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Welcome to the poppr google group

This group is for users of the R package poppr to post and discuss questions related to analysis of population genetic data using poppr.

Citation for poppr:

Kamvar ZN, Tabima JF, & Grünwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281 doi: 10.7717/peerj.281

for version 2.0:

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208. doi:10.3389/fgene.2015.00208

Please see the Posting Guidelines before posting.

Links: Poppr Manual | Poppr on CRAN | Poppr on Github

Bug Reports/Feature Requests: Anonymous | Github user

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Gabriella Scatà, Zhian Kamvar4

Jul 29

ANOVA completely different results w pegas OR ade4 implementation...??

Also, can I ask: in my pegas amova results ( see below again): - is it correct that the sigma^2 for

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ANOVA completely different results w pegas OR ade4 implementation...??

Also, can I ask: in my pegas amova results ( see below again): - is it correct that the sigma^2 for

Jul 29

Gabriella Scatà

Jul 26

AMOVA coefficients

Hi everyone, I just tested the AMOVa this week with the pegas implementation (as I understood that

unread,

AMOVA coefficients

Hi everyone, I just tested the AMOVa this week with the pegas implementation (as I understood that

Jul 26

Gabriella Scatà

Jul 26

AMOVA questions

Hi, I just started using amova in poppr and I have a few questions: - 1. if i want to use Nei's

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AMOVA questions

Hi, I just started using amova in poppr and I have a few questions: - 1. if i want to use Nei's

Jul 26

Kristopher Wojtusik, … Gabriella Scatà3

Jul 26

P-Value for pegas amova

Hi, I was just wondering whether you need to calculate adjustment of p-values when using poppr::amova

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P-Value for pegas amova

Hi, I was just wondering whether you need to calculate adjustment of p-values when using poppr::amova

Jul 26

Kristopher Wojtusik, … Gabriella Scatà4

Jul 26

PhiST with AMOVA

Hi, I ran poppr::amova with correction = NULL (method = pegas), because I provided my own geentic

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PhiST with AMOVA

Hi, I ran poppr::amova with correction = NULL (method = pegas), because I provided my own geentic

Jul 26

massub....@gmail.com, Zhian Kamvar2

May 5

NOTE: Without seeing the code you used to get this error, I can only speculate. I suspect that you

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NOTE: Without seeing the code you used to get this error, I can only speculate. I suspect that you

May 5

Sofie V, Zhian Kamvar2

Apr 26

keeping MLGs with psex>0.05 for diversity_ci

Hello, You can use the custom MLLs in order to do this. Here's the documentation: https://

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keeping MLGs with psex>0.05 for diversity_ci

Hello, You can use the custom MLLs in order to do this. Here's the documentation: https://

Apr 26

Tamanna Batra, Zhian Kamvar4

Apr 17

Doing Bootstrapping of phylogenetic tree

Thank you for reply I have one more query regarding this. i am working on the co-dominant markers. I

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Doing Bootstrapping of phylogenetic tree

Thank you for reply I have one more query regarding this. i am working on the co-dominant markers. I

Apr 17

Zoe Meziere, Zhian Kamvar2

Apr 16

Private alleles biased by population size

At the moment, poppr does not have this functionality. There was a feature request for something like

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Private alleles biased by population size

At the moment, poppr does not have this functionality. There was a feature request for something like

Apr 16

Vanina Castroagudin, Zhian Kamvar2

Apr 1

Association mapping

Not sure about the association mapping, but you can use the results from DAPC to pull out the loci

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Association mapping

Not sure about the association mapping, but you can use the results from DAPC to pull out the loci

Apr 1

Pooja Pathania, Zhian Kamvar2

Jan 5

data conversion

Hello, You will probably want to use the {vcfR} package to read in the data, filter by quality, and

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data conversion

Hello, You will probably want to use the {vcfR} package to read in the data, filter by quality, and

Jan 5

Sarah G, Zhian Kamvar2

11/25/23

Hello, the purpose of imsn() is to provide you with code that you can use to reproduce the network

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Hello, the purpose of imsn() is to provide you with code that you can use to reproduce the network

11/25/23

mnow...@utk.edu, Zhian Kamvar2

11/11/23

Mixed ploidy -> diploid simulation

I'm afraid I would be just as lost as you are right now. If anyone has something that may be able

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Mixed ploidy -> diploid simulation

I'm afraid I would be just as lost as you are right now. If anyone has something that may be able

11/11/23

genetist, Zhian Kamvar2

11/11/23

how to plot population ancestry values as DAPC plots?

I'm not sure how you are expecting to achieve this, but you can plot the Linear Discriminants by

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how to plot population ancestry values as DAPC plots?

