Hello there,

I am not quite sure how to interpret the output of Rprof (in the following the output I was staring at). I was poking around the web a little bit for documentation but without much success. I guess if I want to figure out what takes so long in my code the 2nd table $by.total and the total.pct column (pct = percent) is the most helpful. What does it mean that [ or [.data.frame is taking so much time, and is there something I could do to improve the situation.

Thanks,

-- D


> summaryRprof(tmp)
$by.self
              self.time self.pct total.time total.pct
eval.with.vis     75.92     22.4     339.18     100.0
[.data.frame      46.28     13.6     186.36      54.9
structure         31.78      9.4      79.92      23.6
inherits          27.28      8.0      29.08       8.6
match             20.38      6.0      53.84      15.9
names             20.20      6.0      20.20       6.0
length             9.68      2.9       9.68       2.9
pmatch             9.02      2.7      10.46       3.1
[                  8.56      2.5     194.92      57.5
eval               5.84      1.7      31.02       9.1
any                5.78      1.7       6.88       2.0
match.arg          5.68      1.7      40.54      12.0
is.factor          4.68      1.4      32.28       9.5
cor                4.66      1.4      67.44      19.9
[[                 4.32      1.3      13.46       4.0
stopifnot          4.10      1.2      11.94       3.5
<Anonymous>        4.08      1.2       4.56       1.3
deparse            3.86      1.1      23.92       7.1
[[.data.frame      3.70      1.1       9.14       2.7
==                 3.20      0.9       3.20       0.9
vector             2.80      0.8      11.94       3.5
rank               2.40      0.7      22.58       6.7
>                  2.16      0.6       2.16       0.6
!                  1.92      0.6       1.92       0.6
%in%               1.86      0.5      25.48       7.5
switch             1.68      0.5       1.76       0.5
names<-            1.56      0.5       1.78       0.5
<                  1.54      0.5       1.54       0.5
.deparseOpts       1.50      0.4      11.98       3.5
match.call         1.48      0.4       2.84       0.8
.Call              1.34      0.4       1.34       0.4
is.na              1.30      0.4       1.30       0.4
all                1.24      0.4       1.48       0.4
formals            1.22      0.4       2.46       0.7
mode               1.22      0.4       1.32       0.4
sum                1.20      0.4       1.62       0.5
sys.parent         1.14      0.3       1.14       0.3
as.character       0.98      0.3       0.98       0.3
parent.frame       0.96      0.3       0.96       0.3
attributes<-       0.90      0.3       0.90       0.3
sys.call           0.86      0.3       1.36       0.4
list               0.82      0.2       0.82       0.2
&                  0.74      0.2       0.74       0.2
sys.function       0.58      0.2       1.22       0.4
attr<-             0.58      0.2       0.58       0.2
is.logical         0.56      0.2       0.56       0.2
Rank               0.54      0.2      23.18       6.8
!=                 0.54      0.2       0.54       0.2
:                  0.52      0.2       0.52       0.2
-                  0.46      0.1       0.46       0.1
as.vector          0.44      0.1       0.44       0.1
.subset2           0.36      0.1       0.36       0.1
min                0.34      0.1       0.34       0.1
seq_along          0.34      0.1       0.34       0.1
max                0.32      0.1       0.32       0.1
is.data.frame      0.24      0.1       1.72       0.5
is.character       0.18      0.1       0.18       0.1
is.matrix          0.18      0.1       0.18       0.1
oldClass<-         0.18      0.1       0.18       0.1
is.list            0.16      0.0       0.16       0.0
(                  0.14      0.0       0.14       0.0
dim                0.14      0.0       0.14       0.0
^                  0.12      0.0       0.12       0.0
is.pairlist        0.10      0.0       0.10       0.0
is.null            0.08      0.0       0.08       0.0
attributes         0.06      0.0       0.06       0.0
is.atomic          0.06      0.0       0.06       0.0
baseenv            0.04      0.0       0.04       0.0
