<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><p>The j-expression is evaluated from within C for each group (unless they’re optimised with GForce - a new initiative in data.table). And <code>eval(.SD)</code> or <code>eval(anything(.SD))</code> is costly. </p>
<p>You can get around it by listing the columns by yourself and using <code>.I</code> instead, as follows:</p>
<pre><code>test[test[, .I[length(unique(list(x1,x2,x3))[[1L]]) > 1L], by=id]$V1]
# 0.140 0.001 0.142
</code></pre>
<p>Takes about 0.14 seconds. </p>
<hr>
<p>An even faster way is:</p>
<pre><code>system.time({
ans = test[test[, .I[.N > 1], by=id]$V1] # (1)
ans = ans[, .N, by=names(ans)] # (2)
ans = ans[ans[, .I[.N > 1L], by=id]$V1] # (3)
})
# 0.026 0.000 0.027
</code></pre>
<p>The idea for the second case is: </p>
<p>(1) remove all entries where there’s just 1 row corresponding to that <code>id</code>.<br>
(2) Aggregate this result by all the columns now and get the number of rows in the column <code>N</code> (we won’t have to use this column though).<br>
(3) Now, if we aggregate by <code>id</code> and if any id has just 1 row, then it’d mean that that <code>id</code> has had more than 1 rows (step (1) filtering ensures this), but all of them are same and we don’t need them. So we just filter for those where .N > 1L.</p>
<p>HTH</p>
<p><style>body{font-family:Helvetica,Arial;font-size:13px}</style><style>body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
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p, blockquote, ul, ol, dl, li, table, pre {
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table {
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color: rgb(51, 51, 51);
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padding: 0; }
table tr:nth-child(2n) {
background-color: #f8f8f8; }
table tr th {
font-weight: bold;
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table tr th :first-child, table tr td :first-child {
margin-top: 0; }
table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
.send { color:#77bb77; }
.server { color:#7799bb; }
.error { color:#AA0000; }</style></p><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div> <div id="bloop_sign_1402709866978106112" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">Arun</div></div> <div style="color:black"><br>From: <span style="color:black">Ron Hylton</span> <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>Reply: <span style="color:black">Ron Hylton</span> <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>Date: <span style="color:black">June 14, 2014 at 3:30:55 AM</span><br>To: <span style="color:black">datatable-help@lists.r-forge.r-project.org</span> <a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a><br>Subject: <span style="color:black"> Re: [datatable-help] data.table is asking for help <br></span></div><br> <blockquote type="cite" class="clean_bq"><span><div lang="EN-US" link="blue" vlink="purple" xml:lang="EN-US"><div></div><div>
<!--[if gte mso 9]><xml>
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<title></title>
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
The performance is what puzzles me; the results are correct so the
warnings don’t matter, and not all the variations I’ve tried have
warnings. On the real dataset (~800,000 rows) datatable takes
about 1.5 times longer than dataframe + ddply. I expected it
to be substantially faster.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
</span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b>
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Arunkumar
Srinivasan [mailto:aragorn168b@gmail.com]<br>
<b>Sent:</b> Friday, June 13, 2014 8:57 PM<br>
<b>To:</b> Ron Hylton;
datatable-help@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [datatable-help] data.table is asking for
help</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<div id="bloop_customfont">
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
However there’s another aspect. While I’m relatively new to R
my understanding is that a function argument should be modifiable
within the function body without affecting the caller, which
perhaps conflicts with the behavior of .SD.</span></p>
</div>
</div>
</blockquote>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Helvetica","sans-serif"">`data.table`
is designed for working with *really large* data sets in
mind (> 100 or 200 GB in memory even). And therefore, as a
design feature, it trades in "referential transparency" for
manipulating data objects *as efficient as possible* in terms of
both *speed* and *memory usage* (most of the times they go
hand-in-hand).</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Helvetica","sans-serif"">This is perhaps the biggest
design choice one needs to be aware of when working/choosing
data.tables. It is possible to modify objects by reference using
data.table - All the functions that begin with "set*" modify
objects by reference. The only other non "set*" function is `:=`
operator.</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Helvetica","sans-serif"">HTH</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">
Arun</span></p>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">
<br>
From: Ron Hylton <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>
Reply: Ron Hylton <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>
Date: June 14, 2014 at 2:52:04 AM<br>
To: <a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a>
<a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a><br>
Subject: Re: [datatable-help] data.table is asking for
help</span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif""><br>
<br></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
I suspected it was something like this. As one clarification,
there is a setkey(test,id) before any setkey(.SD). If
setkey(test,id) is changed to setkey(test) so all columns are in
the original datatable key then the warning goes away.</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
However there’s another aspect. While I’m relatively new to R
my understanding is that a function argument should be modifiable
within the function body without affecting the caller, which
perhaps conflicts with the behavior of .SD.</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
</span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
<b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
From:</span></b> <span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Arunkumar
Srinivasan [<a href="mailto:aragorn168b@gmail.com">mailto:aragorn168b@gmail.com</a>]<br>
<b>Sent:</b> Friday, June 13, 2014 8:23 PM<br>
<b>To:</b> Ron Hylton; <a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [datatable-help] data.table is asking for
help</span></p>
</div>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Nicely
reproducible post. Reproducible in v1.9.3 (latest commit) as
well.</span></p>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">This is a
tricky one. It happens because you’re setting key on</span>
<code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">which
should normally not be allowed. What happens is, when you set key
the first time, there’s no key set (here) and therefore key is set
on all the columns</span> <code><span style="font-size:10.0pt">x1</span></code><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">,</span>
<code><span style="font-size:10.0pt">x2</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">and</span>
<code><span style="font-size:10.0pt">x3</span></code><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">.</span></p>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Now, the
next group (in the</span> <code><span style="font-size:10.0pt">by=.</span></code><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">) is passed
to your function, it’ll have the</span> <code><span style="font-size:10.0pt">key</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">already set
to</span> <code><span style="font-size:10.0pt">x1,x2,x3</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">(because</span>
<code><span style="font-size:10.0pt">setkey</span></code>
<span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">modifies
the object by reference), but</span> <code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">has
obtained <strong><span style="font-family:"Helvetica","sans-serif"">new</span></strong> data
corresponding to <em><span style="font-family:"Helvetica","sans-serif"">this</span></em> group.
