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`prospectr::duplex()`: Avoid error "1:nrow(d) : argument of length 0" when`2 * k` is`nrow(X)`.#48

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l-ramirez-lopez merged 6 commits intol-ramirez-lopez:mainfromspectral-cockpit:fix/duplex-do-not-drop-D-dims

Oct 31, 2022

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`prospectr::duplex()`: Avoid error "1:nrow(d) : argument of length 0" when`2 * k` is`nrow(X)`.#48

l-ramirez-lopez merged 6 commits intol-ramirez-lopez:mainfromspectral-cockpit:fix/duplex-do-not-drop-D-dims

Oct 31, 2022

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philipp-baumann commentedOct 22, 2022•
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While working on a cLHS-DUPLEX sampling problem within clusters, I encountered an unlikely but unlucky case that threw an error (see next message). Because I first select spectra that are representative in terms of the distributions of spectral variables --- subject to reference analysis via conditioned latin hypercube sampling --- the next DUPLEX step decides for calibration/tuning or validation. Here, there is the situation ofntot_cluster_ref = 2 * k_duplex_fun. Meaning that half of the pool of spectra to be subjected to reference analysis at this stage go to calibration and half to validation roles, so that if run DUPLEX successfully in the end there is no spectra left.

However, for some edge cases, if there is only 1 possible sample left for "test" in thewhile (i < k) conditional, "Error in 1:nrow(d) : argument of length 0" occurs. This is because1:nrow(d) is called after whend results in a 2L vector instead of a matrix expected, e.g. because of the implicitdrop = TRUE default in[ for matrices/dfs. To be on the safe side, this PR both explicitly does not drop any dims when removing previously assigned samples viadrop = FALSE and replaces1:nrow(d) withseq_len(nrow(d)). The commits in this branch try to avoid any unintended side effects.

Philipp Baumann added4 commits

October 22, 2022 23:38

Avoid error "1:nrow(d) : argument of lenght 0" when k is nrow(X).

b135348

for consitency (F -> FALSE)

4f27a71

Also error when2 * k > nrow(X)

c667d3d

saferseq_along(x) instead of1:nrow(x)

4f25df8

philipp-baumann changed the title~~prospectr::duplex(): Avoid error "1:nrow(d) : argument of lenght 0" when k is nrow(X).~~prospectr::duplex(): Avoid error "1:nrow(d) : argument of lenght 0" when2 * k isnrow(X).

Oct 22, 2022

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philipp-baumann commentedOct 22, 2022

this is a reprex before:

library("prospectr")#> �[34mprospectr version 0.2.6 -- �[39m'chicago'#> �[34mcheck the github repository at: https://github.com/l-ramirez-lopez/prospectr/�[39mdata(NIRsoil)spec<-NIRsoil$spcspec_pca<-stats::prcomp(spec,center=TRUE,scale.=FALSE)# arbitrarily assuming 3 PCs would explain the desired variance threshold# in total 6 samples for lab analysis, where 3 serve the purpose of calibration# and 3 validationscores<- as.data.frame(spec_pca$x)[1:6,1:3]duplex(X=scores,k= nrow(scores)/2,metric="mahal")#> Error in 1:nrow(d): argument of length 0

^{Created on 2022-10-23 by thereprex package (v2.0.1)}

seq_len(nrow(X)) required for matrices/dfs; fixes previous commit

2eb7a17

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philipp-baumann commentedOct 22, 2022

sorry2eb7a17 is now a correct fix across rows.

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philipp-baumann commentedOct 22, 2022

Now with this PR branch:

