xpose not working

[DimitrisVoul]

Hello,

I am having an issue with xpose after fitting a model. Specifically during the conversion step:

xpose_data_nlmixr(fitexpon)

Error in data.frame(data_a, full.dat) : 
  arguments imply differing number of rows: 6272, 0

`R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] xpose.nlmixr_0.1.4 xpose_0.4.8 ggplot2_3.3.0

loaded via a namespace (and not attached): [1] tidyselect_0.2.5 xfun_0.11 purrr_0.3.3 lattice_0.20-38 colorspace_1.4-1
[6] RxODE_0.9.2-0 generics_0.0.2 vctrs_0.2.0 vpc_1.1.0 nlmixr_1.1.1-7
[11] rlang_0.4.1 huxtable_4.7.0 pillar_1.4.2 glue_1.3.1 withr_2.1.2
[16] tweenr_1.0.1 lifecycle_0.1.0 stringr_1.4.0 munsell_0.5.0 n1qn1_6.0.1-3
[21] gtable_0.3.0 mvnfast_0.2.5 memoise_1.1.0 knitr_1.26 RcppArmadillo_0.9.800.1.0 [26] rex_1.1.2 parallel_3.6.1 Rcpp_1.0.3 scales_1.0.0 backports_1.1.5
[31] farver_2.0.1 brew_1.0-6 ggforce_0.3.1 digest_0.6.22 lotri_0.1.1
[36] stringi_1.4.3 dplyr_0.8.3 polyclip_1.10-0 grid_3.6.1 tools_3.6.1
[41] magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3 PreciseSums_0.3 crayon_1.3.4
[46] tidyr_1.0.0 pkgconfig_2.0.3 zeallot_0.1.0 MASS_7.3-51.4 Matrix_1.2-17
[51] data.table_1.12.6 assertthat_0.2.1 rstudioapi_0.10 R6_2.4.1 units_0.6-5
[56] nlme_3.1-140 compiler_3.6.1 `

[mattfidler]

Hi @DimitrisVoul,

We need a reproducible example; If you cannot share the data, please simulate something that causes the same issue.

[DimitrisVoul]

Sure, I am uploading test data and the code

data.zip

expon <- function() { ini({ tV0 <- -2 tkgrow <- -3 prop.err <- 0.3

eta.V0 ~ 0.5
eta.kgrow ~ 0.5

}) model({ V0 <- exp(tV0+eta.V0) KGROW <- exp(tkgrow + eta.kgrow) V(0) =V0;

d/dt(V) = KGROW * V
V~prop(prop.err)

}) }

fitexpon <- nlmixr(expon, data, 'focei')

library(xpose.nlmixr) xpdb <- xpose_data_nlmixr(fitexpon)

[kestrel99]

Thanks @DimitrisVoul. On it

[kestrel99]

I've now had a chance to check this (RxODE 0.9.2.0/GitHub, nlmixr 1.1.1-7/GitHub, xpose 0.4.8/GitHub, xpose.nlmixr 0.1.5, all freshly installed this morning on R 3.6.2) - and it works for me. Can you refresh and let me know if the outcome is different?

[DimitrisVoul]

Hello,

I had some issues installing nlmixr from scratch on my laptop and that why I have been using the window installer to do so. There is an update feature now and I used this to update the software. The current version is RxODE 0.9.2.0/GitHub, nlmixr 1.1.1-7/GitHub, xpose 0.4.8/GitHub, xpose.nlmixr 0.1.4 on R 3.6.1 and I still have the same issue.

I am not sure what the problem is because xpose used to work fine some time ago and never had any issues.

[kestrel99]

We're often chasing a moving target with both the tidyverse and xpose - changes to either of those packages often have a knock-on effect for us (e.g. the impending changes to dplyr are likely to be disruptive).

Can you try upgrading to xpose.nlmixr 0.1.5 (GitHub) to see if that does any good?

[DimitrisVoul]

Yes, it might me some clash with another package because it was a sudden change as well.

What command can I use to do that?

[kestrel99]

devtools::install_github("nlmixrdevelopment/xpose.nlmixr")

[DimitrisVoul]

When I try to install I get an error that the previous installation of dplyr cannot be removed.

[kestrel99]

Try using install.packages("dplyr") from a clean restart of R - this has happened to me a lot as well and is down to having libraries loaded in the background. When all the packages it wants have been upgraded this way, try install_github again.

[DimitrisVoul]

I did it and it worked! Thank you very much for all the help. I just needed to install dplyr and it did the trick.

[kestrel99]

Excellent!