TUTORIAL 1 - Default training database • ResNatSeed

library(ResNatSeed)

When the user uses default settings, the training database refers to the vegetation surveys from the Piedmont Region - North-Western Italy, which includes 248 plant species eligible to modeling. Such a list can be extracted through the command data("cep.piem"). Species names follow the Flora Alpina nomenclature (Aeschimann et al. 2004) and they are associated with the ‘cep.names’ code, an eight-letter abbreviation of species names according to the Cornell Ecology Programs (CEP).

data("cep.piem")

head(cep.piem)
#>                      species cep.names
#> 1 Achillea millefolium aggr.  Achiaggr
#> 2             Acinos alpinus  Acinalpi
#> 3            Agrostis alpina  Agroalpi
#> 4        Agrostis capillaris  Agrocapi
#> 5         Agrostis rupestris  Agrorupe
#> 6      Agrostis schraderiana  Agroschr

From this list is possible to create the mixture or donor grassland composition database, which is characterized by two columns:

First column: species code abbreviated in CEP names format
Second column: abundance of each species. Abundance must be a number bounded between 0 and 100, which can be either a species relative abundance or a species cover (sensu (Pittarello et al. 2016); (Verdinelli et al. 2022)).

In this example, the donor grassland composition is characterized by five species:

Bromus erectus (CEP name: Bromere), relative abundance: 25%
Brachypodium rupestre (CEP name: Bracrupe), relative abundance: 18%
Festuca ovina aggr. (CEP name: Festaggr), relative abundance: 22%
Knautia arvensis (CEP name: Knauarve), relative abundance: 8%
Silene vulgaris (CEP name: Silevulg), relative abundance: 5%

Total abundances amount to 78%. The total abundance of the seed mixture or donor grassland composition should not necessarily amount 100%.

We can generate the dataframe of the donor grassland composition:

donor.composition<-data.frame(
  species=c("Bromere","Bracrupe","Festaggr","Knauarve","Silevulg"),
  abundance=c(25,18,22,8,5)
)

donor.composition
#>    species abundance
#> 1  Bromere        25
#> 2 Bracrupe        18
#> 3 Festaggr        22
#> 4 Knauarve         8
#> 5 Silevulg         5

It is now possible to use the RestInd function to calculate the Suitability Index (SI) and Reliability Index (RI) by means of the donor grassland composition (dataframe ‘donor.composition’) and of the elevation, slope, and aspect of restoration site:

elevation: 2300 m a.s.l
slope: 15°
aspect: 135° N

RestInd(trainingDB = NULL, 
        composition=donor.composition,  
        elevation=2300, 
        slope=15, 
        aspect=135
        )
#> $DESCRIPTIVES
#>          cep.names               species n.obs min.ele max.ele min.slope
#> Bracrupe  Bracrupe Brachypodium rupestre    50     494    2367       3.5
#> Festaggr  Festaggr   Festuca ovina aggr.    67     489    2756       1.7
#> Knauarve  Knauarve      Knautia arvensis    49     494    2368      0.86
#> Silevulg  Silevulg       Silene vulgaris    62     204    2436      0.18
#>          max.slope min.south max.south
#> Bracrupe        42       7.1       179
#> Festaggr        56       2.1       177
#> Knauarve        45       9.4       177
#> Silevulg        51       5.1       173
#> 
#> $SPECIES_ABUNDANCES
#>   cep.names               species  PMA  POA ratio R2.adj RMSE SmDgA    EA
#> 1  Bracrupe Brachypodium rupestre 40.9 90.5  0.45   0.52 19.6    18  8.10
#> 2  Festaggr   Festuca ovina aggr. 80.7 92.2  0.88   0.77 12.2    22 19.36
#> 3  Knauarve      Knautia arvensis  8.6 36.7  0.23   0.30  6.2     8  1.84
#> 4  Silevulg       Silene vulgaris  6.7 15.6  0.43   0.10  7.5     5  2.15
#> 
#> $INDEXES
#>     SI   RI
#> 1 0.59 0.68

References

Aeschimann, D, K Lauber, D Martin Moser, and J D Theurillat. 2004. Flora Alpina. Bologna: Zanichelli.

Pittarello, Marco, Massimiliano Probo, Michele Lonati, and Giampiero Lombardi. 2016. “Restoration of Sub-Alpine Shrub-Encroached Grasslands Through Pastoral Practices: Effects on Vegetation Structure and Botanical Composition.” Edited by Vigdis Vandvik. Applied Vegetation Science 19 (3): 381–90. https://doi.org/10.1111/avsc.12222.

Verdinelli, Marcello, Marco Pittarello, Maria Carmela Caria, Giovanna Piga, Pier Paolo Roggero, Gian Marco Marrosu, Stefano Arrizza, et al. 2022. “Congruent Responses of Vascular Plant and Ant Communities to Pastoral Land-Use Abandonment in Mountain Areas Throughout Different Biogeographic Regions.” Ecological Processes 11 (1): 35. https://doi.org/10.1186/s13717-022-00379-9.

TUTORIAL 1 - Default training database

Marco Pittarello and Davide Barberis

References