fix R conversion

judithabk6 · Dec 21, 2023 · f4a87be · f4a87be
1 parent 2cd241c
commit f4a87be
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/src/med_bench/mediation.py b/src/med_bench/mediation.py
@@ -957,7 +957,7 @@ def r_mediation_DML(y, t, m, x, trim=0.05, order=1):
             Polynomials/interactions are created using the Generate.
             Powers command of the LARF package.
     """
-    x_r, t_r, m_r, y_r = [base.as_matrix(_convert_array_to_R(uu)) for uu in
+    x_r, t_r, m_r, y_r = [_convert_array_to_R(uu) for uu in
                           (x, t, m, y)]
     res = causalweight.medDML(y_r, t_r, m_r, x_r, trim=trim, order=order)
     raw_res_R = np.array(res.rx2('results'))

diff --git a/src/med_bench/utils/utils.py b/src/med_bench/utils/utils.py
@@ -2,7 +2,11 @@
 
 import rpy2.robjects as robjects
 import rpy2.robjects.packages as rpackages
-from rpy2.robjects import pandas2ri, numpy2ri
+import rpy2.rinterface as ri
+
+ri.initr()
+matrix = ri.baseenv["matrix"]
+
 
 def get_interactions(interaction, *args):
     """
@@ -59,5 +63,5 @@ def _convert_array_to_R(x):
     if len(x.shape) == 1:
         return robjects.FloatVector(x)
     elif len(x.shape) == 2:
-        return robjects.r.matrix(robjects.FloatVector(x.ravel()),
-                                 nrow=x.shape[0], byrow='TRUE')
+        return matrix(robjects.FloatVector(x.ravel()),
+                      nrow=x.shape[0], byrow='TRUE')