README.md

NINA package

The goal of NINA is the the analysis and implementation of biotic interactions into environmental niche models using kernel density estimations.

Installation

You can install NINA from github repository with:

devtools::install_github("agarciaEE/NINA")

Example

This is a basic example which shows you how to use NINA’s functions:

library(NINA)
#> Registered S3 methods overwritten by 'adehabitatMA':
#>   method                       from
#>   print.SpatialPixelsDataFrame sp  
#>   print.SpatialPixels          sp

Estimate Environmental Niche Models:

First group of species

g1_EN = EN_model(env_data, occ_data1, cluster = "env", n.clus = 5)
#> Carrying out unique EN model...
#> Occurrence dataset ... OK
#> Environmental dataset ... OK
#>  - Conforming environmental space...
#>  - Clustering environmental variables...
#>  - Regions:
#> [1] "A" "B" "C" "D" "E"
#>  - Carrying out species EN models in region A...
#>      - Modelling spA Environmental Niche...
#>      - Estimating spA niche response in region A...
#>      - Modelling spB Environmental Niche...
#>      - Estimating spB niche response in region A...
#>      - Modelling spC Environmental Niche...
#>      - Estimating spC niche response in region A...
#>      - Modelling spD Environmental Niche...
#>      - Estimating spD niche response in region A...
#>      - Modelling spE Environmental Niche...
#>      - Estimating spE niche response in region A...
#>  - Carrying out species EN models in region B...
#>      - Modelling spA Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of spA in region B.
#>      - Modelling spB Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of spB in region B.
#>      - Modelling spC Environmental Niche...
#>      - Estimating spC niche response in region B...
#>      - Modelling spD Environmental Niche...
#>      - Estimating spD niche response in region B...
#>  - Carrying out species EN models in region C...
#>      - Modelling spA Environmental Niche...
#>      - Estimating spA niche response in region C...
#>      - Modelling spB Environmental Niche...
#>      - Estimating spB niche response in region C...
#>      - Modelling spC Environmental Niche...
#>      - Estimating spC niche response in region C...
#>      - Modelling spD Environmental Niche...
#>      - Estimating spD niche response in region C...
#>      - Modelling spE Environmental Niche...
#>      - Estimating spE niche response in region C...
#>  - Carrying out species EN models in region D...
#>      - Modelling spA Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of spA in region D.
#>      - Modelling spB Environmental Niche...
#>      - Estimating spB niche response in region D...
#>      - Modelling spC Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of spC in region D.
#>      - Modelling spD Environmental Niche...
#>      - Estimating spD niche response in region D...
#>      - Modelling spE Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of spE in region D.
#>  - Carrying out species EN models in region E...
#>      - Modelling spA Environmental Niche...
#>      - Estimating spA niche response in region E...
#>      - Modelling spB Environmental Niche...
#>      - Estimating spB niche response in region E...
#>      - Modelling spC Environmental Niche...
#>      - Estimating spC niche response in region E...
#>      - Modelling spD Environmental Niche...
#>      - Estimating spD niche response in region E...
#>      - Modelling spE Environmental Niche...
#>      - Estimating spE niche response in region E...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, :
#> Model failed to predict the following species due to lack of observations
#>   region species
#> 1      B     spA
#> 2      B     spB
#> 3      D     spA
...
#> Species EN models succesfully completed!

2nd group of species

g2_EN = EN_model(env_data, occ_data2, cluster = g1_EN$clus)
#> Carrying out unique EN model...
#> Occurrence dataset ... OK
#> Environmental dataset ... OK
#>  - Conforming environmental space...
#>  - Clustering based on provided regions...
#>  - Regions:
#> [1] "A" "B" "C" "D" "E"
#>  - Carrying out species EN models in region A...
#>      - Modelling sp1 Environmental Niche...
#>      - Estimating sp1 niche response in region A...
#>      - Modelling sp2 Environmental Niche...
#>      - Estimating sp2 niche response in region A...
#>      - Modelling sp3 Environmental Niche...
#>      - Estimating sp3 niche response in region A...
#>      - Modelling sp4 Environmental Niche...
#>      - Estimating sp4 niche response in region A...
#>      - Modelling sp5 Environmental Niche...
#>      - Estimating sp5 niche response in region A...
#>  - Carrying out species EN models in region B...
#>      - Modelling sp1 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp1 in region B.
#>      - Modelling sp3 Environmental Niche...
#>      - Estimating sp3 niche response in region B...
#>      - Modelling sp4 Environmental Niche...
#>      - Estimating sp4 niche response in region B...
#>      - Modelling sp5 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp5 in region B.
#>  - Carrying out species EN models in region C...
#>      - Modelling sp1 Environmental Niche...
#>      - Estimating sp1 niche response in region C...
#>      - Modelling sp2 Environmental Niche...
#>      - Estimating sp2 niche response in region C...
#>      - Modelling sp3 Environmental Niche...
#>      - Estimating sp3 niche response in region C...
#>      - Modelling sp4 Environmental Niche...
#>      - Estimating sp4 niche response in region C...
#>      - Modelling sp5 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp5 in region C.
#>  - Carrying out species EN models in region D...
#>      - Modelling sp1 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp1 in region D.
#>      - Modelling sp3 Environmental Niche...
#>      - Estimating sp3 niche response in region D...
#>      - Modelling sp4 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp4 in region D.
#>  - Carrying out species EN models in region E...
#>      - Modelling sp1 Environmental Niche...
#>      - Estimating sp1 niche response in region E...
#>      - Modelling sp2 Environmental Niche...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, : Not
#> enough observations of sp2 in region E.
#>      - Modelling sp3 Environmental Niche...
#>      - Estimating sp3 niche response in region E...
#>      - Modelling sp4 Environmental Niche...
#>      - Estimating sp4 niche response in region E...
#>      - Modelling sp5 Environmental Niche...
#>      - Estimating sp5 niche response in region E...
#> Warning in EN_model_(env, occ, res = res, nstart = nstart, k.max = k.max, :
#> Model failed to predict the following species due to lack of observations
#>   region species
#> 1      B     sp1
#> 2      B     sp5
#> 3      C     sp5
...
#> Species EN models succesfully completed!

