SoilProfileCollection into a list based on types of horizon logic errorsR/splitLogicErrors.R
splitLogicErrors.RdUses checkHzDepthLogic() to identify presence of depth logic errors, same depths, missing depths, and overlaps/gaps between the horizons of each profile in a SoilProfileCollection.
splitLogicErrors(object, interact = FALSE, ...)A named list of SoilProfileCollections (or NULL), with names: "depthLogic", "sameDepth", "missingDepth", "overlapOrGap". If interact = TRUE then the list elements groups determined by interaction() of the error types.
data(sp4)
depths(sp4) <- id ~ top + bottom
# no errors (all four list elements return NULL)
splitLogicErrors(sp4)
#> $depthLogic
#> NULL
#>
#> $sameDepth
#> NULL
#>
#> $missingDepth
#> NULL
#>
#> $overlapOrGap
#> NULL
#>
# NA in top depth triggers depth logic and missing depth errors
data(sp4)
sp4$top[1] <- NA
depths(sp4) <- id ~ top + bottom
#> This is already a SoilProfileCollection-class object, doing nothing.
splitLogicErrors(sp4)
#> $depthLogic
#> SoilProfileCollection with 1 profiles and 4 horizons
#> profile ID: id | horizon ID: hzID
#> Depth range: 42 - 42 cm
#>
#> ----- Horizons (4 / 4 rows | 10 / 14 columns) -----
#> id hzID top bottom name K Mg Ca CEC_7 ex_Ca_to_Mg
#> colusa 1 NA 3 A 0.3 25.7 9.0 23.0 0.35
#> colusa 2 3 8 ABt 0.2 23.7 5.6 21.4 0.23
#> colusa 3 8 30 Bt1 0.1 23.2 1.9 23.7 0.08
#> colusa 4 30 42 Bt2 0.1 44.3 0.3 43.0 0.01
#>
#> ----- Sites (1 / 1 rows | 1 / 1 columns) -----
#> id
#> colusa
#>
#> Spatial Data:
#> [EMPTY]
#>
#> $sameDepth
#> NULL
#>
#> $missingDepth
#> SoilProfileCollection with 1 profiles and 4 horizons
#> profile ID: id | horizon ID: hzID
#> Depth range: 42 - 42 cm
#>
#> ----- Horizons (4 / 4 rows | 10 / 14 columns) -----
#> id hzID top bottom name K Mg Ca CEC_7 ex_Ca_to_Mg
#> colusa 1 NA 3 A 0.3 25.7 9.0 23.0 0.35
#> colusa 2 3 8 ABt 0.2 23.7 5.6 21.4 0.23
#> colusa 3 8 30 Bt1 0.1 23.2 1.9 23.7 0.08
#> colusa 4 30 42 Bt2 0.1 44.3 0.3 43.0 0.01
#>
#> ----- Sites (1 / 1 rows | 1 / 1 columns) -----
#> id
#> colusa
#>
#> Spatial Data:
#> [EMPTY]
#>
#> $overlapOrGap
#> NULL
#>
# interact = TRUE gets errors for profile 1 in same group
# and allows you to pass extra arguments to split.default()
splitLogicErrors(sp4, interact = TRUE, sep = "_", drop = TRUE)
#> $`___`
#> SoilProfileCollection with 9 profiles and 26 horizons
#> profile ID: id | horizon ID: hzID
#> Depth range: 16 - 49 cm
#>
#> ----- Horizons (6 / 26 rows | 10 / 14 columns) -----
#> id hzID top bottom name K Mg Ca CEC_7 ex_Ca_to_Mg
#> glenn 5 0 9 A 0.2 21.9 4.4 18.8 0.20
#> glenn 6 9 34 Bt 0.3 18.9 4.5 27.5 0.20
#> kings 7 0 4 A 0.2 12.1 1.4 23.7 0.58
#> kings 8 4 13 Bt1 0.6 12.1 7.0 18.0 0.51
#> kings 9 13 40 Bt2 0.8 17.7 4.4 20.0 0.25
#> mariposa 10 0 3 A 0.6 28.3 5.8 29.3 0.20
#> [... more horizons ...]
#>
#> ----- Sites (6 / 9 rows | 1 / 1 columns) -----
#> id
#> glenn
#> kings
#> mariposa
#> mendocino
#> napa
#> san benito
#> [... more sites ...]
#>
#> Spatial Data:
#> [EMPTY]
#>
#> $depthLogic__missingDepth_
#> SoilProfileCollection with 1 profiles and 4 horizons
#> profile ID: id | horizon ID: hzID
#> Depth range: 42 - 42 cm
#>
#> ----- Horizons (4 / 4 rows | 10 / 14 columns) -----
#> id hzID top bottom name K Mg Ca CEC_7 ex_Ca_to_Mg
#> colusa 1 NA 3 A 0.3 25.7 9.0 23.0 0.35
#> colusa 2 3 8 ABt 0.2 23.7 5.6 21.4 0.23
#> colusa 3 8 30 Bt1 0.1 23.2 1.9 23.7 0.08
#> colusa 4 30 42 Bt2 0.1 44.3 0.3 43.0 0.01
#>
#> ----- Sites (1 / 1 rows | 1 / 1 columns) -----
#> id
#> colusa
#>
#> Spatial Data:
#> [EMPTY]
#>