Create-compatible-crown-delineation-file
Source:vignettes/Create-compatible-crown-delineation-file.Rmd
Create-compatible-crown-delineation-file.RmdRequirements
The extraction of crown images and crown indices requires a
compatible crown delineation file. The function check_crownFile()
tests each requirement of the file and return the necessary
modifications to do to make the file compatible.
To be compatible with the package functions the crown delineation
file must have :
- at least the variables ‘id’, ‘species’, ‘genus’ and ‘family’
- ‘species’, ‘genus’ and ‘family’ should not have NA. Replace them by
‘indet’
- ‘id’ should not have duplicated values.
Check the compatibility and adapt the file
The following example shows how to adjust the crown delineation file to make it compatible. It uses data from the
library(canObsR)
library(dplyr)
data(crownFile)
glimpse(crownFile)
#> Rows: 189
#> Columns: 5
#> $ id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1…
#> $ tx_sp_lvl <chr> "Piptadeniastrum africanum", "Musanga cecropioides", "Distem…
#> $ tax_gen <chr> "Piptadeniastrum", "Musanga", "Distemonanthus", "Celtis", "D…
#> $ tax_fam <chr> "Fabaceae", "Urticaceae", "Fabaceae", "Cannabaceae", "Fabace…
#> $ geom <POLYGON [m]> POLYGON ((257776.3 352837.7..., POLYGON ((257817.3 3…
plot(crownFile$geom, col = 'red')
Crown delineation file
Adjust the variable names
Check if the variables ‘id’, ‘species’, ‘genus’ and ‘family’ are in
the file. Change the variable names or create empty variables if you do
not have the information. id must be
check_crownFile(crownFile)
#> ########## VARIABLES CHECK ##########
#>
#> ✅ id
#> ❌ family variable missing or not well named
#> ❌ genus variable missing or not well named
#> ❌ species variable missing or not well named
#>
#> ########## NA VARIABLES CHECK ##########
#>
#> ✅ No NA for the variable id
#>
#>
#> ########## CRS ##########
#>
#> CRS : WGS 84 / UTM zone 33N
#>
#>
#> ########## DUPLICATED ID CHECK ##########
#>
#> ✅ There is no duplicated id
crownFile = crownFile %>%
rename(
family = tax_fam, # Rename the corresponding variable as 'family'
genus = tax_gen, # Rename the corresponding variable as 'genus'
species = tx_sp_lvl # Rename the corresponding variable as 'species'
)Replace NA by ‘indet’
Check if you have NA in ‘id’, ‘species’, ‘genus’ and ‘family’ variables. NA from ‘species’, ‘genus’ and ‘family’ must be replace by ‘indet’ and just NA from ‘id’.
check_crownFile(crownFile)
#> ########## VARIABLES CHECK ##########
#>
#> ✅ id
#> ✅ family
#> ✅ genus
#> ✅ species
#>
#> ########## NA VARIABLES CHECK ##########
#>
#> ✅ No NA for the variable id
#> ❌ Transform NA to 'indet' for the variable -> family
#> ❌ Transform NA to 'indet' for the variable -> genus
#> ❌ Transform NA to 'indet' for the variable -> species
#>
#>
#> ########## CRS ##########
#>
#> CRS : WGS 84 / UTM zone 33N
#>
#>
#> ########## DUPLICATED ID CHECK ##########
#>
#> ✅ There is no duplicated id
crownFile = crownFile %>% mutate(
# Rename NA to 'indet' in the family variable
family = case_when(is.na(family)~ 'indet', TRUE ~ family),
# Same for genus
genus = case_when(is.na(genus)~ 'indet', TRUE ~ genus),
# Same for species
species = case_when(is.na(species)~ paste(genus, 'indet'), TRUE ~ species)
) %>%
filter(!is.na(id))Last check
When the function does not indicate error, the file is compatible !
check_crownFile(crownFile)
#> ########## VARIABLES CHECK ##########
#>
#> ✅ id
#> ✅ family
#> ✅ genus
#> ✅ species
#>
#> ########## NA VARIABLES CHECK ##########
#>
#> ✅ No NA for the variable id
#> ✅ No NA for the variable family
#> ✅ No NA for the variable genus
#> ✅ No NA for the variable species
#>
#>
#> ########## CRS ##########
#>
#> CRS : WGS 84 / UTM zone 33N
#>
#>
#> ########## DUPLICATED ID CHECK ##########
#>
#> ✅ There is no duplicated id