This document identifies computational bottlenecks in functions from benchmark.R.

Tables of most expensive function calls

Below, two tables for all test functions present profiling results with set_default_options() and set_fast_options() respectively.

Function: bfast.olscusum

f time rel_time
(TOTAL) 9.330 1.0000000
bfast 9.330 1.0000000
breakpoints 9.160 0.9817792
breakpoints.formula 8.410 0.9013934
recresid 5.660 0.6066452
recresid.default 5.645 0.6050375
extend.RSS.table 2.520 0.2700965
as.vector 1.380 0.1479100
outer 1.265 0.1355841
breakpoints.breakpointsfull 0.930 0.0996785
summary.breakpointsfull 0.880 0.0943194
RSS 0.815 0.0873526
confint.breakpointsfull 0.470 0.0503751
as.character 0.400 0.0428725
lm.fit 0.315 0.0337621
lm 0.280 0.0300107
%*% 0.250 0.0267953
breakfactor 0.200 0.0214362
f time rel_time
(TOTAL) 2.010 1.0000000
bfast 2.010 1.0000000
breakpoints 1.830 0.9104478
breakpoints.breakpointsfull 1.130 0.5621891
summary.breakpointsfull 1.060 0.5273632
breakpoints.formula 0.925 0.4601990
confint.breakpointsfull 0.550 0.2736318
lm 0.325 0.1616915
RSS 0.270 0.1343284
breakfactor 0.245 0.1218905
residuals.breakpointsfull 0.225 0.1119403
as.character 0.185 0.0920398
breakdates 0.060 0.0298507
breakdates.breakpoints 0.060 0.0298507
pargmaxV 0.045 0.0223881

Function: bfast.olsmosum

f time rel_time
(TOTAL) 8.270 1.0000000
bfast 8.270 1.0000000
breakpoints 7.935 0.9594921
breakpoints.formula 7.160 0.8657799
recresid 4.435 0.5362757
recresid.default 4.415 0.5338573
extend.RSS.table 2.465 0.2980653
as.vector 1.045 0.1263603
breakpoints.breakpointsfull 0.990 0.1197098
outer 0.950 0.1148730
summary.breakpointsfull 0.915 0.1106409
RSS 0.885 0.1070133
confint.breakpointsfull 0.500 0.0604595
as.character 0.390 0.0471584
lm.fit 0.320 0.0386941
lm 0.255 0.0308343
%*% 0.195 0.0235792
breakfactor 0.195 0.0235792
residuals.breakpointsfull 0.195 0.0235792
sctest 0.190 0.0229746
pvalue.efp 0.170 0.0205562
sctest.efp 0.170 0.0205562
f time rel_time
(TOTAL) 2.115 1.0000000
bfast 2.115 1.0000000
breakpoints 1.935 0.9148936
breakpoints.breakpointsfull 1.175 0.5555556
summary.breakpointsfull 1.105 0.5224586
breakpoints.formula 1.005 0.4751773
confint.breakpointsfull 0.575 0.2718676
RSS 0.325 0.1536643
lm 0.315 0.1489362
breakfactor 0.245 0.1158392
residuals.breakpointsfull 0.240 0.1134752
as.character 0.170 0.0803783
pargmaxV 0.045 0.0212766

Function: bfast.reccusum

f time rel_time
(TOTAL) 7.925 1.0000000
bfast 7.925 1.0000000
breakpoints 7.685 0.9697161
breakpoints.formula 6.990 0.8820189
recresid 4.430 0.5589905
recresid.default 4.415 0.5570978
extend.RSS.table 2.415 0.3047319
as.vector 1.065 0.1343849
outer 0.935 0.1179811
breakpoints.breakpointsfull 0.875 0.1104101
RSS 0.855 0.1078864
summary.breakpointsfull 0.840 0.1059937
confint.breakpointsfull 0.455 0.0574132
as.character 0.355 0.0447950
lm.fit 0.260 0.0328076
lm 0.235 0.0296530
residuals.breakpointsfull 0.190 0.0239748
%*% 0.180 0.0227129
breakfactor 0.170 0.0214511
f time rel_time
(TOTAL) 1.980 1.0000000
bfast 1.980 1.0000000
breakpoints 1.805 0.9116162
breakpoints.breakpointsfull 1.095 0.5530303
summary.breakpointsfull 1.050 0.5303030
breakpoints.formula 0.925 0.4671717
confint.breakpointsfull 0.530 0.2676768
RSS 0.310 0.1565657
lm 0.280 0.1414141
residuals.breakpointsfull 0.230 0.1161616
breakfactor 0.220 0.1111111
as.character 0.165 0.0833333
breakdates 0.120 0.0606061
breakdates.breakpoints 0.120 0.0606061

