Comments (4)
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 rowsCreated 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)
#> classInt 0.4-3 2020-04-07 [1] CRAN (R 4.0.3)
#> 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)
#> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
#> doParallel 1.0.16 2020-10-16 [1] CRAN (R 4.0.3)
#> dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.3)
#> e1071 1.7-4 2020-10-14 [1] CRAN (R 4.0.3)
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
#> fasterize 1.0.3 2020-07-27 [1] CRAN (R 4.0.3)
#> foreach 1.5.1 2020-10-15 [1] CRAN (R 4.0.3)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
#> generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3)
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.3)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.3)
#> iterators 1.0.13 2020-10-15 [1] CRAN (R 4.0.3)
#> KernSmooth 2.23-18 2020-10-29 [1] CRAN (R 4.0.3)
#> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.3)
#> lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.3)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.3)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.3)
#> 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)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.3)
#> 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)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.3)
#> ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
#> 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)
#> Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.3)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.3)
#> rgeos 0.5-5 2020-09-07 [1] CRAN (R 4.0.3)
#> rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.3)
#> rmarkdown 2.5 2020-10-21 [1] CRAN (R 4.0.3)
#> 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)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
#> sf 0.9-6 2020-09-13 [1] CRAN (R 4.0.3)
#> sp 1.4-4 2020-10-07 [1] CRAN (R 4.0.3)
#> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.3)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.3)
#> testthat 3.0.0 2020-10-31 [1] CRAN (R 4.0.3)
#> tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
#> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.3)
#> units 0.6-7 2020-06-13 [1] CRAN (R 4.0.3)
#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.3)
#> utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.3)
#> vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.3)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
#> xfun 0.19 2020-10-30 [1] CRAN (R 4.0.3)
#> 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/libraryThere 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?
from rbien.
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
from rbien.
OndrejMottl
commented on June 16, 2024
Is there any development with the Issue? I am still getting the same problem as @Rekyt.
from rbien.
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()
from rbien.
Related Issues (20)
- Bulk download speed-up
- Clarify "ID" field in BIEN_traits_traits output
- Consistency in species name
- Some species names are not capitalized HOT 4
- all "BIEN_taxonomy_*()" queries list class as "Equisetopsida" HOT 3
- vignette("BIEN") responds with vignette 'BIEN' not found HOT 1
- Feature Request: A trait table conversion between BIEN traits and TRY trait IDs HOT 5
- Error in an observation of whole plant vegetative phenology
- BIEN out of CRAN HOT 4
- How can we match all the traits for each species at each site? HOT 8
- BIEN_ranges_load_species fails with hardcoded proj4string
- Comparison BIEN4/GBIF
- Strange values for leaf dry mass
- One trait name is capitalized in database
- Species occurrence download from a list does not work HOT 3
- get the species list (spp) for a given genus
- Unable to complete queries HOT 4
- markdown formatting error in vignettes HOT 2
- There was a problem with the query... HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rbien.