review joss

[ibarraespinosa]

10.21105.joss.08091_revsie1.pdf

I started the review of the submissions here openjournals/joss-reviews#8091

This is the manuscript.

i will start checking the code

[ibarraespinosa]

reamde.. how to guides?

[ibarraespinosa]

codecov 0%

[ibarraespinosa]

hey, my review thttps://github.com/openjournals/joss-reviews/issues/8091#issuecomment-3042494680 is here. Can you provide an URL to download the .dat files required to run the examples?

[jonsampedro]

Hi @ibarraespinosa. Thank you for your comments. Some answers below:

• The "How to" link in the README file has been now corrected in this commit

• The codecov has also been corrected.

• The .dat file to run the Step-by-step example is provided in the repository. This can be used to run all the functions in the package.

Just let me know if you have any issue you when running the package functions. Thank you again for your time and feedback,

[ibarraespinosa]

Installation guide is still confusing. For instance, cloning the repo is optional, but required to run the examples with the .dat file. Guides and examples should provide link and steps to download the .dat file

[jonsampedro]

Hi @ibarraespinosa ,

The installation guide has now been completely re-structured to improve clarity.

Also, the test_rhap file is now stored in the inst/extdata/ directory and included in the data folder, so it can be directly loaded. Now there is no need to clone the package to access the test file, as also clarified in the vignette

[goldingn]

Hi @ibarraespinosa are you happy with the edits to the installation guide and data?

[ibarraespinosa]

I'm not seeing the plots, what I'm missing?

library(rhap)
# Set your project and scenario names
my_prj_name  <- rhap::test_rhap  # Name of the .dat project file (avoid spaces). Note that rhap::test_rhap loads the example project file included in the package

my_scen_name <- "Reference"       # Name of the GCAM scenario to process (or vector of scenarios)

# Run the RHAP model
hap_damages <- calc_hap_impacts(
  prj_name     = my_prj_name,
  scen_name    = my_scen_name,
  final_db_year = 2050,
  saveOutput   = TRUE,
  map          = FALSE,
  anim         = TRUE,
  HIA_var      = "deaths",
  normalized   = TRUE,
  by_gr        = FALSE
)

# Preview the results
head(hap_damages)

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Denver
tzcode source: system (glibc)

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

other attached packages:
[1] rhap_0.1.0

loaded via a namespace (and not attached):
 [1] gcamdata_5.1      dplyr_1.1.4       compiler_4.4.1    tidyselect_1.2.1 
 [5] Rcpp_1.1.0        collapse_2.1.2    xml2_1.3.8        stringr_1.5.1    
 [9] parallel_4.4.1    assertthat_0.2.1  tidyr_1.3.1       lattice_0.22-6   
[13] readr_2.1.5       R6_2.6.1          maxLik_1.5-2.1    generics_0.1.4   
[17] lmtest_0.9-40     Formula_1.2-5     rbibutils_2.3     MASS_7.3-61      
[21] bdsmatrix_1.3-7   tibble_3.3.0      lubridate_1.9.4   pillar_1.11.0    
[25] tzdb_0.5.0        rlang_1.1.6       utf8_1.2.6        stringi_1.8.7    
[29] rgcam_1.2.0       timechange_0.3.0  cli_3.6.5         withr_3.0.2      
[33] magrittr_2.0.3    Rdpack_2.6.4      digest_0.6.37     grid_4.4.1       
[37] rstudioapi_0.17.1 plm_2.6-6         hms_1.1.3         sandwich_3.1-1   
[41] nlme_3.1-166      lifecycle_1.0.4   miscTools_0.6-28  vctrs_0.6.5      
[45] glue_1.8.0        data.table_1.17.8 zoo_1.8-14        purrr_1.1.0      
[49] httr_1.4.7        tools_4.4.1       pkgconfig_2.0.3  
> 

[ibarraespinosa]

Ohh, doh, It was

  map          = TRUE,

[ibarraespinosa]

Well, now I can run the example, that is a step forward

[ibarraespinosa]

https://github.com/bc3LC/rhap/blob/main/R/create_panel.R#L74 Why not using

system.file("extdata", package = "rhap")

[jonsampedro]

Thank you for your comments @ibarraespinosa!

Given the current progress on the JOSS publication and the version archiving, we will note these suggestions and implement the changes once that process is complete. I hope that works for you!