220 add bruvos between

[davefol]

Closes #220

bruvo.between() exposes the same api as bruvo.dist() except for the extra required argument ref.
It also returns the same object except for NaN for distances that are not a comparison between query and ref.

Internally it uses bruvo_between() which skips unneeded values and fills them with 100, later converted to NaN.

[zkamvar]

That was quick and thorough! I'm a bit surprised you used the micro-update feature (I haven't used that myself in quite a while). Your approach to not re-invent the wheel is fantastic and will make this code easier to maintain in the long run. I admit that I wasn't quite sure what I was expecting with this approach, but now that I see it, it makes a lot of sense.

Thank you for the effort 💯

I do see a couple of things that can be improved:

1. Since you're adding a new function, you should change your role as "aut" in the DESCRIPTION
2. Please add an @export tag in the bruvo.between documentation
3. The matrix got flipped somewhere in the C implementation, because I'm getting the following:

library("poppr")
#> Loading required package: adegenet
#> Loading required package: ade4
#> Registered S3 method overwritten by 'spdep':
#>   method   from
#>   plot.mst ape
#> 
#>    /// adegenet 2.1.3 is loaded ////////////
#> 
#>    > overview: '?adegenet'
#>    > tutorials/doc/questions: 'adegenetWeb()' 
#>    > bug reports/feature requests: adegenetIssues()
#> Registered S3 method overwritten by 'pegas':
#>   method      from
#>   print.amova ade4
#> This is poppr version 2.8.6.99.8. To get started, type package?poppr
#> OMP parallel support: available
#> 
#> This version of poppr is under development.
#> If you find any bugs, please report them at https://github.com/grunwaldlab/poppr/issues
data(nancycats)
n3 <- nancycats[pop = 3]
n4 <- nancycats[pop = 4]
btwn <- poppr:::bruvo.between(n3[1:3], n4[1:5], replen = rep(2, 9), by_locus = TRUE)
btwn
#> $fca8
#>           N24       N25       N26       N35       N36       N37       N38
#> N25        NA                                                            
#> N26        NA        NA                                                  
#> N35 0.7500000 0.7500000 0.7500000                                        
#> N36 0.3750000 0.3750000 0.3750000        NA                              
#> N37 0.4921875 0.4921875 0.4921875        NA 0.2500000                    
#> N38 0.4921875 0.4921875 0.4921875 0.8437500 0.4687500        NA          
#> N39 0.0000000 0.0000000 0.0000000 0.4687500 0.7480469 0.8437500 0.4687500
#> 
#> $fca23
#>           N24       N25       N26       N35       N36       N37       N38
#> N25 0.2500000                                                            
#> N26 0.4687500 0.7187500                                                  
#> N35 0.7480469        NA 0.3750000                                        
#> N36 0.3750000        NA 0.3750000 0.3750000                              
#> N37 0.0000000 0.7500000        NA 0.0000000 0.8437500                    
#> N38 0.4375000 0.7500000 0.3750000 0.0000000 0.3750000 0.0000000          
#> N39 0.0000000 0.0000000 0.8437500 0.3750000 0.0000000        NA        NA
#> 
#> $fca43
#>           N24       N25       N26       N35       N36       N37       N38
#> N25 0.4921875                                                            
#> N26 0.4921875 0.4375000                                                  
#> N35 0.4843750 0.3750000 0.4375000                                        
#> N36 0.4843750 0.3750000 0.4375000 0.9375000                              
#> N37 0.4375000 0.0000000 0.4843750 0.9062500 0.9843750                    
#> N38        NA 0.3750000        NA 0.8750000        NA 0.8125000          
#> N39 0.4375000 0.3750000        NA 0.9843750 0.8437500 0.8750000 0.4921875
#> 
#> $fca45
#>           N24       N25       N26       N35       N36       N37       N38
#> N25 0.4921875                                                            
#> N26 0.8437500        NA                                                  
#> N35 0.8125000 0.0000000        NA                                        
#> N36 0.8750000 0.4375000 0.2500000 0.4687500                              
#> N37 0.4921875 0.4375000 0.4687500 0.7187500 0.3750000                    
#> N38 0.4921875 0.6250000 0.4687500 0.9375000 0.9375000        NA          
#> N39        NA 0.4375000 0.3750000 0.9375000        NA 0.8437500 0.8437500
#> 
#> $fca77
#>           N24       N25       N26       N35       N36       N37       N38
#> N25 0.8437500                                                            
#> N26 0.0000000 0.7500000                                                  
#> N35 0.4687500 0.7500000 0.4687500                                        
#> N36        NA 0.8437500        NA 0.8745117                              
#> N37 0.4921875 0.8437500        NA 0.8745117 0.4980469                    
#> N38 0.4921875 0.8437500 0.4980469 0.0000000 0.4995117 0.8745117          
#> N39 0.4921875 0.0000000 0.4995117        NA 0.8745117 0.0000000 0.4980469
#> 
#> $fca78
#>           N24       N25       N26       N35       N36       N37       N38
#> N25 0.4995117                                                            
#> N26 0.8745117 0.7187500                                                  
#> N35 0.8745117 0.0000000 0.7187500                                        
#> N36 0.0000000 0.4921875 0.0000000 0.4375000                              
#> N37        NA 0.0000000 0.4921875 0.5000000        NA                    
#> N38        NA        NA 0.0000000 0.7460938        NA        NA          
#> N39 0.4375000 0.4375000 0.7187500 0.5000000        NA        NA        NA
#> 
#> $fca90
#>     N24 N25 N26 N35 N36 N37 N38
#> N25  NA                        
#> N26  NA  NA                    
#> N35  NA  NA  NA                
#> N36  NA  NA  NA  NA            
#> N37  NA  NA  NA  NA  NA        
#> N38  NA  NA  NA  NA  NA  NA    
#> N39  NA  NA  NA  NA  NA  NA  NA
#> 
#> $fca96
#>     N24 N25 N26 N35 N36 N37 N38
#> N25  NA                        
#> N26  NA  NA                    
#> N35  NA  NA  NA                
#> N36  NA  NA  NA  NA            
#> N37  NA  NA  NA  NA  NA        
#> N38  NA  NA  NA  NA  NA  NA    
#> N39  NA  NA  NA  NA  NA  NA  NA
#> 
#> $fca37
#>     N24 N25 N26 N35 N36 N37 N38
#> N25  NA                        
#> N26  NA  NA                    
#> N35  NA  NA  NA                
#> N36  NA  NA  NA  NA            
#> N37  NA  NA  NA  NA  NA        
#> N38  NA  NA  NA  NA  NA  NA    
#> N39  NA  NA  NA  NA  NA  NA  NA
# 3 * 5 * 9
sum(!is.na(unlist(btwn)))
#> [1] 135

^{Created on 2020-06-22 by the reprex package (v0.3.0)}

The numbers are correct, they are just in the wrong order. It would be good to add a test for that.

That being said, I can take care of these on the weekend if you don't have time to get to these this week.

[davefol]

Hi Zhian, I think I handled everything in d862c3e

Let me know if I missed anything.

[zkamvar]

It looks good to me! The documentation needed to be re-roxygenized and NEWS updated, but I can take care of that. Thank you for the contribution!

[davefol]

Thanks for making it so easy. Would love to dig into the library more and contribute where needed.