is.call            0.04      0.0       0.04       0.0
is.name            0.04      0.0       0.04       0.0
is.expression      0.02      0.0       0.02       0.0
source             0.00      0.0     339.18     100.0
$by.total
              total.time total.pct self.time self.pct
eval.with.vis     339.18     100.0     75.92     22.4
source            339.18     100.0      0.00      0.0
[                 194.92      57.5      8.56      2.5
[.data.frame      186.36      54.9     46.28     13.6
structure          79.92      23.6     31.78      9.4
cor                67.44      19.9      4.66      1.4
match              53.84      15.9     20.38      6.0
match.arg          40.54      12.0      5.68      1.7
is.factor          32.28       9.5      4.68      1.4
eval               31.02       9.1      5.84      1.7
inherits           29.08       8.6     27.28      8.0
%in%               25.48       7.5      1.86      0.5
deparse            23.92       7.1      3.86      1.1
Rank               23.18       6.8      0.54      0.2
rank               22.58       6.7      2.40      0.7
names              20.20       6.0     20.20      6.0
[[                 13.46       4.0      4.32      1.3
.deparseOpts       11.98       3.5      1.50      0.4
stopifnot          11.94       3.5      4.10      1.2
vector             11.94       3.5      2.80      0.8
pmatch             10.46       3.1      9.02      2.7
length              9.68       2.9      9.68      2.9
[[.data.frame       9.14       2.7      3.70      1.1
any                 6.88       2.0      5.78      1.7
<Anonymous>         4.56       1.3      4.08      1.2
==                  3.20       0.9      3.20      0.9
match.call          2.84       0.8      1.48      0.4
formals             2.46       0.7      1.22      0.4
>                   2.16       0.6      2.16      0.6
!                   1.92       0.6      1.92      0.6
names<-             1.78       0.5      1.56      0.5
switch              1.76       0.5      1.68      0.5
is.data.frame       1.72       0.5      0.24      0.1
sum                 1.62       0.5      1.20      0.4
<                   1.54       0.5      1.54      0.5
all                 1.48       0.4      1.24      0.4
sys.call            1.36       0.4      0.86      0.3
.Call               1.34       0.4      1.34      0.4
mode                1.32       0.4      1.22      0.4
is.na               1.30       0.4      1.30      0.4
sys.function        1.22       0.4      0.58      0.2
sys.parent          1.14       0.3      1.14      0.3
as.character        0.98       0.3      0.98      0.3
parent.frame        0.96       0.3      0.96      0.3
attributes<-        0.90       0.3      0.90      0.3
list                0.82       0.2      0.82      0.2
&                   0.74       0.2      0.74      0.2
attr<-              0.58       0.2      0.58      0.2
is.logical          0.56       0.2      0.56      0.2
!=                  0.54       0.2      0.54      0.2
:                   0.52       0.2      0.52      0.2
-                   0.46       0.1      0.46      0.1
as.vector           0.44       0.1      0.44      0.1
.subset2            0.36       0.1      0.36      0.1
min                 0.34       0.1      0.34      0.1
seq_along           0.34       0.1      0.34      0.1
max                 0.32       0.1      0.32      0.1
is.character        0.18       0.1      0.18      0.1
is.matrix           0.18       0.1      0.18      0.1
oldClass<-          0.18       0.1      0.18      0.1
is.list             0.16       0.0      0.16      0.0
(                   0.14       0.0      0.14      0.0
dim                 0.14       0.0      0.14      0.0
^                   0.12       0.0      0.12      0.0
is.pairlist         0.10       0.0      0.10      0.0
is.null             0.08       0.0      0.08      0.0
attributes          0.06       0.0      0.06      0.0
is.atomic           0.06       0.0      0.06      0.0
baseenv             0.04       0.0      0.04      0.0
is.call             0.04       0.0      0.04      0.0
is.name             0.04       0.0      0.04      0.0
is.expression       0.02       0.0      0.02      0.0
$sampling.time
[1] 339.18

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