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can't use the aggregate function #731

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khalilT opened this issue Jan 22, 2025 · 13 comments
Open

can't use the aggregate function #731

khalilT opened this issue Jan 22, 2025 · 13 comments
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reprex needed

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@khalilT
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khalilT commented Jan 22, 2025

Hello,
I can't call the aggregate function from the stars package, although I can see it in the documentation and methods.

> methods(class = "stars")

 [1] [                 [[<-              [<-               %in%              $<-               adrop             aggregate         aperm            
 [9] as.data.frame     as.POSIXct        c                 coerce            contour           cut               dim               dimnames         
[17] dimnames<-        droplevels        expand_dimensions hist              image             initialize        is.na             Math             
[25] merge             Ops               plot              prcomp            predict           print             show              slotsFromS3      
[33] split             st_apply          st_area           st_as_sf          st_as_sfc         st_as_stars       st_bbox           st_coordinates   
[41] st_crop           st_crs            st_crs<-          st_dimensions     st_dimensions<-   st_downsample     st_extract        st_geometry      
[49] st_geotransform   st_geotransform<- st_interpolate_aw st_intersects     st_join           st_mosaic         st_normalize      st_redimension   
[57] st_rotate         st_sample         st_set_bbox       st_transform      st_write          time              write_stars      
see '?methods' for accessing help and source code

I use R version 4.4.1, and I have both dependencies sf and terra

here is my sessioninfo:

Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
@edzer
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edzer commented Jan 22, 2025

That's not a sessionInfo().

> library(stars)
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
> methods(class = "stars")
 [1] [                 [[<-              [<-               %in%             
 [5] $<-               adrop             aggregate         aperm            
 [9] as.data.frame     as.POSIXct        c                 coerce           
[13] contour           cut               dim               dimnames         
[17] dimnames<-        droplevels        expand_dimensions hist             
[21] image             initialize        is.na             Math             
[25] merge             Ops               plot              prcomp           
[29] predict           print             show              slotsFromS3      
[33] split             st_apply          st_area           st_as_sf         
[37] st_as_sfc         st_as_stars       st_bbox           st_coordinates   
[41] st_crop           st_crs            st_crs<-          st_dimensions    
[45] st_dimensions<-   st_downsample     st_extract        st_geometry      
[49] st_geotransform   st_geotransform<- st_interpolate_aw st_intersects    
[53] st_join           st_mosaic         st_normalize      st_redimension   
[57] st_rotate         st_sample         st_set_bbox       st_transform     
[61] st_write          time              write_stars      
see '?methods' for accessing help and source code
> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 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-r0.3.26.so;  LAPACK version 3.12.0

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

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] stars_0.6-8 sf_1.0-20   abind_1.4-8

loaded via a namespace (and not attached):
 [1] e1071_1.7-16       magrittr_2.0.3     KernSmooth_2.23-26 parallel_4.4.2    
 [5] classInt_0.4-11    cli_3.6.3          grid_4.4.2         DBI_1.2.3         
 [9] proxy_0.4-27       class_7.3-23       compiler_4.4.2     tools_4.4.2       
[13] Rcpp_1.0.13-1      rlang_1.1.4        units_0.8-6

@khalilT
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khalilT commented Jan 22, 2025

I am really sorry I didn't notice the last part was truncated.
Here is everything again (also the message when loading stars)

Loading required package: abind
Loading required package: sf
Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

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               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] stars_0.6-8  sf_1.0-19    abind_1.4-8  terra_1.8-12

loaded via a namespace (and not attached):
 [1] codetools_0.2-20   e1071_1.7-16       magrittr_2.0.3     KernSmooth_2.23-24 parallel_4.4.1     classInt_0.4-11    cli_3.6.3         
 [8] grid_4.4.1         DBI_1.2.3          proxy_0.4-27       class_7.3-22       compiler_4.4.1     rstudioapi_0.16.0  tools_4.4.1       
[15] Rcpp_1.0.14        rlang_1.1.5        units_0.8-5

@edzer
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edzer commented Jan 22, 2025

Did you load library(stars)?

@khalilT
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khalilT commented Jan 22, 2025

of course.
I can't call the function even this way stars::aggregate()

Image

@edzer
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edzer commented Jan 22, 2025

Please give the full output, starting from a clean R session (no other packages loaded), when you run

library(stars)
methods(class = "stars")
sessionInfo()

@khalilT
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khalilT commented Jan 22, 2025

sure. Here it is:


> library(stars)
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
> methods(class = "stars")
 [1] [                 [[<-              [<-               %in%              $<-               adrop             aggregate         aperm            
 [9] as.data.frame     as.POSIXct        c                 coerce            contour           cut               dim               dimnames         
[17] dimnames<-        droplevels        expand_dimensions filter            hist              image             initialize        is.na            
[25] Math              merge             Ops               plot              prcomp            predict           print             show             
[33] slotsFromS3       split             st_apply          st_area           st_as_sf          st_as_sfc         st_as_stars       st_bbox          
[41] st_coordinates    st_crop           st_crs            st_crs<-          st_dimensions     st_dimensions<-   st_downsample     st_extract       
[49] st_geometry       st_geotransform   st_geotransform<- st_interpolate_aw st_intersects     st_join           st_mosaic         st_normalize     
[57] st_redimension    st_rotate         st_sample         st_set_bbox       st_transform      st_write          time              write_stars      
see '?methods' for accessing help and source code
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