And</span> <code><span style="font-size:10.0pt">data.table</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">sorts this
data, knowing that it already has key set.. but if the key is set
then the order must be 1:n. But it wouldn’t be, as this data isn’t
sorted.</span> <code><span style="font-size:10.0pt">data.table</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">warns in
those scenarios.. and that’s why you get the warning.</span></p>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">To verify
this, you can try:</span></p>
<div style="border:solid #CCCCCC 1.0pt;padding:3.0pt 6.0pt 3.0pt 6.0pt">
<pre style="background:#F8F8F8"><code>conflictsTable1 <- function(f, address) {</code>
</pre>
<pre style="background:#F8F8F8"><code> u <- unique(setkey(f))</code>
</pre>
<pre style="background:#F8F8F8"><code> setattr(f, 'sorted', NULL)</code>
</pre>
<pre style="background:#F8F8F8"><code> if (nrow(u) == 1) return(NULL)</code>
</pre>
<pre style="background:#F8F8F8"><code> u</code>
</pre>
<pre style="background:#F8F8F8"><code>}</code>
</pre></div>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Basically,
we set the key of</span> <code><span style="font-size:10.0pt">f</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">(which is
equal to</span> <code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">as it’s
only modified by reference) to</span> <code><span style="font-size:10.0pt">NULL</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">everytime
after.. so that</span> <code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">for the new
group will not have the key set.</span></p>
<p><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">The ideal
scenario here, IIUC, is that</span> <code><span style="font-size:10.0pt">setkey(.SD)</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">or things
pointing to</span> <code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">should not
be possible (locking binding doesn’t seem to affect things done by
reference..).</span> <code><span style="font-size:10.0pt">.SD</span></code> <span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">however
should retain the key of the data.table, if a key was set, wherever
possible.</span></p>
<div id="bloop_customfont">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif""> </span></p>
</div>
<div id="bloop_sign_1402704505278157056">
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Arun</span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"><br>
From: Ron Hylton <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>
Reply: Ron Hylton <a href="mailto:rhylton@verizon.net">rhylton@verizon.net</a><br>
Date: June 14, 2014 at 1:55:53 AM<br>
To: <a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a>
<a href="mailto:datatable-help@lists.r-forge.r-project.org">datatable-help@lists.r-forge.r-project.org</a><br>
Subject: [datatable-help] data.table is asking for
help</span></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"> </p>
<blockquote style="margin-left:0in;margin-top:11.25pt;margin-right:0in;margin-bottom:11.25pt">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The code below
generates the warning:</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;word-break:break-all">
<span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5">
In setkeyv(x, cols, verbose = verbose) :</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;word-break:break-all">
<span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5">
Already keyed by this key but had invalid row order, key
rebuilt. If you didn't go under the hood please let datatable-help
know so the root cause can be fixed.</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;word-break:break-all">
<span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5">
</span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This is my
first attempt at using datatable so I probably did something dumb,
but maybe that‘s useful for someone. The first case is the
one that gives the warnings.</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’m also
surprised at the timings. I wrote the original algorithm
using dataframe & ddply and I expected datatable to be
substantially faster; the opposite is true.</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The algorithm
does the following: Certain columns in the table are keys and
others are values in the sense that each row with the same set of
keys should have the same set of values. Find all the key
sets for which this is not true and return the keys sets +
conflicting value sets.</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Insight into
the performance would be appreciated.</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Regards,</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Ron</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
library(data.table)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
library(plyr)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
conflictsTable1 <- function(f) {</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u <-
unique(setkey(f))</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> if
(nrow(u) == 1) return(NULL)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">}</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
conflictsTable2 <- function(f) {</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u <-
unique(f)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> if
(nrow(u) == 1) return(NULL)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">}</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">conflictsFrame
<- function(f) {</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u <-
unique(f)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> if
(nrow(u) == 1) return(NULL)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> u</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">}</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">N <-
10000</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">test <-
data.table(id=as.character(10000*sample(1:N,N,replace=TRUE)),
x1=rnorm(N), x2=rnorm(N), x3=rnorm(N))</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
setkey(test,id)</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
print(system.time(ut1 <- test[, conflictsTable1(.SD),
by=id]))</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
print(system.time(ut2 <- test[, conflictsTable2(.SD),
by=id]))</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
print(system.time(uf <- ddply(test, .(id), conflictsFrame)))</p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">
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