The function allows to compute the Suitability Index (SI) and Reliability Index (RI) for a seed mixture or
donor grassland composition to be used in a restoration site based on topographic features: elevation, slope and aspect.
see vignettes for additional details and examples
Arguments
- trainingDB
dataframe with the species eligible for the statistical modelling, selected on the basis of their frequency and abundance in the vegetation and topographical variables database. Each species is associated with the values of topographic variables (elevation, slope and aspect) and its abundance. Default is NULL. When NULL, the training database is derived from 4081 vegetation surveys carried out in Piedmont Region, (North-Western Italy), which it includes 248 plant species eligible for modeling. A customized training database can be generated with
trainingDB.- composition
dataframe with the seed mixture or donor grassland composition. It consists of two columns: 1) species code abbreviated in CEP names format and 2) abundance of the species. When "trainingDB" is NULL, the species CEP names are retrievable from
cep.piemdata. When "trainingDB" is not NULL, i.e. the user does not use default settings, species CEP names are retrievable fromtrainingDB, which generates CEP names of species suitable for modeling from a customized training database.- elevation
Elevation of restoration site, expressed in meters above sea level (m a.s.l.)
- slope
Slope of restoration site, expressed in degrees (°)
- aspect
Aspect of restoration site, expressed in degrees from North (°N)
Value
A list with three outputs:
DESCRIPTIVES: dataframe with the descriptive information related to modeled plant species:
- cep.names
Species name in CEP format
- species
Full species name
- n.obs
Number of observations of each species selected for modeling
- min.ele
Minimum elevation at which a species occurred
- max.ele
Maximum elevation at which a species occurred
- min.slope
Minimum slope at which a species occurred
- max.slope
Maximum slope at which a species occurred
- min.south
Minimum southness value at which a species occurred
- max.south
Maximum southness value at which a species occurred
SPECIES ABUNDANCES: dataframe with the following information:
- cep.names
Species name in CEP format
- species
Full species name
- PMA
Predicted Maximum Abundance. It is the maximum achievable abundance of a species in the restoration site, as predicted by the best model
- POA
Predicted Optimal Abundance. It is the maximum achievable abundance of a species in its optimal ecological condition, based on all possible combinations of elevation, slope and southness.
- ratio
Ratio between the PMA and POA. This ratio indicates how far (ratio = 0) or close (ratio = 1) a species is from its ecological optimum.
- R2.adj
R square adjusted of the best Generalized Additive Model
- RMSE
Root Mean Squared Error of the best Generalized Additive Model
- SmDgA
Seed mixture or Donor grassland Abundance. Abundance of a species listed in the seed mixture or donor grassland composition imported by the user and eligible for modeling
- EA
Expected Abundance. The highest achievable abundance of a species in a restoration site, based on how far the species is from the ecological optimum (i.e. computed from the multiplication of SmDgA by the ratio)
INDEXES:
- SI
Suitability Index (SI). Suitability of a seed mixture or donor grassland to restore a site with specific topographic characteristics. It ranges between 0 and 1. When SI=0 the restoration site is totally beyond the optimal ecological ranges of all species of the seed mixture or donor grassland, which is therefore not appropriate for the site restoration. Conversely, when SI=1 the restoration site has the optimal ecological conditions for all species of the seed mixture or donor grassland, which is therefore perfectly appropriate for the site restoration.
- RI
Reliability Index (RI). Index of the reliability of the Suitability Index (SI). The RI ranges between 0 and 1. When RI is close to 0 it means that few to none species contribute to the computation of the SI, whereas when RI is close to 1 the SI is computed with most to all species. Therefore, the higher is the RI, the most reliable is the SI. Not all the species of the seed mixture and donor grassland composition may modeled as i) they can be missing from the training database or ii) the values of the topographic factors of the restoration site are beyond their ecological ranges (e.g. if the elevation of the restoration site is 250 m and a species as an elevation range bounded between 1000 and 3000 m, such a species cannot be modeled).
Examples
#creation of seed mixture dataframe by retrieving species CEP names from ResNatSeed::cep.piem
mixture_composition<-data.frame(species=c("Festrubr","Chaehirs","Phleprat","Onobmont"),
sc=c(5,40,20,20))
#run function
ResNatSeed::RestInd(trainingDB = NULL,
composition = mixture_composition,
elevation = 1500,
aspect = 30,
slope = 5)
#> $DESCRIPTIVES
#> cep.names species n.obs min.ele max.ele min.slope
#> Chaehirs Chaehirs Chaerophyllum hirsutum 43 623 2248 2
#> Festrubr Festrubr Festuca rubra 60 494 2743 2
#> Onobmont Onobmont Onobrychis montana 40 1395 2501 0.97
#> Phleprat Phleprat Phleum pratense 51 848 2439 2.6
#> max.slope min.south max.south
#> Chaehirs 49 4.2 178
#> Festrubr 51 0.33 180
#> Onobmont 45 2.5 177
#> Phleprat 43 9 179
#>
#> $SPECIES_ABUNDANCES
#> cep.names species PMA POA ratio R2.adj RMSE SmDgA EA
#> 1 Chaehirs Chaerophyllum hirsutum 50.0 57.7 0.87 0.27 14.7 40 34.8
#> 2 Festrubr Festuca rubra 90.4 96.4 0.94 0.89 8.5 5 4.7
#> 3 Onobmont Onobrychis montana 20.2 85.6 0.24 0.57 15.3 20 4.8
#> 4 Phleprat Phleum pratense 9.2 34.2 0.27 0.47 8.8 20 5.4
#>
#> $INDEXES
#> SI RI
#> 1 0.58 1
#>