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               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] stars_0.6-8 sf_1.0-19   abind_1.4-8

loaded via a namespace (and not attached):
 [1] gtable_0.3.5       dplyr_1.1.4        compiler_4.4.1     tidyselect_1.2.1   Rcpp_1.0.14        parallel_4.4.1     gridExtra_2.3     
 [8] scales_1.3.0       ggplot2_3.5.1      R6_2.5.1           generics_0.1.3     classInt_0.4-11    MASS_7.3-61        polyclip_1.10-7   
[15] tibble_3.2.1       units_0.8-5        munsell_0.5.1      DBI_1.2.3          pillar_1.9.0       rlang_1.1.5        utf8_1.2.4        
[22] terra_1.8-12       cli_3.6.3          withr_3.0.1        magrittr_2.0.3     tweenr_2.0.3       class_7.3-22       grid_4.4.1        
[29] rstudioapi_0.16.0  ggforce_0.4.2      lifecycle_1.0.4    vctrs_0.6.5        KernSmooth_2.23-24 proxy_0.4-27       glue_1.7.0        
[36] farver_2.1.2       codetools_0.2-20   fansi_1.0.6        e1071_1.7-16       colorspace_2.1-1   tools_4.4.1        pkgconfig_2.0.3   ```

@edzer
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edzer commented Jan 22, 2025

You have 41 packages loaded via namespace, I have 17, it's possible that the problem lies in that difference. I asked you to do this in a clean R session.

@khalilT
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khalilT commented Jan 22, 2025

I restarted the session (ctl + shift + F10) but it was still loading when I copied the output.
I closed the project, and this is from a clean R session (also only 17 base packages are loaded, the problem is still there though)

Loading required package: abind
Loading required package: sf
Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE
> methods(class = "stars")
 [1] [                 [[<-              [<-               %in%              $<-               adrop             aggregate         aperm            
 [9] as.data.frame     as.POSIXct        c                 coerce            contour           cut               dim               dimnames         
[17] dimnames<-        droplevels        expand_dimensions hist              image             initialize        is.na             Math             
[25] merge             Ops               plot              prcomp            predict           print             show              slotsFromS3      
[33] split             st_apply          st_area           st_as_sf          st_as_sfc         st_as_stars       st_bbox           st_coordinates   
[41] st_crop           st_crs            st_crs<-          st_dimensions     st_dimensions<-   st_downsample     st_extract        st_geometry      
[49] st_geotransform   st_geotransform<- st_interpolate_aw st_intersects     st_join           st_mosaic         st_normalize      st_redimension   
[57] st_rotate         st_sample         st_set_bbox       st_transform      st_write          time              write_stars      
see '?methods' for accessing help and source code
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

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               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] stars_0.6-8 sf_1.0-19   abind_1.4-8

loaded via a namespace (and not attached):
 [1] e1071_1.7-16       magrittr_2.0.3     KernSmooth_2.23-24 parallel_4.4.1     classInt_0.4-11    cli_3.6.3          grid_4.4.1        
 [8] DBI_1.2.3          proxy_0.4-27       class_7.3-22       compiler_4.4.1     rstudioapi_0.16.0  tools_4.4.1        Rcpp_1.0.14       
[15] rlang_1.1.5        units_0.8-5  ```

@edzer
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edzer commented Jan 22, 2025

the problem is still there though

it looks like it's gone.

@edzer
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edzer commented Jan 22, 2025

It was already gone in #731 (comment) - we forgot to scroll right.

@khalilT
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khalilT commented Jan 22, 2025

As I said, I see it when I call methods(class = "stars") and it is in the documentation, but I can't call it even with stars::aggregate().

@edzer
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edzer commented Jan 22, 2025

It's normal that you can't call stars::aggregate() because

> stars::aggregate
Error: 'aggregate' is not an exported object from 'namespace:stars'
  • it's an exported method, the generic is in stats.

@khalilT
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khalilT commented Jan 22, 2025

maybe I am missing something very obvious, but this function for example used to work 6 months ago or so, and it is based on the aggregate method for stars objects.

agg_by_refregion <- function(x,y,f) {
  #'@title agg_by_refregion
  #'
  #'@description applies a function f on a raster x cropped by a multi-polygon object y
  #'@description and returns the aggregated result for every subset x[y]
  #'
  #'@param x: multi-dim raster object of type stars
  #'@param y: multi-polygon vector object of type sf
  #'@param f: function to apply
  st_crs(x) <- st_crs(y)
  result_sf <- aggregate(x, y, f)
  result_df <- result_sf %>% as.data.frame()
  result_df_all <- left_join(result_df, y, by="geometry")
  names(result_df_all)[3] <- "fvalue"
  return(result_df_all)
}

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