Landscape genetic analysis

[laiajulianamu]

Dear developers. I am trying to make an isolation by distance but I need to build my own landscape. My question is if you have some advise that I could use for making mine, I tried with github repository but I can´t open the [landscape.sim) file

[mijangos81]

Hi Laia,

You don't need to build a landscape to perform an isolation by distance analysis, you only need your data loaded into dartR and the coordinates for each individual. You can open the help page of the function by typing: ?gl.ibd

You can also have a look at some of our tutorials, which can be downloaded from: http://georges.biomatix.org/dartR

Please let us know if we can help you with anything else.

Cheers, Luis

[laiajulianamu]

Hi Luis

Thank you for your reply, the thing is that I have this error Error in wassermann(gen.mat = gd, eucl.mat = eucl, cost.mats = list(cost = cost), : object 'cost' not found and for generating the cost object I am trying to use: cost <- costdistances(landscape = , locs = coords, method = "leastcost", NN = 8) But I don´t have a landscape :(

On Wed, 11 Aug 2021 at 21:43, luis mijangos @.***> wrote:

Hi Laia,

You don't need to build a landscape to perform an isolation by distance analysis, you only need your data loaded into dartR and the coordinates for each individual. You can open the help page of the function by typing: ?gl.ibd

You can also have a look at some of our tutorials, which can be downloaded from: http://georges.biomatix.org/dartR

Please let us know if we can help you with anything else.

Cheers, Luis

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/green-striped-gecko/dartR/issues/185#issuecomment-897303999, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJNRBMP5R4JBAB2JUSTT4MYOLANCNFSM5B76CNYA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

[green-striped-gecko]

Hi Laia,

You cannot calculate costdistances without a landscape.

For an ibd approach use gl.ibd and provide a genlight object with coordinates.

To check if you have the correct format available you can try:

gl.map.interactive(genlightobject) if this results in a map with your data then you are fine.

Cheers, Bernd

============================================================================== Dr Bernd Gruber )/ .--..---"-,--c_ Professor Ecological Modelling |..' ._O) Tel: (02) 6206 3804 ,=. .+ ..--( / Fax: (02) 6201 2328 \.-''.-' \ ( _ Institute for Applied Ecology '''\ /\ Faculty of Science and Technology ') University of Canberra ACT 2601 AUSTRALIA Email: @.**@.> WWW: bernd-gruberhttps://researchprofiles.canberra.edu.au/en/persons/bernd-gruber

Australian Government Higher Education Provider Number CRICOS #00212K NOTICE & DISCLAIMER: This email and any files transmitted with it may contain confidential or copyright material and are for the attention of the addressee only. If you have received this email in error please notify us by email reply and delete it from your system. The University of Canberra accepts no liability for any damage caused by any virus transmitted by this email.

From: laiajulianamu @.> Sent: Thursday, 12 August 2021 13:52 To: green-striped-gecko/dartR @.> Cc: Subscribed @.***> Subject: Re: [green-striped-gecko/dartR] Landscape genetic analysis (#185)

Hi Luis

Thank you for your reply, the thing is that I have this error Error in wassermann(gen.mat = gd, eucl.mat = eucl, cost.mats = list(cost = cost), : object 'cost' not found and for generating the cost object I am trying to use: cost <- costdistances(landscape = , locs = coords, method = "leastcost", NN = 8) But I don´t have a landscape :(

On Wed, 11 Aug 2021 at 21:43, luis mijangos @.<mailto:@.>> wrote:

Hi Laia,

You don't need to build a landscape to perform an isolation by distance analysis, you only need your data loaded into dartR and the coordinates for each individual. You can open the help page of the function by typing: ?gl.ibd

You can also have a look at some of our tutorials, which can be downloaded from: http://georges.biomatix.org/dartRhttp://georges.biomatix.org/dartR

Please let us know if we can help you with anything else.

