General Information

This data_availability directory contains all of the scripts and results necessary to recreate the analyses and plots used in the paper "Reatini et. al. 2026. Local exclusion and regional decline of an endemic Galápagos tree species (Psidium galapageium) by an invasive relative (P. guajava)."

Below is a description of the results files, the meaning of the column names within those files, and the corresponding analyses and plots for which they were used. A description of the scripts used to carry out the analyses follows.

Results Files

Below is a brief description of each of the results files and the figures they were used to produce:

The SDM subdirectory (SDMs.zip) contains the output of the final ensemble models for both species, including the species distribution models named gal_ensemble_cont.tif (continuous), gal_ensemble_bin.tif (binary), gua_ensemble_cont.tif (continuous),
gua_ensemble_bin.tif (binary). Presence data used to generate the SDMs can be found in galapageium.csv and guayava.csv; hyperparameters used to generate the models can be found in all_hyperparameters.xlsx, and model performance results files for both species can be found in gal_all_models_performance.csv and gua_all_models_performance.csv. All SDMs and associated results were generated via R_analyses.R

The niche_overlap subdirectory (niche_overlap.zip) contains the input data and results for all niche comparisons between species. Complete_distributions.csv includes all presence data for both species. gal_background_points.csv and
gua_background_points.csv contain all background points used in SDMs and were used to define the background environmental space on the islands. favorability.csv contains the difference in suitability scores (from the SDMs) for each presence location. All input data and associated niche overlap and comparison analyses were generated via R_analyses.R

The exclusion subdirectory (exclusion.zip) contains the input data for all exclusion analyses. favorability_ecos.csv contains the landcover classification type for each presence locality located with predicted sympatry. gal_CMCR_quadrats.csv and gal_GO_quadrats.csv contain the demographic structure data within the two sympatric and allopatric study sites. gal_fruit_set_perflower.csv and gua_fruit_set_perflower.csv
contain the input data for per-flower rate of fruit set for both species.
gal_seed_set.csv and gua_seed_set.csv contain the seed set input data used to assess reproductive fitness in sympatry. gal_decline.csv contains the input data on the relative position of P. galapageium populations within predicted sympatry, used to assess landscape-level patterns of exclusion. All of these input data and the associated results were processed and generated via R_analyses.R

Column Names

galapageium.csv and guayava.csv

1. long - longitude
2. lat - latitude
3. pr_ab - presence classification (0 or 1)

all_hyperparameters.xlsx

1. species - species for SDM model
2. model - model type
3. regmult - multiplier
4. classes - classes of response modeled
5. mtry - values modeled for "mtry" variable
6. size - values modeled for "size" variable
7. decay - values modeled for "decay" variable

gal_all_models_performance.csv and gal_all_models_performance.csv

1. model_ID - model number
2. model - model type
3. threshold - threshold type for binary prediction of presence
4. thr_value - threshold value for binary prediction of presence
5. n_presences - number of presence points
6. n_absences - number of absence points
7. the following columns are mean values and standard deviations for the following statistics: TPR, TNR, SORENSEN,  JACCARD, FPB, OR, TSS, AUC, BOYCE, IMAE
8. regmult - value used for the "regmult" variable
9. classes - value used for the "classes" variable
10. mtry size - value used for the "mtry" variable
11. decay - value used for the "decay" variable

complete_distributions.csv

1. ID - individual ID
2. source - source of datum
3. species - species of datum
4. island - island of occurrence
5. Date - date collected
6. latitude - latitude
7. longitude - longitude
8. altitude - elevation (m)

favorability.csv

1. OBJECTID - point ID number
2. species - species of occurrence
3. island - island of occurrence
4. dd_long - longitude
5. dd_lat - latitude
6. favorability_difference - difference in favorability score

gal_background_points.csv and gua_background_points.csv

1. x - longitude
2. y - latitude
3. pr_ab - presence type
4. .part - number of partition
5. the following columns are the values extracted at the background point for the following variables: mean_diurnal_rn, temp_annual_rng, annual_precip, precip_coldest_qtr, dem, ecos

favorability_ecos.csv

1. fav_species - species of occurrence
2. FID_Galapagos_Agroecosystems_LandCover2018 - ID number of layer
3. Level_1 - level 1 classification of land cover
4. Level_2 - level 2 classification of land cover
5. Level_3 - level 3 classification of land cover
6. Level_4 - level 4 classification of land cover
7. Level_5 - level 5 classification of land cover
8. Island - island of occurrence
9. Area_m2 - area in square meters
10. Shape_Length - perimeter of polygon
11. Shape_Area - area of polygon

gal_CRCM_quadrats.csv and gal_GO_quadrats

1. height - height of plant in meters
2. species - species of plant
3. site - site ID
4. quadrat - quadrat number
5. type - type of site

gal_fruit_set_perflower.csv and gua_fruit_set_perflower.csv

1. flower - flower number
2. site - site ID
3. type - type of site
4. individual - individual ID
5. branch - branch ID
6. fruitset - fruitset condition (0 or 1)

gal_seed_set.csv and gua_seed_set.csv

1. seeds - number of seeds
2. species - species of fruit
3. site - site ID
4. type - type of site
5. direction - side of island of site pair

gal_decline.csv

1. OBJECTID - ID number of point
2. species - species of point
3. dd_long - longitude
4. dd_lat - latitude
5. Island - island of point
6. centroid_to_edge - distance from centroid to edge of sympatry
7. point_to_edge - distance from point to edge of sympatry
8. normalized_centroid_to_point - relative position within sympatry