Error in using some cover types (ball and restrained)

[20choudharysa]

Hi,

@corybrunson, @20demkowiczbr and I installed the latest version of Mapper and have been using the examples from your vignette to explore the functionality of the package. We have been trying to change the cover type from fixed interval to ball and restrained, however we have been receiving errors which are shown below. These cover types were outlined in the covers_available() function.

Thanks and we hope to hear from you soon.

library(Mapper)

t <- seq(-0.5*pi, (3/2)*pi, length.out = 100) + runif(100, max = 0.01)
eight <- cbind(x1=cos(t), x2=sin(t)*cos(t))
f_x <- matrix(cos(t))

m <- MapperRef$new(X = eight)$
  use_filter(filter= f_x)$
  use_cover(cover = "restrained interval", number_intervals = 10, percent_overlap = 20)$
  use_clustering_algorithm(cl = "single")$
  construct_k_skeleton(k = 1L)
#> Error in self$cover$neighborhood(self$filter, k): unused argument (k)

m <- MapperRef$new(X = eight)$
  use_filter(filter= f_x)$
  use_cover(cover = "ball", epsilon = 1)$
  use_clustering_algorithm(cl = "single")$
  construct_k_skeleton(k = 1L)
#> Error in self$cover$neighborhood(self$filter, k): unused argument (k)

sessioninfo::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_United States.1252  
#>  ctype    English_United States.1252  
#>  tz       America/New_York            
#>  date     2019-07-23                  
#> 
#> - Packages --------------------------------------------------------------
#>  ! package      * version date       lib
#>    assertthat     0.2.1   2019-03-21 [1]
#>    cli            1.1.0   2019-03-19 [1]
#>    codetools      0.2-16  2018-12-24 [2]
#>    crayon         1.3.4   2017-09-16 [1]
#>    digest         0.6.20  2019-07-04 [1]
#>    evaluate       0.14    2019-05-28 [1]
#>    fastcluster    1.1.25  2018-06-07 [1]
#>    highr          0.8     2019-03-20 [1]
#>    htmltools      0.3.6   2017-04-28 [1]
#>    knitr          1.23    2019-05-18 [1]
#>    magrittr       1.5     2014-11-22 [1]
#>    Mapper       * 0.9.1   2019-07-23 [1]
#>    parallelDist   0.2.4   2018-12-12 [1]
#>    proxy          0.4-23  2019-03-05 [1]
#>    R6             2.4.0   2019-02-14 [1]
#>    RANN           2.6.1   2019-01-08 [1]
#>    Rcpp           1.0.1   2019-03-17 [1]
#>  D RcppParallel   4.4.3   2019-05-22 [1]
#>    rmarkdown      1.13    2019-05-22 [1]
#>    sessioninfo    1.1.1   2018-11-05 [1]
#>    simplextree    0.9.1   2019-07-23 [1]
#>    stringi        1.4.3   2019-03-12 [1]
#>    stringr        1.4.0   2019-02-10 [1]
#>    withr          2.1.2   2018-03-15 [1]
#>    xfun           0.8     2019-06-25 [1]
#>    yaml           2.2.0   2018-07-25 [1]
#>  source                             
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.1)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  Github (peekxc/Mapper@52a8985)     
#>  CRAN (R 3.6.1)                     
#>  CRAN (R 3.6.1)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.1)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.1)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.1)                     
#>  Github (peekxc/simplextree@32a0316)
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#>  CRAN (R 3.6.0)                     
#> 
#> [1] C:/Users/sanma/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.0/library
#> 
#>  D -- DLL MD5 mismatch, broken installation.

^{Created on 2019-07-23 by the reprex package (v0.3.0)}

[Matt Piekenbrock]

Thanks for the issue, sorry for the delayed response. This should be fixed in the newest version. I also expanded the unit tests to actually construct the mappers with the other covers. Here's the reprex.

library(Mapper)

t <- seq(-0.5*pi, (3/2)*pi, length.out = 100) + runif(100, max = 0.01)
eight <- cbind(x1=cos(t), x2=sin(t)*cos(t))
f_x <- matrix(cos(t))

m <- MapperRef$new(X = eight)$
  use_filter(filter= f_x)$
  use_cover(cover = "restrained interval", number_intervals = 10, percent_overlap = 20)$
  use_clustering_algorithm(cl = "single")$
  construct_k_skeleton(k = 1L)
m$simplicial_complex
#> Simplex Tree with (16, 16) (0, 1)-simplices

m <- MapperRef$new(X = eight)$
  use_filter(filter= f_x)$
  use_cover(cover = "ball", epsilon = 1)$
  use_clustering_algorithm(cl = "single")$
  construct_k_skeleton(k = 1L)
m$simplicial_complex
#> Simplex Tree with (1) (0)-simplices

^{Created on 2019-08-05 by the reprex package (v0.3.0)}

[20choudharysa]

Thank you so much! I installed the latest version and all the cover types seem to be working now.