<div dir="ltr"><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">Hi,<br>I think that the problem is that since a genind object is a list, the nrow is NULL.<br><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">Probably you want to sample from object$tab instead.<br><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">Hope it helps.<br><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">Best<br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br><br></div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><span style="font-family:courier new,monospace">Francesco Montinaro</span></div></div>
<br><div class="gmail_quote">On 23 October 2014 16:04, <span dir="ltr"><<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">adegenet-forum-request@lists.r-forge.r-project.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send adegenet-forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. repooling random rows from genind objects (Spencer Bruce)<br>
2. Re: repooling random rows from genind objects (Jombart, Thibaut)<br>
3. Re: repooling random rows from genind objects (Spencer Bruce)<br>
4. Re: repooling random rows from genind objects (Jombart, Thibaut)<br>
5. Re: repooling random rows from genind objects (Spencer Bruce)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 23 Oct 2014 10:29:10 -0400<br>
From: Spencer Bruce <<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] repooling random rows from genind objects<br>
Message-ID:<br>
<CAGjKGeaQyQ=<a href="mailto:UFFOSerHR1qeKXHSwVzF-0whQf2do83wOV38s5w@mail.gmail.com">UFFOSerHR1qeKXHSwVzF-0whQf2do83wOV38s5w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello All!<br>
<br>
I have three seperate populations as genind objects. What I would like to<br>
do is pull a certain number of random individuals from each, to form a new<br>
single genind population.<br>
<br>
I would then like individuals from this new genind population to mate<br>
randomly, producing another genind object which would contain their<br>
offspring.<br>
<br>
Below is the code I came up with (which does not work):<br>
<br>
Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1), 750),<br>
], pop2[sample(nrow(pop2), 750), ], n=2000)<br>
<br>
Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],<br>
Year1[sample(nrow(Year1), 1000), ], n=2000)<br>
<br>
<br>
any help would be greatly appreciated!<br>
<br>
Best,<br>
Spencer<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<br>
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Message: 2<br>
Date: Thu, 23 Oct 2014 14:50:24 +0000<br>
From: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
To: Spencer Bruce <<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>>,<br>
"<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] repooling random rows from genind<br>
objects<br>
Message-ID:<br>
<<a href="mailto:2CB2DA8E426F3541AB1907F98ABA6570ABE6AE7F@icexch-m1.ic.ac.uk">2CB2DA8E426F3541AB1907F98ABA6570ABE6AE7F@icexch-m1.ic.ac.uk</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hello,<br>
hard to figure out what is wrong without the error message..<br>
Cheers<br>
Thibaut<br>
________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Spencer Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>]<br>
Sent: 23 October 2014 15:29<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] repooling random rows from genind objects<br>
<br>
Hello All!<br>
<br>
I have three seperate populations as genind objects. What I would like to do is pull a certain number of random individuals from each, to form a new single genind population.<br>
<br>
I would then like individuals from this new genind population to mate randomly, producing another genind object which would contain their offspring.<br>
<br>
Below is the code I came up with (which does not work):<br>
<br>
Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1), 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)<br>
<br>
Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ], Year1[sample(nrow(Year1), 1000), ], n=2000)<br>
<br>
<br>
any help would be greatly appreciated!<br>
<br>
Best,<br>
Spencer<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 23 Oct 2014 10:52:59 -0400<br>
From: Spencer Bruce <<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>><br>
To: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
Cc: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] repooling random rows from genind<br>
objects<br>
Message-ID:<br>
<<a href="mailto:CAGjKGeZhjLhurZbKiMZxSmZV_GFC3quw58FPt06LrXwakRDPeA@mail.gmail.com">CAGjKGeZhjLhurZbKiMZxSmZV_GFC3quw58FPt06LrXwakRDPeA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Error message:<br>
<br>
Error in <a href="http://sample.int" target="_blank">sample.int</a>(length(x), size, replace, prob) :<br>
invalid first argument<br>
<br>
On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><br>
> wrote:<br>
<br>
><br>
> Hello,<br>
> hard to figure out what is wrong without the error message..<br>
> Cheers<br>
> Thibaut<br>
> ------------------------------<br>
> *From:* <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<br>
> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Spencer<br>
> Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>]<br>
> *Sent:* 23 October 2014 15:29<br>
> *To:* <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
> *Subject:* [adegenet-forum] repooling random rows from genind objects<br>
><br>
> Hello All!<br>
><br>
> I have three seperate populations as genind objects. What I would like<br>
> to do is pull a certain number of random individuals from each, to form a<br>
> new single genind population.<br>
><br>
> I would then like individuals from this new genind population to mate<br>
> randomly, producing another genind object which would contain their<br>
> offspring.<br>
><br>
> Below is the code I came up with (which does not work):<br>
><br>
> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),<br>
> 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)<br>
><br>
> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],<br>
> Year1[sample(nrow(Year1), 1000), ], n=2000)<br>
><br>
><br>
> any help would be greatly appreciated!<br>
><br>
> Best,<br>
> Spencer<br>
><br>
> --<br>
> Spencer A Bruce<br>