I'm not sure how you are expecting to achieve this, but you can plot the Linear Discriminants by

11/11/23

Nikki Lukasko, Zhian Kamvar2

11/11/23

How to handle missing population data running amova.test

CCR is the population factor for the model. AMOVA explicitly needs a population factor in order to

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How to handle missing population data running amova.test

CCR is the population factor for the model. AMOVA explicitly needs a population factor in order to

11/11/23

Kerin Law, Zhian Kamvar2

11/11/23

How to ID clonal thresholds within large database across species

Hi Kerin, I think the approach should be turn the vcf into a genclone object, isolate the clonal

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How to ID clonal thresholds within large database across species

Hi Kerin, I think the approach should be turn the vcf into a genclone object, isolate the clonal

11/11/23

Shan Wong, Zhian Kamvar2

11/11/23

Questions - calculating Euclidean distance

If you look at the help for ?summary.dist, you'll find that it tests for the Euclidean nature of

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Questions - calculating Euclidean distance

If you look at the help for ?summary.dist, you'll find that it tests for the Euclidean nature of

11/11/23

Riley A Buchanan, Zhian Kamvar2

11/11/23

Installation error: non-zero exit status of igraph and adegenet

This is an error that you do not have the libicui18n C library, which is required by the {stringi}

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Installation error: non-zero exit status of igraph and adegenet

This is an error that you do not have the libicui18n C library, which is required by the {stringi}

11/11/23

10/11/23

Apologies for SPAM

Hello all, Due to the recent flood of SPAM getting through the filters, all new member posts will be

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Apologies for SPAM

Hello all, Due to the recent flood of SPAM getting through the filters, all new member posts will be

10/11/23

Alexis Díaz, Zhian Kamvar2

8/2/23

preparing genlight file from fasta file

Hello Alexis, You will probably want to use the fasta2genlight() function Best, Zhian On Sun, Jul 30,

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preparing genlight file from fasta file

Hello Alexis, You will probably want to use the fasta2genlight() function Best, Zhian On Sun, Jul 30,

8/2/23

RN Sarma, Zhian Kamvar4

7/21/23

Combing population information from other file in Poppr

I will try it. Thank you On Fri, 21 Jul, 2023, 7:26 pm Zhian Kamvar, <zka...@gmail.com> wrote:

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Combing population information from other file in Poppr

I will try it. Thank you On Fri, 21 Jul, 2023, 7:26 pm Zhian Kamvar, <zka...@gmail.com> wrote:

7/21/23

林子熙, Zhian Kamvar3

5/31/23

Hi, is there any packages or software you know that can do the same thing as DAPC for huge data ？

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Hi, is there any packages or software you know that can do the same thing as DAPC for huge data ？

5/31/23

5/16/23

plot.poppr.msn is not giving the same MLG assignments as mlg.id MLL table.

Hi everyone, Apologies in advance I've only recently started to use poppr and don't know what

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plot.poppr.msn is not giving the same MLG assignments as mlg.id MLL table.

Hi everyone, Apologies in advance I've only recently started to use poppr and don't know what

5/16/23

Mohamad Ali El Chami, Julius Pyton Sserumaga2

4/11/23

Error in loading package "adegenet"

Hello Mohamad. To resolve this issue, you can try updating the htmltools package to a version that is

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Error in loading package "adegenet"

Hello Mohamad. To resolve this issue, you can try updating the htmltools package to a version that is

4/11/23

Daniel Kulik, Zhian Kamvar2

4/4/23

Minimum spanning network for population, included diploid and triploid individuals

This is correct. Bruvo's distance will apply one of the four models to fill in the missing

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Minimum spanning network for population, included diploid and triploid individuals

This is correct. Bruvo's distance will apply one of the four models to fill in the missing

4/4/23

Martin Boys, Zhian Kamvar3

11/11/22

Clustering error

Thank you for the detailed explanation. On Thu, 10 Nov 2022, 20:13 Zhian Kamvar, <zkamvar@gmail.

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Clustering error

Thank you for the detailed explanation. On Thu, 10 Nov 2022, 20:13 Zhian Kamvar, <zkamvar@gmail.

11/11/22

Mattia Schmid, Zhian Kamvar2

11/9/22

Hello, Thank you for providing the data. I think I understand what's happening here. `as.genambig

unread,

Hello, Thank you for providing the data. I think I understand what's happening here. `as.genambig

11/9/22

11/9/22

K-means cluster analysis

Dear Kamvar When I do K-means hierarchial clustering, and when choosing the number of PCs to retain,

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K-means cluster analysis

Dear Kamvar When I do K-means hierarchial clustering, and when choosing the number of PCs to retain,

11/9/22

11/9/22

Phylogenetic tree plot that is cut

Dear Kamvar I have plotted a phylogenetic tree in fan style however, when I try to export the plot,

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Phylogenetic tree plot that is cut

Dear Kamvar I have plotted a phylogenetic tree in fan style however, when I try to export the plot,

11/9/22

Martin Boys, Zhian Kamvar2

11/7/22

You can either use the pdf()/png() functions: https://bookdown.org/ndphillips/YaRrr/saving-plots-to-a

unread,

You can either use the pdf()/png() functions: https://bookdown.org/ndphillips/YaRrr/saving-plots-to-a

11/7/22

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