ignobioR Vignette
my-vignette.Rmd
library(ignobioR)Prepare the data
data(floratus) # Upload the dataset with occurrence data
head(floratus)
#> Taxon Long Lat
#> 101049 Trigonella elegans (Salzm. ex Ser.) Coulot & Rabaute 11.17838 43.1584
#> 101050 Cephalanthera longifolia (L.) Fritsch 11.17838 43.1584
#> 101051 Chaenorhinum minus (L.) Lange subsp. minus 11.17838 43.1584
#> 101052 Chondrilla juncea L. 11.17838 43.1584
#> 101053 Mercurialis annua L. 11.17838 43.1584
#> 101054 Cirsium arvense (L.) Scop. 11.17838 43.1584
#> uncertainty year
#> 101049 1784.124 1985
#> 101050 1784.124 1985
#> 101051 1784.124 1985
#> 101052 1784.124 1985
#> 101053 1784.124 1985
#> 101054 1784.124 1985
data(park) # Upload the study area
data(unsuitablezone) # Unsuitable areas, i.e. zones where floristic records cannot occurDraft the virtual floristic list (VFL)
vfl <- virtual_list(data_flor=floratus, site=park, excl_areas=unsuitablezone, tau=20)
#>
#> ##############################################################################################
#> Please be patient. The process can be very slow, dependeing on the amount of records provided
#> ##############################################################################################
#>
#> Chosen Coordinate Reference System: +init=epsg:3035
#> Unsiuitable areas provided
#> Preparing spatial objects!
#> Drafting the Virtual Floristic List
#>
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#> Virtual floristic List drafting time:0.36862 minutes
#> Done! The files have been saved here: C:/Users/MARCO/Dropbox/Dottorato/Pubblicazioni mie/Paper 3 - Ignorance Map/SUBMISSION PACK_3/ignobioR/vignettes
head(vfl$VFL)
#> taxon
#> 49 Acer campestre L.
#> 155 Aeluropus littoralis (Gouan) Parl. subsp. littoralis
#> 21 Agrostis stolonifera L. subsp. stolonifera
#> 93 Ajuga chamaepitys (L.) Schreb. subsp. chamaepitys
#> 76 Ajuga reptans L.
#> 25 Alisma plantago-aquatica L.
#> Estimated_Spatiotemporal_probability Number_of_records Max_probability
#> 49 100.0 17 92.3
#> 155 100.0 6 84.2
#> 21 100.0 21 92.1
#> 93 13.6 1 13.6
#> 76 100.0 12 92.1
#> 25 85.4 1 85.4
#> Min_probability
#> 49 69.0
#> 155 66.5
#> 21 79.1
#> 93 13.6
#> 76 73.7
#> 25 85.4
vfl$statistics
#> NULLDraft the Map of Floristic Ignorance (MFI)
mfi <- ignorance_map(data_flor=floratus, site=park, excl_areas=unsuitablezone, tau=20, cellsize=2000)
#>
#> ##############################################################################################
#> Please be patient. The process can be very slow, depending on the amount of records provided
#> ##############################################################################################
#>
#> Chosen Coordinate Reference System: +init=epsg:3035
#> Chosen tau: 20
#> Unsuitable areas provided. Plotting
#> Creating spatial objects
#> Plotting
#> Filtering occurrence records having buffers intersecting the study area
#> Creating an empty raster
#> Calculating species richness per cell
#> Preparing preliminary data to draft the Map of Floristic Ignorance
#> Drafting the Map of Floristic Ignorance!
#>
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#> Almost done. Preparing outputs.......
#> Regions defined for each Polygons
#> Regions defined for each Polygons
#> Done! The files have been saved here: C:/Users/MARCO/Dropbox/Dottorato/Pubblicazioni mie/Paper 3 - Ignorance Map/SUBMISSION PACK_3/ignobioR/vignettes
#> Plot Map of Floristic Ignorance (MFI)
#> Plot Species richness Map
#> Plot frequency of occurrences spatial uncertainty
#> Plot frequency of occurrence date
#> Return statistics
