Making custom areacell, outdated vignette and division not showing in the database

[MikkoVihtakari]

I noticed that the Vignette regarding areacell definition is outdated and does not work. The area column in the dataframe should be called name. I am using the GitHub version (6.2.99).

Also the division does not seem to be stored in the schema (tbl(mdb$db,"areacell"))

library(mfdb)
library(tidyverse)

mfdb("test", destroy_schema = TRUE) # Delete 'test' in database for a fresh start
#> 2021-03-15 14:28:19 INFO:mfdb:Schema test removed, connect again to repopulate DB.

mdb <- mfdb("test")
#> 2021-03-15 14:28:20 INFO:mfdb:No schema, creating test
#> 2021-03-15 14:28:20 INFO:mfdb:Creating schema from scratch
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy case_study needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy institute needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy gear needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy vessel_type needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy market_category no updates to make
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy sex needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy maturity_stage needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy species needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy stomach_state needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy digestion_stage needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy index_type needs updating
#> 2021-03-15 14:28:20 INFO:mfdb:Creating indexes

# Out-of-date example:
mfdb_import_area(mdb, 
                 data.frame(area = c('101', '102', '103', '401','402', '403'), 
                            division = c('1', '1', '1', '4', '4', '4')))
#> Error in sanitise_col(mdb, data_in, "name"): Input data is missing 'name'. Columns available: area,division

dt <- data.frame(name = c('101', '102', '103', '401','402', '403')
                 division = c('1', '1', '1', '4', '4', '4'))

mfdb_import_area(mdb, dt)
#> 2021-03-15 14:28:20 INFO:mfdb:Taxonomy areacell needs updating

tbl(mdb$db,"areacell") %>% collect() # No division
#> # A tibble: 6 x 4
#>   areacell_id name  t_group  size
#>         <int> <chr> <chr>   <dbl>
#> 1           1 101   <NA>       NA
#> 2           2 102   <NA>       NA
#> 3           3 103   <NA>       NA
#> 4           4 401   <NA>       NA
#> 5           5 402   <NA>       NA
#> 6           6 403   <NA>       NA


mfdb_import_division(mdb, dt %>% split(.$division) %>% map('name'))

tbl(mdb$db,"areacell") %>% collect() # Stil nothing
#> # A tibble: 6 x 4
#>   areacell_id name  t_group  size
#>         <int> <chr> <chr>   <dbl>
#> 1           1 101   <NA>       NA
#> 2           2 102   <NA>       NA
#> 3           3 103   <NA>       NA
#> 4           4 401   <NA>       NA
#> 5           5 402   <NA>       NA
#> 6           6 403   <NA>       NA

^{Created on 2021-03-15 by the reprex package (v1.0.0)}

[bthe]

Yes, sorry about that. I've edited the gadget-course notes so hopefully they are correct now. I haven't yet included an actual mfdb db when building the course which would have made spotting errors like this a lot easier.