Function: bfast.recmosum

f time rel_time
(TOTAL) 7.945 1.0000000
bfast 7.945 1.0000000
breakpoints 7.700 0.9691630
breakpoints.formula 6.995 0.8804279
recresid 4.515 0.5682819
recresid.default 4.485 0.5645060
extend.RSS.table 2.340 0.2945249
as.vector 1.075 0.1353052
breakpoints.breakpointsfull 0.885 0.1113908
RSS 0.865 0.1088735
summary.breakpointsfull 0.845 0.1063562
outer 0.825 0.1038389
confint.breakpointsfull 0.460 0.0578980
as.character 0.415 0.0522341
lm 0.250 0.0314663
lm.fit 0.225 0.0283197
%*% 0.215 0.0270610
residuals.breakpointsfull 0.180 0.0226558
breakfactor 0.175 0.0220264
f time rel_time
(TOTAL) 2.125 1.0000000
bfast 2.125 1.0000000
breakpoints 1.905 0.8964706
breakpoints.breakpointsfull 1.145 0.5388235
summary.breakpointsfull 1.090 0.5129412
breakpoints.formula 0.980 0.4611765
confint.breakpointsfull 0.575 0.2705882
lm 0.325 0.1529412
RSS 0.275 0.1294118
residuals.breakpointsfull 0.245 0.1152941
breakfactor 0.230 0.1082353
as.character 0.165 0.0776471
breakdates 0.115 0.0541176
breakdates.breakpoints 0.110 0.0517647
sctest 0.045 0.0211765

Function: bfast01.test

f time rel_time
(TOTAL) 5.815 1.0000000
bfast01 5.815 1.0000000
Fstats 4.100 0.7050731
lm.fit 2.830 0.4866724
sctest 0.830 0.1427343
as.matrix 0.665 0.1143594
gefp 0.400 0.0687876
lm 0.325 0.0558899
model.matrix 0.295 0.0507309
sctest.formula 0.285 0.0490112
model.frame 0.195 0.0335340
efp 0.195 0.0335340
efp.formula 0.195 0.0335340
bfastpp 0.165 0.0283749
sctest.gefp 0.140 0.0240757
as.character 0.130 0.0223560
f time rel_time
(TOTAL) 5.975 1.0000000
bfast01 5.975 1.0000000
Fstats 4.255 0.7121339
lm.fit 2.905 0.4861925
sctest 0.765 0.1280335
as.matrix 0.685 0.1146444
gefp 0.385 0.0644351
lm 0.330 0.0552301
model.matrix 0.325 0.0543933
sctest.formula 0.245 0.0410042
model.frame 0.225 0.0376569
efp 0.185 0.0309623
efp.formula 0.185 0.0309623
bfastpp 0.145 0.0242678
sctest.gefp 0.135 0.0225941

Function: bfastmonitor.hist.all

f time rel_time
(TOTAL) 3.105 1.0000000
bfastmonitor 3.105 1.0000000
monitor 0.770 0.2479871
mefp 0.740 0.2383253
mefp.formula 0.740 0.2383253
model.frame 0.690 0.2222222
model.matrix 0.595 0.1916264
efp 0.595 0.1916264
efp.formula 0.590 0.1900161
bfastpp 0.505 0.1626409
lm 0.415 0.1336554
monitor.matrix 0.335 0.1078905
as.character 0.160 0.0515298
factor 0.145 0.0466989
lm.fit 0.125 0.0402576
mefp.efp 0.120 0.0386473
model.response 0.075 0.0241546
f time rel_time
(TOTAL) 1.065 1.0000000
bfastmonitor 1.060 0.9953052
monitor.matrix 0.330 0.3098592
bfastpp 0.290 0.2723005
mefp.matrix 0.200 0.1877934
efp.matrix 0.110 0.1032864
lm.fit 0.090 0.0845070
mefp.efp 0.065 0.0610329
as.matrix 0.025 0.0234742

