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Rekyt avatar Rekyt commented on June 16, 2024 1

Looking into more details it seems that most sampling protocols don't match with what is reported in the view_full_occurrence_individual, these are the protocols I get from the sampling_protocol column in the view:

tibble::as_tibble(BIEN:::.BIEN_sql("SELECT DISTINCT sampling_protocol  FROM view_full_occurrence_individual"))
#> # A tibble: 24 x 1
#>    sampling_protocol                                                            
#>    <chr>                                                                        
#>  1 0.01 ha, stems >= 10 cm dbh; 16 subplots of 10 x 10 m per plot, 4 rows (UU, ~
#>  2 0.1 ha  transect, stems >= 2.5 cm dbh                                        
#>  3 1 ha, stems >= 10 cm dbh                                                     
#>  4 All species recorded in a circle of 5 km radius, centered on the geocoordina~
#>  5 Area of each plot was estimated, not based on actual measurements.           
#>  6 Carolina Vegetation Survey Standard Sampling Method.  See http://www.bio.unc~
#>  7 Cover only                                                                   
#>  8 Cover values are derived from cover below 1m observed in 25 1m^2 plots suppl~
#>  9 CVS protocol.  2 module plot with 150% supersample for trees >=10cm in DBH. ~
#> 10 CVS Protocol.  Pines >=2.5 cm DBH supersampled at 125%                       
#> # ... with 14 more rows

Created on 2020-11-10 by the reprex package (v0.3.0)

Session info
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  French_France.1252          
#>  ctype    French_France.1252          
#>  tz       Europe/Berlin               
#>  date     2020-11-10                  
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version date       lib source        
#>  ape           5.4-1   2020-08-13 [1] CRAN (R 4.0.3)
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.3)
#>  backports     1.2.0   2020-11-02 [1] CRAN (R 4.0.2)
#>  BIEN          1.2.4   2020-02-27 [1] CRAN (R 4.0.3)
#>  callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.3)
#>  class         7.3-17  2020-04-26 [2] CRAN (R 4.0.2)
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#>  cli           2.1.0   2020-10-12 [1] CRAN (R 4.0.3)
#>  codetools     0.2-18  2020-11-04 [1] CRAN (R 4.0.2)
#>  crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.3)
#>  DBI           1.1.0   2019-12-15 [1] CRAN (R 4.0.3)
#>  desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.3)
#>  devtools      2.3.2   2020-09-18 [1] CRAN (R 4.0.3)
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#>  doParallel    1.0.16  2020-10-16 [1] CRAN (R 4.0.3)
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#>  e1071         1.7-4   2020-10-14 [1] CRAN (R 4.0.3)
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#>  nlme          3.1-150 2020-10-24 [1] CRAN (R 4.0.3)
#>  pillar        1.4.6   2020-07-10 [1] CRAN (R 4.0.3)
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#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.3)
#>  pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.3)
#>  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.3)
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#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.3)
#>  R6            2.5.0   2020-10-28 [1] CRAN (R 4.0.3)
#>  raster        3.3-13  2020-07-17 [1] CRAN (R 4.0.3)
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#>  RPostgreSQL   0.6-2   2017-06-24 [1] CRAN (R 4.0.3)
#>  rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.3)
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#>  utf8          1.1.4   2018-05-24 [1] CRAN (R 4.0.3)
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#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.3)
#> 
#> [1] C:/Users/ke76dimu/Documents/R/win-library/4.0
#> [2] C:/Program Files/R/R-4.0.2/library

There is a discrepancy between the sampling_protocol column provided by BIEN::BIEN_plot_list_sampling_protocols() and the sampling_protocol column in view_full_occurrence_individual. Looking at the code of BIEN_plot_list_sampling_protocols() this means there is a discrepancy between the sampling_protocol column in plot_metadata table and view_full_occurrence_individual. So which one should be the good one?

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bmaitner avatar bmaitner commented on June 16, 2024 1

Thanks for letting me know about this @Rekyt . This discrepancy must have crept in during one of the database updates. I'll dig into this and get back to you shortly

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OndrejMottl avatar OndrejMottl commented on June 16, 2024

Is there any development with the Issue? I am still getting the same problem as @Rekyt.

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OndrejMottl avatar OndrejMottl commented on June 16, 2024

The solution presented by @Rekyt does not solve the situation as the sampling_protocol from view_full_occurrence_individual also does not return anything from BIEN::BIEN_plot_sampling_protocol()

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