superheat problems

[carloscinelli]

Hi guys, the package currently does not import the superheat::superheat function, so the user faces an error when using it for the first time, if the superheat package is not already installed in their machine.

When installing the CRAN version of superheat (0.1.0), I get the following error message:

Error in superheat::superheat(te_mat, heat.pal = c("blue", "light blue",  : 
  unused arguments (title.alignment = "center", legend.breaks = round(seq(from = -max(abs(ate_mean)), to = max(abs(ate_mean)), length.out = 5)), legend.vspace = 0.05)

Then I tried installing the development version on GitHub (1.0.0), and now I get the following error message:

Error in if (!alpha || all(lab_in[, 4] == 1)) { : 
  missing value where TRUE/FALSE needed

I am running the first heatmap example with the NHANES data.

Here is the example with the GitHub version of superheat and my session info, in case it helps.

rm(list = ls())
library(TukeySens)
#> Loading required package: tidyverse

# Observed data in treatment group
NHANES_trt <- NHANES %>% dplyr::filter(trt_dbp == 1)
x_trt <- NHANES_trt %>% select(-one_of("trt_dbp", "ave_dbp"))
y_trt <- NHANES_trt %>% select(ave_dbp)

# Observed data in control group 
NHANES_ctrl <- NHANES %>% dplyr::filter(trt_dbp == 0)
x_ctrl <- NHANES_ctrl %>% select(-one_of("trt_dbp", "ave_dbp"))
y_ctrl <- NHANES_ctrl %>% select(ave_dbp)

# ATE Heatmap 
# fit outcome separately
heatmap_ate(x_trt, y_trt, x_ctrl, y_ctrl, largest_effect = 0.05)
#> *****Into main of wbart
#> *****Data:
#> data:n,p,np: 1026, 21, 1456
#> y1,yn: -7.629630, 0.370370
#> x1,x[n*p]: 1.000000, 52.000000
#> xp1,xp[np*p]: 0.000000, 52.000000
#> *****Number of Trees: 200
#> *****Number of Cut Points: 1 ... 33
#> *****burn and ndpost: 100, 1000
#> *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,2.156676,3.000000,0.000000
#> *****sigma: 0.000000
#> *****w (weights): 1.000000 ... 1.000000
#> *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,21,0
#> *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
#> *****printevery: 100
#> *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
#> 
#> MCMC
#> done 0 (out of 1100)
#> done 100 (out of 1100)
#> done 200 (out of 1100)
#> done 300 (out of 1100)
#> done 400 (out of 1100)
#> done 500 (out of 1100)
#> done 600 (out of 1100)
#> done 700 (out of 1100)
#> done 800 (out of 1100)
#> done 900 (out of 1100)
#> done 1000 (out of 1100)
#> time: 11s
#> check counts
#> trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
#> Warning in summary.lm(lmf): essentially perfect fit: summary may be unreliable
#> *****Into main of wbart
#> *****Data:
#> data:n,p,np: 1456, 21, 1026
#> y1,yn: -21.266484, -1.266484
#> x1,x[n*p]: 0.000000, 52.000000
#> xp1,xp[np*p]: 1.000000, 52.000000
#> *****Number of Trees: 200
#> *****Number of Cut Points: 1 ... 37
#> *****burn and ndpost: 100, 1000
#> *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,1.697056,3.000000,0.000000
#> *****sigma: 0.000000
#> *****w (weights): 1.000000 ... 1.000000
#> *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,21,0
#> *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
#> *****printevery: 100
#> *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
#> 
#> MCMC
#> done 0 (out of 1100)
#> done 100 (out of 1100)
#> done 200 (out of 1100)
#> done 300 (out of 1100)
#> done 400 (out of 1100)
#> done 500 (out of 1100)
#> done 600 (out of 1100)
#> done 700 (out of 1100)
#> done 800 (out of 1100)
#> done 900 (out of 1100)
#> done 1000 (out of 1100)
#> time: 14s
#> check counts
#> trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
#> Error in if (!alpha || all(lab_in[, 4] == 1)) {: missing value where TRUE/FALSE needed




sessionInfo()
#> R version 3.6.2 (2019-12-12)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS Catalina 10.15.2
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] TukeySens_0.0.0.9000 forcats_0.4.0        stringr_1.4.0       
#>  [4] dplyr_0.8.3          purrr_0.3.3          readr_1.3.1         
#>  [7] tidyr_1.0.0          tibble_2.1.3         ggplot2_3.2.1       
#> [10] tidyverse_1.3.0     
#> 
#> loaded via a namespace (and not attached):
#>  [1] superheat_1.0.0  tidyselect_0.2.5 xfun_0.12        splines_3.6.2   
#>  [5] haven_2.2.0      lattice_0.20-38  colorspace_1.4-1 vctrs_0.2.1     
#>  [9] generics_0.0.2   htmltools_0.4.0  BART_2.7         yaml_2.2.0      
#> [13] survival_3.1-8   rlang_0.4.2      pillar_1.4.3     withr_2.1.2     
#> [17] glue_1.3.1       DBI_1.1.0        dbplyr_1.4.2     modelr_0.1.5    
#> [21] readxl_1.3.1     lifecycle_0.1.0  munsell_0.5.0    gtable_0.3.0    
#> [25] cellranger_1.1.0 rvest_0.3.5      evaluate_0.14    knitr_1.26      
#> [29] parallel_3.6.2   fansi_0.4.1      highr_0.8        broom_0.5.3     
#> [33] Rcpp_1.0.3       backports_1.1.5  scales_1.1.0     jsonlite_1.6    
#> [37] farver_2.0.1     fs_1.3.1         hms_0.5.3        digest_0.6.23   
#> [41] stringi_1.4.5    grid_3.6.2       cli_2.0.1        tools_3.6.2     
#> [45] magrittr_1.5     lazyeval_0.2.2   crayon_1.3.4     pkgconfig_2.0.3 
#> [49] zeallot_0.1.0    Matrix_1.2-18    xml2_1.2.2       reprex_0.3.0    
#> [53] lubridate_1.7.4  assertthat_0.2.1 rmarkdown_2.0    httr_1.4.1      
#> [57] R6_2.4.1         nnet_7.3-12      nlme_3.1-142     compiler_3.6.2

[carloscinelli]

PS: I saw that you listed superheat in the remotes in the description. Thus, maybe not installing automatically the superheat package could be a devtools issue.