> 200 Washington St.<br>
> Troy, NY 12180<br>
> 518 225 0787<br>
><br>
<br>
<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<br>
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<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 23 Oct 2014 14:54:53 +0000<br>
From: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
To: Spencer Bruce <<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>><br>
Cc: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] repooling random rows from genind<br>
objects<br>
Message-ID:<br>
<<a href="mailto:2CB2DA8E426F3541AB1907F98ABA6570ABE6AE93@icexch-m1.ic.ac.uk">2CB2DA8E426F3541AB1907F98ABA6570ABE6AE93@icexch-m1.ic.ac.uk</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
<br>
What does nrow(F1) and other nrow(...)'s say?<br>
<br>
<br>
<br>
<br>
________________________________<br>
From: Spencer Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>]<br>
Sent: 23 October 2014 15:52<br>
To: Jombart, Thibaut<br>
Cc: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: Re: [adegenet-forum] repooling random rows from genind objects<br>
<br>
Error message:<br>
<br>
Error in <a href="http://sample.int" target="_blank">sample.int</a><<a href="http://sample.int" target="_blank">http://sample.int</a>>(length(x), size, replace, prob) :<br>
invalid first argument<br>
<br>
On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>>> wrote:<br>
<br>
Hello,<br>
hard to figure out what is wrong without the error message..<br>
Cheers<br>
Thibaut<br>
________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>>] on behalf of Spencer Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a><mailto:<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>>]<br>
Sent: 23 October 2014 15:29<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: [adegenet-forum] repooling random rows from genind objects<br>
<br>
Hello All!<br>
<br>
I have three seperate populations as genind objects. What I would like to do is pull a certain number of random individuals from each, to form a new single genind population.<br>
<br>
I would then like individuals from this new genind population to mate randomly, producing another genind object which would contain their offspring.<br>
<br>
Below is the code I came up with (which does not work):<br>
<br>
Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1), 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)<br>
<br>
Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ], Year1[sample(nrow(Year1), 1000), ], n=2000)<br>
<br>
<br>
any help would be greatly appreciated!<br>
<br>
Best,<br>
Spencer<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<tel:518%20225%200787><br>
<br>
<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<br>
-------------- next part --------------<br>
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<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 23 Oct 2014 11:03:54 -0400<br>
From: Spencer Bruce <<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>><br>
To: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
Cc: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] repooling random rows from genind<br>
objects<br>
Message-ID:<br>
<<a href="mailto:CAGjKGeZiyS-27oF2CKb6JBPgS%2BVSyTA1-NS2Q8g2UC0JqOs4VA@mail.gmail.com">CAGjKGeZiyS-27oF2CKb6JBPgS+VSyTA1-NS2Q8g2UC0JqOs4VA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
they both say Null, if I just type them into R.<br>
<br>
Just to be clear these genind objects contains microsat data for 11 loci<br>
for thousands of individuals.<br>
<br>
I'm rather new to R, so I apologize if I'm missing something obvious here...<br>
<br>
On Thu, Oct 23, 2014 at 10:54 AM, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><br>
> wrote:<br>
<br>
><br>
><br>
> What does nrow(F1) and other nrow(...)'s say?<br>
><br>
><br>
><br>
><br>
> ------------------------------<br>
> *From:* Spencer Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>]<br>
> *Sent:* 23 October 2014 15:52<br>
> *To:* Jombart, Thibaut<br>
> *Cc:* <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
> *Subject:* Re: [adegenet-forum] repooling random rows from genind objects<br>
><br>
> Error message:<br>
><br>
> Error in <a href="http://sample.int" target="_blank">sample.int</a>(length(x), size, replace, prob) :<br>
> invalid first argument<br>
><br>
> On Thu, Oct 23, 2014 at 10:50 AM, Jombart, Thibaut <<br>
> <a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>> wrote:<br>
><br>
>><br>
>> Hello,<br>
>> hard to figure out what is wrong without the error message..<br>
>> Cheers<br>
>> Thibaut<br>
>> ------------------------------<br>
>> *From:* <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<br>
>> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Spencer<br>
>> Bruce [<a href="mailto:goatsrunfaster@gmail.com">goatsrunfaster@gmail.com</a>]<br>
>> *Sent:* 23 October 2014 15:29<br>
>> *To:* <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
>> *Subject:* [adegenet-forum] repooling random rows from genind objects<br>
>><br>
>> Hello All!<br>
>><br>
>> I have three seperate populations as genind objects. What I would like<br>
>> to do is pull a certain number of random individuals from each, to form a<br>
>> new single genind population.<br>
>><br>
>> I would then like individuals from this new genind population to mate<br>
>> randomly, producing another genind object which would contain their<br>
>> offspring.<br>
>><br>
>> Below is the code I came up with (which does not work):<br>
>><br>
>> Year1 <- repool(F1[sample(nrow(F1), 500), ], pop1[sample(nrow(pop1),<br>
>> 750), ], pop2[sample(nrow(pop2), 750), ], n=2000)<br>
>><br>
>> Year2 <- hybridize(Year1[sample(nrow(Year1), 1000), ],<br>
>> Year1[sample(nrow(Year1), 1000), ], n=2000)<br>
>><br>
>><br>
>> any help would be greatly appreciated!<br>
>><br>
>> Best,<br>
>> Spencer<br>
>><br>
>> --<br>
>> Spencer A Bruce<br>
>> 200 Washington St.<br>
>> Troy, NY 12180<br>
>> 518 225 0787<br>
>><br>
><br>
><br>
><br>
> --<br>
> Spencer A Bruce<br>
> 200 Washington St.<br>
> Troy, NY 12180<br>
> 518 225 0787<br>
><br>
<br>
<br>
<br>
--<br>
Spencer A Bruce<br>
200 Washington St.<br>
Troy, NY 12180<br>
518 225 0787<br>
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</blockquote></div><br></div>