library("prospectr")#> �[34mprospectr version 0.2.6 -- �[39m'chicago'#> �[34mcheck the github repository at: https://github.com/l-ramirez-lopez/prospectr/�[39mdevtools::session_info()#> ─ Session info ───────────────────────────────────────────────────────────────#>  setting  value#>  version  R version 4.1.3 (2022-03-10)#>  os       Ubuntu 20.04.5 LTS#>  system   x86_64, linux-gnu#>  ui       X11#>  language (EN)#>  collate  en_US.UTF-8#>  ctype    en_US.UTF-8#>  tz       Europe/Zurich#>  date     2022-10-23#>  pandoc   2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown)#>#> ─ Packages ───────────────────────────────────────────────────────────────────#>  package     * version date (UTC) lib source#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.2)#>  cachem        1.0.6   2021-08-19 [1] CRAN (R 4.1.1)#>  callr         3.7.2   2022-08-22 [1] CRAN (R 4.1.3)#>  cli           3.4.0   2022-09-08 [1] CRAN (R 4.1.3)#>  codetools     0.2-18  2020-11-04 [2] CRAN (R 4.1.3)#>  crayon        1.5.1   2022-03-26 [1] CRAN (R 4.1.3)#>  devtools      2.4.2   2021-06-07 [1] CRAN (R 4.1.1)#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.2)#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.2)#>  evaluate      0.16    2022-08-09 [1] CRAN (R 4.1.3)#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.1.3)#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.1)#>  foreach       1.5.2   2022-02-02 [1] CRAN (R 4.1.2)#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.2)#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.2)#>  highr         0.9     2021-04-16 [1] CRAN (R 4.1.2)#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.1.3)#>  iterators     1.0.14  2022-02-05 [1] CRAN (R 4.1.2)#>  knitr         1.38    2022-03-25 [1] CRAN (R 4.1.3)#>  lifecycle     1.0.2   2022-09-09 [1] CRAN (R 4.1.3)#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.1.3)#>  mathjaxr      1.4-0   2021-03-01 [1] CRAN (R 4.1.1)#>  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.1.2)#>  pillar        1.8.1   2022-08-19 [1] CRAN (R 4.1.3)#>  pkgbuild      1.3.1   2021-12-20 [1] CRAN (R 4.1.2)#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.2)#>  pkgload       1.3.0   2022-06-27 [1] CRAN (R 4.1.3)#>  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.1.2)#>  processx      3.7.0   2022-07-07 [1] CRAN (R 4.1.3)#>  prospectr   * 0.2.6   2022-10-22 [1] Github (spectral-cockpit/prospectr@2eb7a17)#>  ps            1.7.1   2022-06-18 [1] CRAN (R 4.1.3)#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.2)#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.2)#>  Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.1.3)#>  remotes       2.4.2   2021-11-30 [1] CRAN (R 4.1.2)#>  reprex        2.0.1   2021-08-05 [1] CRAN (R 4.1.2)#>  rlang         1.0.5   2022-08-31 [1] CRAN (R 4.1.3)#>  rmarkdown     2.13    2022-03-10 [1] CRAN (R 4.1.3)#>  rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.1.3)#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.2)#>  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.2)#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.2)#>  styler        1.5.1   2021-07-13 [1] CRAN (R 4.1.1)#>  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.1.3)#>  usethis       2.1.6   2022-05-25 [1] CRAN (R 4.1.3)#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.2)#>  vctrs         0.4.1   2022-04-13 [1] CRAN (R 4.1.3)#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.3)#>  xfun          0.30    2022-03-02 [1] CRAN (R 4.1.3)#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.1.3)#>#>  [1] /home/philipp/R/x86_64-pc-linux-gnu-library/4.1#>  [2] /opt/R/4.1.3/lib/R/library#>#> ──────────────────────────────────────────────────────────────────────────────data(NIRsoil)spec<-NIRsoil$spcspec_pca<-stats::prcomp(spec,center=TRUE,scale.=FALSE)# arbitrarily assuming 3 PCs would explain the desired variance threshold# in total 6 samples for lab analysis, where 3 serve the purpose of calibration# and 3 validationscores<- as.data.frame(spec_pca$x)[1:6,1:3]duplex(X=scores,k= nrow(scores)/2,metric="mahal")#> $model#> [1] 5 3 4#>#> $test#> [1] 2 1 6

^{Created on 2022-10-23 by thereprex package (v2.0.1)}

philipp-baumann changed the title~~prospectr::duplex(): Avoid error "1:nrow(d) : argument of lenght 0" when2 * k isnrow(X).~~prospectr::duplex(): Avoid error "1:nrow(d) : argument of length 0" when2 * k isnrow(X).

Oct 22, 2022

return early if 'nrow(X) = 4'; avoid returning two identical test sam…

9bd0abf

…ples

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philipp-baumann commentedOct 25, 2022•
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9bd0abf addresses the issue of two identical test samples that were returned whennrow(X) == 4 (because of

prospectr/R/duplex.R

Line 158 inda9b892

id<- c(arrayInd(which.max(D[,-id]), rep(m-2,2)))

). It is again not a very standard case, but in my opinion nice to cover. Somehow thearrayInd method does not work whendim(D) = c(2, 2), hence I thought returning early the two samples (exceptionally 1 ifnrow(X) == 3, what is left) does the job. Maybe you find a more elegant way to program the last special case (promise no more in this PR branch ;))

