Re: [R-sig-phylo] Error in phytools - locate.fossil?

[Lindsey Dehaan]

Great! Thanks for all the help!

Lindsey

On Wed, Jan 11, 2023 at 9:33 AM Liam J. Revell  wrote:

> Dear Lindsey.
>
> You should not adjust tol at all -- use the default. Sorry I wasn't clear
> on that. It is just an (arbitrarily) small value that helps us avoid
> evaluating solutions that are not "legal." (E.g., in your case, trying to
> attach a tip to an edge *below* its parent node.)
>
> All the best, Liam
> Liam J. Revell
> Professor of Biology, University of Massachusetts Boston
> Web: http://faculty.umb.edu/liam.revell/
>
>
> On 1/11/2023 7:58 AM, Lindsey Dehaan wrote:
>
> CAUTION: EXTERNAL SENDER
> Hey Liam,
>
> Thanks alot! I really appreciate it! I installed the new version and I saw
> your edits to the locate.fossil function on github.
>
> I just have one more question, I am new to the tol argument and I am not
> sure what the default should be set to. I've set it to a couple numbers
> (ex, 0.5, 0.1 0.01) and my fossil now places correctly but could you
> possibly tell me what this argument means and what I should be setting it
> to?
>
> Best,
> Lindsey
>
> On Tue, Jan 10, 2023 at 6:07 PM Liam J. Revell 
> wrote:
>
>> Dear Lindsey.
>>
>> Thanks for sharing the code & data. It made the problem pretty easy to
>> resolve.
>>
>> Turns out it is a simple numerical precision issue.
>>
>> I have resolved it by adding an optional argument tol with a sensible
>> default value which most users can probably ignore (but can set to tol=0
>> if they want to guarantee the current behavior of locate.fossil). I
>> pushed this update to *GitHub*:
>> https://github.com/liamrevell/phytools/commit/f1dcddbf56a7ae6bf9bece223cd6a949a57eac5f
>> 
>> .
>>
>> To obtain this updated version of *phytools* I recommend installing the
>> package *remotes* and then running (from a fresh R session):
>>
>> remotes::install_github("liamrevell/phytools")
>>
>> Let us know if this fixes everything!
>>
>> All the best, Liam
>> Liam J. Revell
>> Professor of Biology, University of Massachusetts Boston
>> Web: http://faculty.umb.edu/liam.revell/
>> 
>>
>>
>> On 1/10/2023 4:42 PM, Lindsey Dehaan wrote:
>>
>> CAUTION: EXTERNAL SENDER
>> Hey Liam,
>>
>> Thanks for the fast response.
>>
>> Attached is a simple script with the fossil I am having problems with.
>> All the files should be attached. Let me know if I missed a file or you
>> need anything else.
>>
>> I greatly appreciate your help on this. I have been stuck on this for a
>> while now.
>>
>> Best,
>> Lindsey
>>
>>
>> On Tue, Jan 10, 2023 at 4:23 PM Liam J. Revell 
>> wrote:
>>
>>> Dear Lindsey.
>>>
>>> Thanks for posting your code, but would you mind sending me (it can be
>>> off-list) an example in which I can also pull your data & tree and re-run
>>> it with the real data that is generating the error? This might be helpful
>>> in getting to the bottom of your issue. Thanks!
>>>
>>> All the best, Liam
>>> Liam J. Revell
>>> Professor of Biology, University of Massachusetts Boston
>>> Web: http://faculty.umb.edu/liam.revell/
>>> 
>>>
>>>
>>> On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
>>>
>>> CAUTION: EXTERNAL SENDER
>>>
>>> Hi all,
>>>
>>> I have a question regarding the phytools function locate.fossil().
>>>
>>> I have had a lot of success with this function but there are two fossils of
>>> mine that the function does not like. I give the function my phylogeny, a
>>> max and min age for the fossil, and the edge for the fossil to be placed
>>> on. So I basically just want the function to estimate the branch length
>>> subtending the fossil and the position of where the node subtending the
>>> fossil attaches in the phylogeny.
>>>
>>> For two of my fossils I get the following error.
>>>
>>>
>>>
>>> *Error in bind.tree(tree, tip, where = where, position = pp) :   

Re: [R-sig-phylo] Error in phytools - locate.fossil?

