I don't know this library, but it looks like your infile class is 'list' or 'data frame' and it should be 'matrix' or 'numeric'. Are you sure that your infile has proper structure?

Michal, thanks for your suggestion. My input is in genepop format, which supposed to be input in this package..((

How did you import the file for input? Recently RStudio started using by default readr library which caused some problems for me. Maybe if you use old methods of importing the file you will solve your problem?

I used "readGenepop" function from library "diveRsity", and its works fine. However another fuction of the same library,  "writeBoot", did not((((

hmm, the documentation for this library is a bit messy from my point of view, however as I uderstand it, you should use name of the genepop file directly in function, not the variable to which you assign result of 'readGenepop'. Maybe that will help.

Eh, I tryed this option also of course! Did not work also, however it give anothe error:

> writeBoot(infile = "16032017_genepop_test.gen", outfile = "23032017_10_boot", gp = 3, bootstraps = 10, parallel = T)

Error in match.fun(FUN) : object 'plMake' not found

Оля, привет,

Извини, я не работала никогда с этим ресурсом и вряд ли смогу помочь :-(

Ok I managed to find a working solution. I will write it later cause now I am away from keybord.

wow! looking forward, Michal!

Ok. So as I wrtote earlier, after using readGenepop you will obtain variable of class 'list' which is unsuitable for writeBoot. Instead you need to import your data from your_file.gen to R. There are two problem with it:

1. your file have structure which is a bit problematic to import it straightforward to RStudio (or R generaly) and obtain the correct structure of data needed by writeBoot function.

2. try to use:

> data(Test_data, package = "diveRsity")

you will make new variable Test_data from sample data attached to diveRsity package.

Than using:

>View(Test_data)

You will see the structure of data which works with with writeBoot fuction correctly. I have found that the difference between your_file.gen structure and Test_data is number of digits in cells. Each of population cell is represented by three digits while in correct Test_data you will find that there are 6 digits in each cell. I manually changed each cell with random 6 digits and writeBoot function worked (ok. it did not work when i added three zeros in front of each cell e.g. '245' -> '000245', however i was dealing with other type of file, so maybe when you do it in .gen it will work). So what you need to do is:

A) correct cells to have 6 digits (if you want tu use argument gp = 3, otherwise if you use argument gp = 2, they should have 4 digits) in your_file.gen

B) upload your file like this:

gendata

Michal, it is relly work like this!!!! Thank you very much! you spent so many time and efforts...

The thing is my data haploid: there is why its 3 digits, and not 6, like in Test_data. And "writeBoot" function worked well with my data several months ago... Have no idea what happens now with this script... But anyway. Now I make my data "artificially diploid", like all samples would be homozygotas...and it is work!! even without "readGenepop" step, I just write name of my input in genepop format in a quotes.

Thanks again, many best wishes for you!!!

Glad to hear that :)

Also, all the best!

Hi Olga and Michal,

I'm trying to use the readGenepop function in diveRsity and it won't read my file at all. When I enter:

data

 Hi Sarah,

Could you write which R version you are working with? There were some changes recently and I had problems with other libraries (needed to make changes in source code, since some functions do not exist anymore).  Generally subscript out of bounds, means that your df or matrix has fewer rows/columns than expected by function. Currently I have to much workload, but I will try to solve your problem during weekend, if you can wait.

All the best!

Hi Michal and Sarah,

I used Genepop file which was converted by PGDSpider

The scrip is:

gendata