Sent from my phone. Please excuse my brevity.
On August 22, 2017 5:53:09 AM PDT, raphael.felber at agroscope.admin.ch wrote:
>Dear all
>
>I was thinking about efficient reading data into R and tried several
>ways to test if load(file.Rdata) or readRDS(file.rds) is faster. The
>files file.Rdata and file.rds contain the same data, the first created
>with save(d, ' file.Rdata', compress=F) and the second with saveRDS(d,
>' file.rds', compress=F).
>
>First I used the function microbenchmark() and was a astonished about
>the max value of the output.
>
>FIRST TEST:
>> library(microbenchmark)
>> microbenchmark(
>+ n <- readRDS('file.rds'),
>+ load('file.Rdata')
>+ )
>Unit: milliseconds
>expr min lq
>mean median uq
> max neval
>n <- readRDS(fl1) 106.5956 109.6457 237.3844
> 117.8956 141.9921 10934.162 100
>load(fl2) 295.0654 301.8162 335.6266
> 308.3757 319.6965 1915.706 100
>
>It looks like the max value is an outlier.
>
>So I tried:
>SECOND TEST:
>> sapply(1:10, function(x) system.time(n <- readRDS('file.rds'))[3])
>elapsed elapsed elapsed
>elapsed elapsed elapsed
>elapsed elapsed elapsed
>elapsed
>10.50 0.11 0.11
>0.11 0.10 0.11
>0.11 0.11 0.12
> 0.12
>> sapply(1:10, function(x) system.time(load'flie.Rdata'))[3])
>elapsed elapsed elapsed
>elapsed elapsed elapsed
>elapsed elapsed elapsed
>elapsed
>1.86 0.29 0.31
>0.30 0.30 0.31
>0.30 0.29 0.31
> 0.30
>
>Which confirmed my suspicion; the first time loading the data takes
>much longer than the following times. I suspect that this has something
>to do how the data is assigned and that R doesn't has to 'fully' read
>the data, if it is read the second time.
>
>So the question remains, how can I make a realistic benchmark test?
>From the first test I would conclude that reading the *.rds file is
>faster. But this holds only for a large number of neval. If I set times
>= 1 then reading the *.Rdata would be faster (as also indicated by the
>second test).
>
>Thanks for any help or comments.
>
>Kind regards
>
>Raphael
>------------------------------------------------------------------------------------
>Raphael Felber, PhD
>Scientific Officer, Climate & Air Pollution
>
>Federal Department of Economic Affairs,
>Education and Research EAER
>Agroscope
>Research Division, Agroecology and Environment
>
>Reckenholzstrasse 191, CH-8046 Z?rich
>Phone +41 58 468 75 11
>Fax +41 58 468 72 01
>raphael.felber at agroscope.admin.ch<mailto:raphael.felber at agroscope.admin.ch>
>www.agroscope.ch<http://www.agroscope.ch/>
>
>
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