[Liam J. Revell]

Dear Lindsey.

You should not adjust tol at all -- use the default. Sorry I wasn't 
clear on that. It is just an (arbitrarily) small value that helps us 
avoid evaluating solutions that are not "legal." (E.g., in your case, 
trying to attach a tip to an edge /below/ its parent node.)

All the best, Liam

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/


On 1/11/2023 7:58 AM, Lindsey Dehaan wrote:
> CAUTION: EXTERNAL SENDER
> Hey Liam,
>
> Thanks alot! I really appreciate it! I installed the new version and I 
> saw your edits to the locate.fossil function on github.
>
> I just have one more question, I am new to the tol argument and I am 
> not sure what the default should be set to. I've set it to a couple 
> numbers (ex, 0.5, 0.1 0.01) and my fossil now places correctly but 
> could you possibly tell me what this argument means and what I should 
> be setting it to?
>
> Best,
> Lindsey
>
> On Tue, Jan 10, 2023 at 6:07 PM Liam J. Revell  
> wrote:
>
> Dear Lindsey.
>
> Thanks for sharing the code & data. It made the problem pretty
> easy to resolve.
>
> Turns out it is a simple numerical precision issue.
>
> I have resolved it by adding an optional argument tolwith a
> sensible default value which most users can probably ignore (but
> can set to tol=0 if they want to guarantee the current behavior of
> locate.fossil). I pushed this update to /GitHub/:
> 
> https://github.com/liamrevell/phytools/commit/f1dcddbf56a7ae6bf9bece223cd6a949a57eac5f
> 
> .
>
> To obtain this updated version of /phytools/ I recommend
> installing the package /remotes/ and then running (from a fresh R
> session):
>
> remotes::install_github("liamrevell/phytools")
>
> Let us know if this fixes everything!
>
> All the best, Liam
>
> Liam J. Revell
> Professor of Biology, University of Massachusetts Boston
> Web: http://faculty.umb.edu/liam.revell/
> 
> 
>
>
> On 1/10/2023 4:42 PM, Lindsey Dehaan wrote:
>> CAUTION: EXTERNAL SENDER
>> Hey Liam,
>>
>> Thanks for the fast response.
>>
>> Attached is a simple script with the fossil I am having problems
>> with. All the files should be attached. Let me know if I missed a
>> file or you need anything else.
>>
>> I greatly appreciate your help on this. I have been stuck on this
>> for a while now.
>>
>> Best,
>> Lindsey
>>
>>
>> On Tue, Jan 10, 2023 at 4:23 PM Liam J. Revell
>>  wrote:
>>
>> Dear Lindsey.
>>
>> Thanks for posting your code, but would you mind sending me
>> (it can be off-list) an example in which I can also pull your
>> data & tree and re-run it with the real data that is
>> generating the error? This might be helpful in getting to the
>> bottom of your issue. Thanks!
>>
>> All the best, Liam
>>
>> Liam J. Revell
>> Professor of Biology, University of Massachusetts Boston
>> Web: http://faculty.umb.edu/liam.revell/
>> 
>> 
>>
>>
>> On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
>>> CAUTION: EXTERNAL SENDER
>>>
>>> Hi all,
>>>
>>> I have a question regarding the phytools function locate.fossil().
>>>
>>> I have had a lot of success with this function but there are two 
>>> fossils of
>>> mine that the function does not like. I give the function my 
>>> phylogeny, a
>>> max and min age for the fossil, and the edge for the fossil to be 
>>> placed
>>> on. So I basically just want the function to estimate the branch 
>>> length
>>> subtending the fossil and the position of where the node subtending 
>>> the
>>> 

Re: [R-sig-phylo] Error in phytools - locate.fossil?

