Evaluating a TI method

[SirKuikka]

Hi,

I'm failing in running the example here.

library(dynwrap)
library(dyneval)
library(dynmethods)
library(tidyverse)


dataset <- dyntoy::generate_dataset(model = "bifurcating")


models <- infer_trajectories(dataset, list(ti_comp1(), ti_mst(), ti_shuffle()))




dataset <- add_cell_waypoints(dataset)
models$model <- map(models$model, add_cell_waypoints)

Here is the error I received:

Error: is_wrapper_with_trajectory(trajectory) isn't true.

The code breaks at the last line.

My session info:

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fi_FI.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=fi_FI.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fi_FI.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fi_FI.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] forcats_0.4.0    stringr_1.4.0    dplyr_0.8.4      purrr_0.3.3      readr_1.3.1      tidyr_1.0.2     
 [7] tibble_2.1.3     ggplot2_3.2.1    tidyverse_1.3.0  dynmethods_1.0.5 dyneval_0.9.9    dynwrap_1.1.4   

loaded via a namespace (and not attached):
 [1] nlme_3.1-144          fs_1.3.1              dynutils_1.0.4.9000   bit64_0.9-7          
 [5] lubridate_1.7.4       RColorBrewer_1.1-2    httr_1.4.1            tools_3.6.3          
 [9] backports_1.1.5       R6_2.4.1              rpart_4.1-15          Hmisc_4.3-1          
[13] DBI_1.1.0             lazyeval_0.2.2        colorspace_1.4-1      nnet_7.3-13          
[17] withr_2.1.2           tidyselect_1.0.0      carrier_0.1.0         gridExtra_2.3        
[21] processx_3.4.2        proxyC_0.1.5          bit_1.1-15.2          compiler_3.6.3       
[25] cli_2.0.1             rvest_0.3.5           htmlTable_1.13.3      hdf5r_1.3.1          
[29] xml2_1.2.2            scales_1.1.0          checkmate_2.0.0       mvtnorm_1.0-12       
[33] digest_0.6.23         foreign_0.8-75        base64enc_0.1-3       jpeg_0.1-8.1         
[37] pkgconfig_2.0.3       htmltools_0.4.0       dbplyr_1.4.2          htmlwidgets_1.5.1    
[41] rlang_0.4.4           readxl_1.3.1          rstudioapi_0.11       generics_0.0.2       
[45] jsonlite_1.6.1        acepack_1.4.1         magrittr_1.5          Formula_1.2-3        
[49] Matrix_1.2-18         fansi_0.4.1           Rcpp_1.0.3            munsell_0.5.0        
[53] lifecycle_0.1.0       stringi_1.4.5         yaml_2.2.1            plyr_1.8.5           
[57] grid_3.6.3            crayon_1.3.4          lattice_0.20-40       haven_2.2.0          
[61] splines_3.6.3         hms_0.5.3             dynfeature_1.0.0.9000 knitr_1.28           
[65] ps_1.3.0              pillar_1.4.3          igraph_1.2.4.2        ranger_0.12.1        
[69] babelwhale_1.0.1      reshape2_1.4.3        reprex_0.3.0          glue_1.3.1           
[73] latticeExtra_0.6-29   data.table_1.12.8     remotes_2.1.0         RcppParallel_4.4.4   
[77] modelr_0.1.5          png_0.1-7             vctrs_0.2.2           dynparam_1.0.0       
[81] testthat_2.3.1        cellranger_1.1.0      gtable_0.3.0          assertthat_0.2.1     
[85] xfun_0.12             broom_0.5.4           survival_3.1-8        dyntoy_0.9.9         
[89] cluster_2.1.0         ellipsis_0.3.0       
> 

Thanks for any help in advance.

Best
SirKuikka

[akattapuram-insitro]

@SirKuikka Hi! I am also running into the same issue- did you find a fix ?