check tables from Fieldmap database for inconsistencies

This function retrieves the important fields of tables Trees, Shoots, Deadwood, Regeneration, Regspecies, Vegetation, Herblayer, Plots and Plotdetails (of all periods) from the given database and checks for missing data or wrong input.

check_data_fmdb(database, forest_reserve = "all")

Arguments

database

name of Fieldmap/Access database (with specific Fieldmap structure) including path

forest_reserve

name of forest reserve for which the records in the database should be checked (defaults to "all")

Value

Dataframe with inconsistent data with layer, ID's and additional columns aberrant_field (which column is wrong) and anomaly (what is wrong with the input)

Examples

library(forrescalc)
# (add path to your own fieldmap database here)
path_to_fieldmapdb <-
  system.file("example/database/mdb_bosres.sqlite", package = "forrescalc")
check_data_fmdb(path_to_fieldmapdb)
#> # A tibble: 96 × 14
#>    plot_id tree_measure_id period aberrant_field anomaly    aberrant_value layer
#>      <int> <chr>           <chr>  <chr>          <chr>      <chr>          <chr>
#>  1     204 1               1      iufro_hght     not in lo… 0              Trees
#>  2     204 1               1      iufro_vital    not in lo… 0              Trees
#>  3     204 1               1      iufro_socia    not in lo… 0              Trees
#>  4     204 1540            1      iufro_hght     not in lo… 0              Trees
#>  5     204 1540            1      iufro_vital    not in lo… 0              Trees
#>  6     204 1540            1      iufro_socia    not in lo… 0              Trees
#>  7     204 2               1      iufro_hght     not in lo… 0              Trees
#>  8     204 2               1      iufro_vital    not in lo… 0              Trees
#>  9     204 2               1      iufro_socia    not in lo… 0              Trees
#> 10    1005 23              1      iufro_hght     not in lo… 0              Trees
#> # ℹ 86 more rows
#> # ℹ 7 more variables: shoot_id <int>, lying_deadw_id <int>, subplot_id <int>,
#> #   heightclass_id <int>, regspecies_id <int>, herblayer_id <int>,
#> #   tree_id <chr>
check_data_fmdb(path_to_fieldmapdb, forest_reserve = "Everzwijnbad")
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `min_period = min(.data$period)`.
#> Caused by warning in `min()`:
#> ! no non-missing arguments to min; returning Inf
#> # A tibble: 2 × 14
#>   plot_id tree_measure_id period aberrant_field  anomaly    aberrant_value layer
#>     <int> <chr>           <chr>  <chr>           <chr>      <chr>          <chr>
#> 1     101 NA              1      max_diameter_mm too low    10             Dead…
#> 2     101 NA              1      alive_dead      tree alive 11             Dead…
#> # ℹ 7 more variables: shoot_id <int>, lying_deadw_id <int>, subplot_id <int>,
#> #   heightclass_id <int>, regspecies_id <int>, herblayer_id <int>, old_id <chr>