[Lindsey Dehaan]

Hey Liam,

Thanks alot! I really appreciate it! I installed the new version and I saw
your edits to the locate.fossil function on github.

I just have one more question, I am new to the tol argument and I am not
sure what the default should be set to. I've set it to a couple numbers
(ex, 0.5, 0.1 0.01) and my fossil now places correctly but could you
possibly tell me what this argument means and what I should be setting it
to?

Best,
Lindsey

On Tue, Jan 10, 2023 at 6:07 PM Liam J. Revell  wrote:

> Dear Lindsey.
>
> Thanks for sharing the code & data. It made the problem pretty easy to
> resolve.
>
> Turns out it is a simple numerical precision issue.
>
> I have resolved it by adding an optional argument tol with a sensible
> default value which most users can probably ignore (but can set to tol=0
> if they want to guarantee the current behavior of locate.fossil). I
> pushed this update to *GitHub*:
> https://github.com/liamrevell/phytools/commit/f1dcddbf56a7ae6bf9bece223cd6a949a57eac5f
> .
>
> To obtain this updated version of *phytools* I recommend installing the
> package *remotes* and then running (from a fresh R session):
>
> remotes::install_github("liamrevell/phytools")
>
> Let us know if this fixes everything!
>
> All the best, Liam
> Liam J. Revell
> Professor of Biology, University of Massachusetts Boston
> Web: http://faculty.umb.edu/liam.revell/
>
>
> On 1/10/2023 4:42 PM, Lindsey Dehaan wrote:
>
> CAUTION: EXTERNAL SENDER
> Hey Liam,
>
> Thanks for the fast response.
>
> Attached is a simple script with the fossil I am having problems with. All
> the files should be attached. Let me know if I missed a file or you need
> anything else.
>
> I greatly appreciate your help on this. I have been stuck on this for a
> while now.
>
> Best,
> Lindsey
>
>
> On Tue, Jan 10, 2023 at 4:23 PM Liam J. Revell 
> wrote:
>
>> Dear Lindsey.
>>
>> Thanks for posting your code, but would you mind sending me (it can be
>> off-list) an example in which I can also pull your data & tree and re-run
>> it with the real data that is generating the error? This might be helpful
>> in getting to the bottom of your issue. Thanks!
>>
>> All the best, Liam
>> Liam J. Revell
>> Professor of Biology, University of Massachusetts Boston
>> Web: http://faculty.umb.edu/liam.revell/
>> 
>>
>>
>> On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
>>
>> CAUTION: EXTERNAL SENDER
>>
>> Hi all,
>>
>> I have a question regarding the phytools function locate.fossil().
>>
>> I have had a lot of success with this function but there are two fossils of
>> mine that the function does not like. I give the function my phylogeny, a
>> max and min age for the fossil, and the edge for the fossil to be placed
>> on. So I basically just want the function to estimate the branch length
>> subtending the fossil and the position of where the node subtending the
>> fossil attaches in the phylogeny.
>>
>> For two of my fossils I get the following error.
>>
>>
>>
>> *Error in bind.tree(tree, tip, where = where, position = pp) :   'position'
>> is larger than the branch length*
>>
>> The function does not seem to like my edge constraint with these two
>> fossils. When I remove my edge constraint it works and the fossil is placed
>> in the correct time interval but just on a different edge estimated using
>> ML. For one of my fossils, the edge I place my fossil on ranges from 42 mya
>> to 4 mya and the age range for the fossil is between 33 and 28 mya. I am
>> confused why the function does not like the edge constraints I am giving
>> it. The error that I receive makes me believe that the position the
>> function is estimating for my fossil may be older than the edge constraint
>> I am giving it or I could just be missing something, most likely the
>> latter...
>>
>> Below is my code. This code works for almost all my fossils except for two
>> of them.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *fossil_to_add<-fossil_trait_data[13,] locate_fossil_data<-rbind(extant_data,
>> fossil_to_add) # used this data in
>> locate.fossil()extant_sister_clade<-rownames(extant_data)[c(grep(fossil_info[13,7],
>> rownames(extant_data)), grep(fossil_info[13,8],
>> rownames(extant_data)))]mrca<-getMRCA(tree,
>> extant_sister_clade)edge<-mrcamin_time<- depth - fossil_info[13,4] # depth
>> is the root age of the phylogeny max_time<-depth - fossil_info[13,3] # the
>> max and min ages are positive numbers time_constraints<-c(max_time,
>> min_time)locate_fossil_tree<-locate.fossil(tree, locate_fossil_data,
>> time.constraint=time_constraints,edge.constraint=edge, plot=TRUE)*
>>
>> Any help or advice, would be 