Correct EN models by biotic interactions:

g2_BC <- BC_model(g2_EN, g1_EN, A.matrix = int_matrix, type = "region")
#> Estimating biotic constrains of species in region A...
#>  Adding biotic constrains to sp1...  ...Success!
#>  Adding biotic constrains to sp2...  ...Success!
#>  Adding biotic constrains to sp3...  ...Success!
#>  Adding biotic constrains to sp4...  ...Success!
#>  Adding biotic constrains to sp5...  ...Success!
#> Estimating biotic constrains of species in region C...
#>  Adding biotic constrains to sp1...  ...Success!
#>  Adding biotic constrains to sp2...  ...Success!
#>  Adding biotic constrains to sp3...  ...Success!
#>  Adding biotic constrains to sp4...  ...Success!
#> Estimating biotic constrains of species in region E...
#>  Adding biotic constrains to sp1...  ...Success!
#>  Adding biotic constrains to sp3...  ...Success!
#>  Adding biotic constrains to sp4...  ...Success!
#>  Adding biotic constrains to sp5...  ...Success!
#> Estimating biotic constrains of species in region B...
#>  Adding biotic constrains to sp3...  ...Success!
#>  Adding biotic constrains to sp4...  ...Success!
#> Estimating biotic constrains of species in region D...
#>  Adding biotic constrains to sp3...  ...Success!
#>  - Carrying out models evaluations...
#> Observations ... OK
#> Environmental predictors ... OK
#> Model predictions ... OK
#> Sampling pseudo_absences... 
#> Performing models evaluation...
#>  ...Evaluating sp1 niche model...
#>  ...Evaluating sp2 niche model...
#>  ...Evaluating sp3 niche model...
#>  ...Evaluating sp4 niche model...
#>  ...Evaluating sp5 niche model...
#> Models evaluation performed.
#> Models successfully corrected!

Transform environmental niche space into ecological niche space (prioritizing the effect of biotic interactions).

g2_EC <- EC_model(g2_BC, type = "region")
#> Transforming niche space of species in region A...
#>  Estimating ecological niche of sp1...   ...Success!
#>  Estimating ecological niche of sp2...   ...Success!
#>  Estimating ecological niche of sp3...   ...Success!
#>  Estimating ecological niche of sp4...   ...Success!
#>  Estimating ecological niche of sp5...   ...Success!
#> Transforming niche space of species in region C...
#>  Estimating ecological niche of sp1...   ...Success!
#>  Estimating ecological niche of sp2...   ...Success!
#>  Estimating ecological niche of sp3...   ...Success!
#>  Estimating ecological niche of sp4...   ...Success!
#> Transforming niche space of species in region E...
#>  Estimating ecological niche of sp1...   ...Success!
#>  Estimating ecological niche of sp3...   ...Success!
#>  Estimating ecological niche of sp4...   ...Success!
#>  Estimating ecological niche of sp5...   ...Success!
#> Transforming niche space of species in region B...
#>  Estimating ecological niche of sp3...   ...Success!
#>  Estimating ecological niche of sp4...   ...Success!
#> Transforming niche space of species in region D...
#>  Estimating ecological niche of sp3...   ...Success!
#> Models successfully transformed!

You can summarize the output by using summary function or print:

summary(g1_EN)
#> Niche model type:
#> Environmental-only
#> Predictors:
#> bio1 bio2 bio3 bio4 bio5 bio6
#> 2 axis-components used
#> Class: pca dudi
#> Call: dudi.pca(df = stats::na.exclude(env[, env.var]), center = T, 
#>     scale = T, scannf = F, nf = 2)
...
#> TRUE
#> Geographical extents:
#> 5
#>   spA spB spC spD spE
#> A   1   1   1   1   1
#> C   1   1   1   1   1
#> E   1   1   1   1   1
...
#> FALSE
#> Failures or warnings:
#> TRUE
#>   region species
#> 1      B     spA
#> 2      B     spB
#> 3      D     spA
...
#> FALSE
print(g2_BC)
#> Object class: NINA
#> 
#> Niche model type:
#> Environmental-constrained
#> Predictors:
#> bio1 bio2 bio3 bio4 bio5 bio6
#> Spatially constrained:
#> TRUE
#> Geographical extents:
#> 5
#> Ensemble of regional models:
#> FALSE
#> Number of species:
#> 5
#> Failures or warnings:
#> TRUE
#> Models evaluation:
#> TRUE

You can also plot a summary of the output model using plot function:

plot(g2_BC)
#> Ploting only the first four species maps of a total of 5

Models can be evaluated using models_evaluation function and visualize it by plotting the output.

eval <- models_evaluation(g2_BC)
#> Observations ... OK
#> Environmental predictors ... OK
#> Model predictions ... OK
#> Sampling pseudo_absences...
#> Performing models evaluation...
#>  ...Evaluating sp1 niche model...
#>  ...Evaluating sp2 niche model...
#>  ...Evaluating sp3 niche model...
#>  ...Evaluating sp4 niche model...
#>  ...Evaluating sp5 niche model...
#> Models evaluation performed.
plot(eval)