Function: bfastmonitor.hist.bp

f time rel_time
(TOTAL) 6.855 1.0000000
bfastmonitor 6.855 1.0000000
history_break 6.820 0.9948942
breakpoints 6.820 0.9948942
breakpoints.formula 6.790 0.9905179
recresid 6.580 0.9598833
recresid.default 6.530 0.9525894
as.vector 1.560 0.2275711
outer 1.235 0.1801605
%*% 0.575 0.0838804
lm.fit 0.385 0.0561634
extend.RSS.table 0.155 0.0226112
f time rel_time
(TOTAL) 0.795 1.0000000
bfastmonitor 0.795 1.0000000
history_break.matrix 0.780 0.9811321
breakpoints.matrix 0.755 0.9496855
breakpoints 0.065 0.0817610
breakpoints.breakpointsfull 0.065 0.0817610
summary.breakpointsfull 0.055 0.0691824

Function: bfastmonitor.hist.roc

f time rel_time
(TOTAL) 6.765 1.0000000
bfastmonitor 6.765 1.0000000
efp 4.415 0.6526238
efp.formula 4.410 0.6518847
history_roc 4.005 0.5920177
history_roc.formula 4.005 0.5920177
recresid 3.400 0.5025868
recresid.default 3.395 0.5018477
model.frame 0.860 0.1271249
as.vector 0.845 0.1249076
outer 0.730 0.1079084
model.matrix 0.660 0.0975610
mefp 0.650 0.0960828
mefp.formula 0.650 0.0960828
monitor 0.605 0.0894309
bfastpp 0.445 0.0657797
lm 0.365 0.0539542
lm.fit 0.285 0.0421286
%*% 0.265 0.0391722
monitor.matrix 0.230 0.0339985
as.character 0.220 0.0325203
model.response 0.155 0.0229120
f time rel_time
(TOTAL) 1.675 1.0000000
bfastmonitor 1.675 1.0000000
efp.matrix 0.675 0.4029851
history_roc.matrix 0.670 0.4000000
recresid 0.470 0.2805970
recresid.default 0.465 0.2776119
monitor.matrix 0.305 0.1820896
bfastpp 0.240 0.1432836
mefp.matrix 0.165 0.0985075
lm.fit 0.110 0.0656716
mefp.efp 0.070 0.0417910
ts 0.050 0.0298507
sctest 0.040 0.0238806
sctest.efp 0.040 0.0238806

Function: bfastmonitor.ME

f time rel_time
(TOTAL) 7.670 1.0000000
bfastmonitor 7.665 0.9993481
efp 6.410 0.8357236
efp.formula 6.410 0.8357236
mefp 5.840 0.7614081
mefp.formula 5.840 0.7614081
root.matrix.crossprod 5.520 0.7196871
root.matrix 3.270 0.4263364
root.matrix 3.270 0.4263364
lm.fit 0.905 0.1179922
monitor 0.870 0.1134289
monitor.matrix 0.815 0.1062581
history_roc 0.620 0.0808344
history_roc.formula 0.615 0.0801825
recresid 0.535 0.0697523
recresid.default 0.535 0.0697523
as.matrix 0.290 0.0378096
f time rel_time
(TOTAL) 1.240 1.0000000
bfastmonitor 1.240 1.0000000
efp.matrix 0.615 0.4959677
mefp.matrix 0.530 0.4274194
monitor.matrix 0.505 0.4072581
root.matrix.crossprod 0.330 0.2661290
history_roc.matrix 0.105 0.0846774
recresid 0.085 0.0685484
recresid.default 0.080 0.0645161
lm.fit 0.065 0.0524194
bfastpp 0.045 0.0362903