Re: [R-sig-phylo] Error in phytools - locate.fossil?

[Liam J. Revell]

Dear Lindsey.

Thanks for sharing the code & data. It made the problem pretty easy to 
resolve.

Turns out it is a simple numerical precision issue.

I have resolved it by adding an optional argument tolwith a sensible 
default value which most users can probably ignore (but can set to tol=0 
if they want to guarantee the current behavior of locate.fossil). I 
pushed this update to /GitHub/: 
https://github.com/liamrevell/phytools/commit/f1dcddbf56a7ae6bf9bece223cd6a949a57eac5f.

To obtain this updated version of /phytools/ I recommend installing the 
package /remotes/ and then running (from a fresh R session):

remotes::install_github("liamrevell/phytools")

Let us know if this fixes everything!

All the best, Liam

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/


On 1/10/2023 4:42 PM, Lindsey Dehaan wrote:
> CAUTION: EXTERNAL SENDER
> Hey Liam,
>
> Thanks for the fast response.
>
> Attached is a simple script with the fossil I am having problems with. 
> All the files should be attached. Let me know if I missed a file or 
> you need anything else.
>
> I greatly appreciate your help on this. I have been stuck on this for 
> a while now.
>
> Best,
> Lindsey
>
>
> On Tue, Jan 10, 2023 at 4:23 PM Liam J. Revell  
> wrote:
>
> Dear Lindsey.
>
> Thanks for posting your code, but would you mind sending me (it
> can be off-list) an example in which I can also pull your data &
> tree and re-run it with the real data that is generating the
> error? This might be helpful in getting to the bottom of your
> issue. Thanks!
>
> All the best, Liam
>
> Liam J. Revell
> Professor of Biology, University of Massachusetts Boston
> Web: http://faculty.umb.edu/liam.revell/
> 
> 
>
>
> On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
>> CAUTION: EXTERNAL SENDER
>>
>> Hi all,
>>
>> I have a question regarding the phytools function locate.fossil().
>>
>> I have had a lot of success with this function but there are two fossils 
>> of
>> mine that the function does not like. I give the function my phylogeny, a
>> max and min age for the fossil, and the edge for the fossil to be placed
>> on. So I basically just want the function to estimate the branch length
>> subtending the fossil and the position of where the node subtending the
>> fossil attaches in the phylogeny.
>>
>> For two of my fossils I get the following error.
>>
>>
>>
>> *Error in bind.tree(tree, tip, where = where, position = pp) :   
>> 'position'
>> is larger than the branch length*
>>
>> The function does not seem to like my edge constraint with these two
>> fossils. When I remove my edge constraint it works and the fossil is 
>> placed
>> in the correct time interval but just on a different edge estimated using
>> ML. For one of my fossils, the edge I place my fossil on ranges from 42 
>> mya
>> to 4 mya and the age range for the fossil is between 33 and 28 mya. I am
>> confused why the function does not like the edge constraints I am giving
>> it. The error that I receive makes me believe that the position the
>> function is estimating for my fossil may be older than the edge 
>> constraint
>> I am giving it or I could just be missing something, most likely the
>> latter...
>>
>> Below is my code. This code works for almost all my fossils except for 
>> two
>> of them.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *fossil_to_add<-fossil_trait_data[13,] 
>> locate_fossil_data<-rbind(extant_data,
>> fossil_to_add) # used this data in
>> 
>> locate.fossil()extant_sister_clade<-rownames(extant_data)[c(grep(fossil_info[13,7],
>> rownames(extant_data)), grep(fossil_info[13,8],
>> rownames(extant_data)))]mrca<-getMRCA(tree,
>> extant_sister_clade)edge<-mrcamin_time<- depth - fossil_info[13,4] # 
>> depth
>> is the root age of the phylogeny max_time<-depth - fossil_info[13,3] # 
>> the
>> max and min ages are positive numbers time_constraints<-c(max_time,
>> min_time)locate_fossil_tree<-locate.fossil(tree, locate_fossil_data,
>> time.constraint=time_constraints,edge.constraint=edge, plot=TRUE)*
>>
>> Any help or advice, would be greatly appreciated!
>>
>> Best,
>> Lindsey
>> --
>> Lindsey DeHaan
>> Ph.D. Candidate
>> Department of Earth and Environmental Sciences
>> University of Michigan
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> R-sig-phylo 

