aggregate_area function rework

[andybeet]

New functions

• Added check_Argument_validation.r - some logic to determine conflicting argument parameter choices. To safeguard from running get_comland_data incorrectly.

Function changes

• get_comland_data - Reduce two arguments into one. applyPropLand and applyPropValue into applyProp. Included section in function to explain how some arguments are dependent on others
• aggregate_areas - rework code to use single applyProp argument
• get_comland_raw_data - fixed default filteByArea to pull up to the curent year (if no year is supplied)

linked Discussion

[sgaichas]

this all looks good but I may have introduced an error by upgrading to the latest sf package?

I can run get_comland_data(channel=channel) up to the point

Disaggregating little and winter skates from skates(ns)

when it errors out with

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/sgaichas/R/x86_64-pc-linux-gnu-library/4.3/sf/libs/sf.so':
  /home/sgaichas/R/x86_64-pc-linux-gnu-library/4.3/sf/libs/sf.so: undefined symbol: GEOSLineMergeDirected_r

I got the same error when trying to build the site with pkgdown, when it tries to build the ForeignCatchCompare21A21B.Rmd vignette:

The error ocurrs in that when I run this line

comlandr/vignettes/ForeignCatchCompare21A21B.Rmd

Lines 66 to 67 in b868a1e

	statAreas <- sf::st_read(system.file("extdata",package="comlandr"),layer="Statistical_Areas_2010",quiet=T)
	sf::st_crs(statAreas) <- 4269

so it is possibly an issue with the sf package that I didn't have when I was running an older sf version

My current sf is

> packageVersion("sf")
[1] '1.0.17'

my current setup:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
[1] C

time zone: EST
tzcode source: system (glibc)

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

other attached packages:
[1] patchwork_1.2.0   magrittr_2.0.3    data.table_1.15.4 ROracle_1.3-1.1   DBI_1.2.3        
[6] comlandr_0.3.0   

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1   viridisLite_0.4.2  dplyr_1.1.4        farver_2.1.2      
 [5] fastmap_1.1.1      tweenr_2.0.3       digest_0.6.35      survdat_1.0       
 [9] lifecycle_1.0.4    processx_3.8.4     compiler_4.3.1     rlang_1.1.3       
[13] tools_4.3.1        utf8_1.2.4         yaml_2.3.8         knitr_1.46        
[17] bit_4.0.5          classInt_0.4-10    xml2_1.3.6         KernSmooth_2.23-21
[21] withr_3.0.0        purrr_1.0.2        desc_1.4.3         grid_4.3.1        
[25] polyclip_1.10-4    fansi_1.0.6        dbutils_0.3.0      e1071_1.7-14      
[29] colorspace_2.1-0   ggplot2_3.5.1      scales_1.3.0       MASS_7.3-60       
[33] cli_3.6.2          rmarkdown_2.26     crayon_1.5.2       generics_0.1.3    
[37] rstudioapi_0.16.0  tzdb_0.4.0         cachem_1.0.8       ggforce_0.4.2     
[41] proxy_0.4-27       stringr_1.5.0      parallel_4.3.1     vctrs_0.6.5       
[45] jsonlite_1.8.8     callr_3.7.6        hms_1.1.3          bit64_4.0.5       
[49] systemfonts_1.0.6  tidyr_1.3.1        units_0.8-5        glue_1.7.0        
[53] pkgdown_2.0.7      ps_1.7.6           stringi_1.8.4      gtable_0.3.5      
[57] munsell_0.5.1      tibble_3.2.1       pillar_1.9.0       htmltools_0.5.8.1 
[61] R6_2.5.1           vroom_1.6.3        evaluate_0.23      kableExtra_1.4.0  
[65] readr_2.1.4        memoise_2.0.1      class_7.3-22       Rcpp_1.0.12       
[69] svglite_2.1.3      xfun_0.43          getPass_0.2-2      fs_1.6.4          
[73] pkgconfig_2.0.3   

I see there is no version for sf in the comlandr imports; which version are you running?

[andybeet]

so i have 1.0.16 on my windows machine. it builds ok. The Rstudio container (linux) has 1.0.17. It builds ok.

I think you got the same error because in the dissaggregate_skate_hakes function, there is an identical line of code.

Do you have any other shapefiles on your machine (if not i'll point you to one)? Can you try to read a different one using sf::st_read and see if this is a general problem using this function?

[sgaichas]

probably me:

> sf::st_read("data/EPU_NOESTUARIES")
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/sgaichas/R/x86_64-pc-linux-gnu-library/4.3/sf/libs/sf.so':
  /home/sgaichas/R/x86_64-pc-linux-gnu-library/4.3/sf/libs/sf.so: undefined symbol: GEOSLineMergeDirected_r

[sgaichas]

why don't I go ahead and pull this into dev, this issue shouldn't stop you working on it