Function: bfastmonitor.modis

f time rel_time
(TOTAL) 9.980 1.0000000
bfastmonitor 7.040 0.7054108
efp 4.415 0.4423848
efp.formula 4.410 0.4418838
history_roc 4.060 0.4068136
history_roc.formula 4.060 0.4068136
recresid 3.350 0.3356713
recresid.default 3.350 0.3356713
bfastts 2.365 0.2369739
as.vector 1.005 0.1007014
model.frame 0.840 0.0841683
outer 0.795 0.0796593
as.ts 0.720 0.0721443
model.matrix 0.675 0.0676353
mefp 0.655 0.0656313
mefp.formula 0.655 0.0656313
monitor 0.650 0.0651303
bfastpp 0.575 0.0576152
factor 0.515 0.0516032
as.character 0.480 0.0480962
lm 0.425 0.0425852
%*% 0.375 0.0375752
monitor.matrix 0.305 0.0305611
lm.fit 0.295 0.0295591
f time rel_time
(TOTAL) 3.095 1.0000000
bfastmonitor 1.760 0.5686591
bfastts 0.770 0.2487884
history_roc.matrix 0.715 0.2310178
efp.matrix 0.675 0.2180937
recresid 0.505 0.1631664
recresid.default 0.505 0.1631664
monitor.matrix 0.335 0.1082391
bfastpp 0.215 0.0694669
mefp.matrix 0.215 0.0694669
ts 0.135 0.0436187
as.ts 0.110 0.0355412
lm.fit 0.095 0.0306947
mefp.efp 0.090 0.0290792
sctest 0.075 0.0242326
sctest.efp 0.075 0.0242326

Function: bfastmonitor.olscusum

f time rel_time
(TOTAL) 6.775 1.0000000
bfastmonitor 6.770 0.9992620
efp 4.415 0.6516605
efp.formula 4.415 0.6516605
history_roc 4.055 0.5985240
history_roc.formula 4.055 0.5985240
recresid 3.330 0.4915129
recresid.default 3.330 0.4915129
model.matrix 0.930 0.1372694
model.frame 0.900 0.1328413
outer 0.820 0.1210332
as.vector 0.810 0.1195572
monitor 0.620 0.0915129
mefp 0.615 0.0907749
mefp.formula 0.610 0.0900369
bfastpp 0.520 0.0767528
lm 0.375 0.0553506
lm.fit 0.305 0.0450185
%*% 0.285 0.0420664
as.character 0.220 0.0324723
factor 0.145 0.0214022
f time rel_time
(TOTAL) 1.365 1.0000000
bfastmonitor 1.365 1.0000000
history_roc.matrix 0.670 0.4908425
efp.matrix 0.620 0.4542125
recresid 0.495 0.3626374
recresid.default 0.490 0.3589744
bfastpp 0.230 0.1684982
mefp.matrix 0.210 0.1538462
mefp.efp 0.120 0.0879121
lm.fit 0.085 0.0622711
sctest 0.075 0.0549451
sctest.efp 0.075 0.0549451
monitor.matrix 0.055 0.0402930

Function: bfastmonitor.RE

f time rel_time
(TOTAL) 5.010 1.0000000
bfastmonitor 5.010 1.0000000
efp 4.660 0.9301397
efp.formula 4.660 0.9301397
mefp 4.310 0.8602794
mefp.formula 4.310 0.8602794
root.matrix.crossprod 3.515 0.7015968
root.matrix 2.135 0.4261477
root.matrix 2.135 0.4261477
lm.fit 0.790 0.1576846
history_roc 0.385 0.0768463
history_roc.formula 0.380 0.0758483
recresid 0.340 0.0678643
recresid.default 0.340 0.0678643
as.matrix 0.195 0.0389222
monitor 0.155 0.0309381
monitor.matrix 0.130 0.0259481
f time rel_time
(TOTAL) 0.540 1.0000000
bfastmonitor 0.535 0.9907407
efp.matrix 0.395 0.7314815
mefp.matrix 0.355 0.6574074
monitor.matrix 0.095 0.1759259
lm.fit 0.090 0.1666667
history_roc.matrix 0.065 0.1203704
recresid 0.045 0.0833333
recresid.default 0.045 0.0833333
mefp.efp 0.020 0.0370370

Graphs of most expensive function calls

The following graphs present call graphs of most expensive operations. Given percentages represent the time a function needs to complete relative to the overall computation time. For all test functions, two graphs with set_default_options() and set_fast_options() respectively are shown.

This report has been generated on 2017-01-06 13:23:37.