Re: [R-sig-phylo] Error in phytools - locate.fossil?

[Liam J. Revell]

Dear Lindsey.

Thanks for posting your code, but would you mind sending me (it can be 
off-list) an example in which I can also pull your data & tree and 
re-run it with the real data that is generating the error? This might be 
helpful in getting to the bottom of your issue. Thanks!

All the best, Liam

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/


On 1/10/2023 4:20 PM, Lindsey Dehaan wrote:
> CAUTION: EXTERNAL SENDER
>
> Hi all,
>
> I have a question regarding the phytools function locate.fossil().
>
> I have had a lot of success with this function but there are two fossils of
> mine that the function does not like. I give the function my phylogeny, a
> max and min age for the fossil, and the edge for the fossil to be placed
> on. So I basically just want the function to estimate the branch length
> subtending the fossil and the position of where the node subtending the
> fossil attaches in the phylogeny.
>
> For two of my fossils I get the following error.
>
>
>
> *Error in bind.tree(tree, tip, where = where, position = pp) :   'position'
> is larger than the branch length*
>
> The function does not seem to like my edge constraint with these two
> fossils. When I remove my edge constraint it works and the fossil is placed
> in the correct time interval but just on a different edge estimated using
> ML. For one of my fossils, the edge I place my fossil on ranges from 42 mya
> to 4 mya and the age range for the fossil is between 33 and 28 mya. I am
> confused why the function does not like the edge constraints I am giving
> it. The error that I receive makes me believe that the position the
> function is estimating for my fossil may be older than the edge constraint
> I am giving it or I could just be missing something, most likely the
> latter...
>
> Below is my code. This code works for almost all my fossils except for two
> of them.
>
>
>
>
>
>
>
>
>
>
>
> *fossil_to_add<-fossil_trait_data[13,] locate_fossil_data<-rbind(extant_data,
> fossil_to_add) # used this data in
> locate.fossil()extant_sister_clade<-rownames(extant_data)[c(grep(fossil_info[13,7],
> rownames(extant_data)), grep(fossil_info[13,8],
> rownames(extant_data)))]mrca<-getMRCA(tree,
> extant_sister_clade)edge<-mrcamin_time<- depth - fossil_info[13,4] # depth
> is the root age of the phylogeny max_time<-depth - fossil_info[13,3] # the
> max and min ages are positive numbers time_constraints<-c(max_time,
> min_time)locate_fossil_tree<-locate.fossil(tree, locate_fossil_data,
> time.constraint=time_constraints,edge.constraint=edge, plot=TRUE)*
>
> Any help or advice, would be greatly appreciated!
>
> Best,
> Lindsey
> --
> Lindsey DeHaan
> Ph.D. Candidate
> Department of Earth and Environmental Sciences
> University of Michigan
>
>  [[alternative HTML version deleted]]
>
> ___
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