtrand.pyx", line 687, in mtrand.RandomState.seed
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> py_call_impl ->     .Call
Execution halted

Answer 1

首先，通过导入numpy模块 np <- import("numpy", convert = FALSE)。

然后，您可以使用int64重新创建具有显式类型reticulate::np_array(datainput, dtype = np$int64)的numpy数组。

您可以在this tutorial中了解有关如何操作和创建数组的详细信息。

希望这有帮助。

Answer 2

Yuan的教程（上面的答案中的链接）包含允许我回答问题的建议。以下是我修订的R代码，截至目前，该代码有效：

np <- import("numpy", convert = FALSE)
(limmbo$core$vdbootstrap$LiMMBo(datainput, timing = TRUE, iterations = np_array(10, dtype = "int64"), S = np_array(2, dtype = "int64")) -> foo)
limmbo$core$vdbootstrap$LiMMBo$runBootstrapCovarianceEstimation(foo, cpus = np$int(1), seed = np_array(1232, dtype = "int64"))

R，python，网状和limmbo：将数组'float64'强制转换为'int64'错误

2 个答案: