mikldk / dnatools Goto Github PK

Perhaps these suggestions are helpful?

• The following sentence is a bit hard to understand, e.g. what does "which" refer to? I suggest to split it into two shorter sentences to clarify: "With increasing number of STR markers, the random match probabilities are in the order of $10^{-20}$, which some people regard the random match probabilities associated with DNA evidence as just too small or basically unsupportable."Maybe: "With increasing number of STR markers, the probability of a random match between to unrelated samples is small (in the order of $10^{-20}$). Some people regard such small probabilities associated with DNA evidence as just too small or basically unsupportable."
• Typo / clarity: "researchers looking at the efficicy of new multiplexes". That should probably be "efficacy"? Maybe the authors can clarify what "efficacy of new multiplexes" means?
• Typos in the db_vignette vignette:
  - "Applying this method to yields" - should probably be "Applying the plot method to the
  summary yields".
  - "distribution is interesting part" - should probably be "distribution is interesting".
  - "Both functions implements" - should be "Both functions implement".
• Typos in the dna_vignette vignette:
  - "constituted by a abbritary" should be "constituted by an arbitrary".
• Typos in the noa_vignette vignette:
  - "which implies is can be" should be "which implies it can be"

The first three lines of the "Getting started" section of the main README are, in my opinion, the content that any potential user needs to see first. Installation instructions, issue trackers, examples, etc., are all good, but first and foremost a user needs to see What does this software do? Who is it designed for?

In general I think the documentation for DNAtools is very good, but I think this change would make it even better for newcomers.

dbCompare() seems to fail for one marker (I'm using the cran version, is the GitHub newer?):

 library(DNAtools, quietly = T)
#> 
#> Attaching package: 'DNAtools'
#> The following object is masked from 'package:stats':
#> 
#>     convolve
 freq <-  list(p1 = c(0.5, 0.5))
 simdb <- dbSimulate(freq,n = 2)
 dbCompare(simdb)
#> Error in apply(x[, -1], 1, function(y) any(y == 0)): dim(X) must have a positive length

^{Created on 2023-01-02 with reprex v2.0.2}

Installing DNAtools on a computer with no internet connection isn't possible with the provided instructions. Only an occasional R user and not an R developer, it took me a while to figure this out.

• download DNAtools as a .tar.gz archive from GitHub, transfer to computer using removable media
• install devtools and DNAtools pre-requisites (multicool, Rcpp, RcppParallel, RcppProgress, Rsolnp)
• install DNAtools in R using devtools::install_local

It may be helpful for you to include some instructions for offline installation.