Here a short reprex:

library("prospectr")# current version on github main branch; see session info#> �[34mprospectr version 0.2.6 -- �[39m'chicago'#> �[34mcheck the github repository at: https://github.com/l-ramirez-lopez/prospectr/�[39m# belowdata(NIRsoil)spec<-NIRsoil$spcspec_pca<-stats::prcomp(spec,center=TRUE,scale.=FALSE)# 4 rows onlyscores<- as.data.frame(spec_pca$x)[1:4,1:3]# returns twice the same row numbers/sample IDs for the test setduplex(X=scores,k= nrow(scores)/2,metric="mahal")#> $model#> [1] 3 1#>#> $test#> [1] 4 4sessioninfo::session_info()#> ─ Session info ───────────────────────────────────────────────────────────────#>  setting  value#>  version  R version 4.1.3 (2022-03-10)#>  os       Ubuntu 20.04.5 LTS#>  system   x86_64, linux-gnu#>  ui       X11#>  language (EN)#>  collate  en_US.UTF-8#>  ctype    en_US.UTF-8#>  tz       Europe/Zurich#>  date     2022-10-25#>  pandoc   2.5 @ /usr/bin/ (via rmarkdown)#>#> ─ Packages ───────────────────────────────────────────────────────────────────#>  ! package     * version date (UTC) lib source#>    cli           3.4.1   2022-09-23 [1] CRAN (R 4.1.3)#>    codetools     0.2-18  2020-11-04 [2] CRAN (R 4.1.3)#>    digest        0.6.30  2022-10-18 [1] CRAN (R 4.1.3)#>    evaluate      0.17    2022-10-07 [1] CRAN (R 4.1.3)#>    fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.3)#>    foreach       1.5.2   2022-02-02 [1] CRAN (R 4.1.3)#>    fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.3)#>    glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.3)#>    highr         0.9     2021-04-16 [1] CRAN (R 4.1.3)#>    htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.1.3)#>    iterators     1.0.14  2022-02-05 [1] CRAN (R 4.1.3)#>    knitr         1.40    2022-08-24 [1] CRAN (R 4.1.3)#>    lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.1.3)#>    magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.1.3)#>    mathjaxr      1.6-0   2022-02-28 [1] CRAN (R 4.1.3)#>    prospectr   * 0.2.6   2022-10-25 [1] Github (l-ramirez-lopez/prospectr@da9b892)#>    Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.1.3)#>    reprex        2.0.2   2022-08-17 [1] CRAN (R 4.1.3)#>    rlang         1.0.6   2022-09-24 [1] CRAN (R 4.1.3)#>    rmarkdown     2.17    2022-10-07 [1] CRAN (R 4.1.3)#>  P sessioninfo   1.2.2   2021-12-06 [?] CRAN (R 4.1.3)#>    stringi       1.7.8   2022-07-11 [1] CRAN (R 4.1.3)#>    stringr       1.4.1   2022-08-20 [1] CRAN (R 4.1.3)#>    withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.3)#>    xfun          0.34    2022-10-18 [1] CRAN (R 4.1.3)#>    yaml          2.3.6   2022-10-18 [1] CRAN (R 4.1.3)#>#>  [1] /home/philipp/git/spectral-cockpit/reprex-prospectr-duplex-no-drop-dims/renv/profiles/origin/renv/library/R-4.1/x86_64-pc-linux-gnu#>  [2] /opt/R/4.1.3/lib/R/library#>#>  P ── Loaded and on-disk path mismatch.#>#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2022-10-25 withreprex v2.0.2}

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l-ramirez-lopez commentedOct 31, 2022

Thank you@philipp-baumann

l-ramirez-lopez merged commit73852db intol-ramirez-lopez:main

Oct 31, 2022

l-ramirez-lopez added a commit that referenced this pull request

Oct 31, 2022

Merge pull request#49from l-ramirez-lopez/main

db62420

incorporate#48

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l-ramirez-lopez commentedFeb 13, 2024

@philipp-baumann: I had to reopen this as I found a problem with some parts of your original solution

l-ramirez-lopez mentioned this pull request

Feb 13, 2024

DUPLEX suggested changes#61

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`prospectr::duplex()`: Avoid error "1:nrow(d) : argument of length 0" when`2 * k` is`nrow(X)`.#48

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prospectr::duplex(): Avoid error "1:nrow(d) : argument of length 0" when2 * k isnrow(X).#48

prospectr::duplex(): Avoid error "1:nrow(d) : argument of length 0" when2 * k isnrow(X).#48

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`prospectr::duplex()`: Avoid error "1:nrow(d) : argument of length 0" when`2 * k` is`nrow(X)`.#48

`prospectr::duplex()`: Avoid error "1:nrow(d) : argument of length 0" when`2 * k` is`nrow(X)`.#48

philipp-baumann commentedOct 22, 2022•
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philipp-baumann commentedOct 25, 2022•
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