Cheers, Luis

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/green-striped-gecko/dartR/issues/185#issuecomment-897303999<https://github.com/green-striped-gecko/dartR/issues/185#issuecomment-897303999>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJNRBMP5R4JBAB2JUSTT4MYOLANCNFSM5B76CNYA<https://github.com/notifications/unsubscribe-auth/ALV6WJNRBMP5R4JBAB2JUSTT4MYOLANCNFSM5B76CNYA> . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email<https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

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[laiajulianamu]

Hi Bernd

Thank you for your response and sorry again for bothering you.

I have my files: [image: image.png]

I created a gl object gl <- gl.read.dart(filename = "YFT2.csv", ind.metafile = "meta2.csv")

and then I used:

iso <- gl.ibd(gl, projected = TRUE) xs <- @.$latlong[, "lon"], pop(gl), mean) ys <- @.$latlong[, "lat"], pop(gl), mean) plot(gl)points(xs,ys, pch = 16) text(xs, ys, popNames(gl), col = "orange")

coords <- cbind(xs, ys) eucl <- as.matrix(dist(coords))

If I use the "gl.map.interactive(gl)" the map looks good but if I use the iso object I have a error

[image: image.png]

And then when creating the cost. or when I try to create a landscape plot I have the follow error:

cost <- costdistances(landscape = landscape.sim,

• locs = coords, method = "leastcost", NN =
• 8) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘transition’ for signature ‘"data.frame"’

  plot(landsape.sim) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': object 'landsape.sim' not found plot(landscape.sim) Error in plot.window(...) : need finite 'ylim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf

On Wed, 11 Aug 2021 at 22:55, Bernd Gruber @.***> wrote:

Hi Laia,

You cannot calculate costdistances without a landscape.

For an ibd approach use gl.ibd and provide a genlight object with coordinates.

To check if you have the correct format available you can try:

gl.map.interactive(genlightobject) if this results in a map with your data then you are fine.

Cheers, Bernd

==============================================================================

Dr Bernd Gruber )/ .--..---"-,--c_ Professor Ecological Modelling |..' ._O) Tel: (02) 6206 3804 ,=. .+ ..--( / Fax: (02) 6201 2328 \.-''.-' \ ( _ Institute for Applied Ecology '''\ /\ Faculty of Science and Technology ') University of Canberra ACT 2601 AUSTRALIA Email: @.**@.> WWW: bernd-gruber< https://researchprofiles.canberra.edu.au/en/persons/bernd-gruber>

Australian Government Higher Education Provider Number CRICOS #00212K NOTICE & DISCLAIMER: This email and any files transmitted with it may contain confidential or copyright material and are for the attention of the addressee only. If you have received this email in error please notify us by email reply and delete it from your system. The University of Canberra accepts no liability for any damage caused by any virus transmitted by this email.

From: laiajulianamu @.> Sent: Thursday, 12 August 2021 13:52 To: green-striped-gecko/dartR @.> Cc: Subscribed @.***> Subject: Re: [green-striped-gecko/dartR] Landscape genetic analysis (#185)

Hi Luis

Thank you for your reply, the thing is that I have this error Error in wassermann(gen.mat = gd, eucl.mat = eucl, cost.mats = list(cost = cost), : object 'cost' not found and for generating the cost object I am trying to use: cost <- costdistances(landscape = , locs = coords, method = "leastcost", NN = 8) But I don´t have a landscape :(

On Wed, 11 Aug 2021 at 21:43, luis mijangos @.<mailto:@.>>

wrote:

Hi Laia,

You don't need to build a landscape to perform an isolation by distance analysis, you only need your data loaded into dartR and the coordinates for each individual. You can open the help page of the function by typing: ?gl.ibd

You can also have a look at some of our tutorials, which can be downloaded from: http://georges.biomatix.org/dartR< http://georges.biomatix.org/dartR>

Please let us know if we can help you with anything else.

Cheers, Luis

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