Introduction
This R Markdown file is used to bring together all of the results
generated from the High Performance Computer (HPC)
that will then be saved as combined spreadsheets saved to dropbox. Some
of the basic numeric results will be included in this markdown, but all
of the data visualization will be left for the 4th and final step of
this analysis.
As a reminder, the co-abundance models were implemented on this R
script: scripts/HPC_code/HPC_co-abundance_model_final.R. However, the
each JAGS model with long MCMC settings is too heavy to download
(i.e., several GB per model), so we only saved spreadsheets
from the model on the HPC.
Description of results
Total models completed
A total of 258 co-abundance models out of 258 were successfully
completed and downloaded from the HPC. The models are composed of
194 ‘community models’ across the entire eligible
community, and 64 ‘preferred models’ based on large
carnivore dietary preferences. There were a total of 117 community
top-down models and 32 preferred top-down models. There were a total of
77 community bottom-up models and 32 preferred bottom-up models.
When examining pairwise comparisons of species, each species-pair
(regardless of the direction) can produce one result that is either
top-down, bottom-up, or unsupported. There were a total of 16
species-pairs supporting top-down regulation, a total of
29 species-pairs supporting bottom-up regulation, and a
total of 98 species-pairs supporting no associations.
These results can be further sub-divided into preferred & community
results:
For the preferred species-pairs, there were 2
species-pairs supporting top-down regulation, a total of 12
species-pairs supporting bottom-up regulation, and a total of 18
species-pairs supporting no associations.
For the community species-pairs, there were 14
species-pairs supporting top-down regulation, a total of 17
species-pairs supporting bottom-up regulation, and a total of 80
species-pairs supporting no associations.
The settings used on the HPC to complete these models are composed of
258 models with long settings, 0 models with middle settings, and 0
models with short settings.
If there are any uncompleted preferred models, the
names of those species-pairs will appear here: .
Model diagnostics
It is important to inspect the diagnostics of the models before we
interpret results, and there are four key diagnostic features to
inspect.
The first key value we are interested in is the parameter
convergence (known as R-hat) around the species interaction value
(SIV), where parameters are converged if values are between 1
and 1.1. The median Rhat for the SIV is 1.001 with a standard
deviation of 6.176. In total, 41 models failed to generate a
convergent SIV. This is composed of 11 preferred models and 30 community
models.
The second key value is the Bayesian p-value denoting
model goodness-of-fit, where models are deemed to be a good fit
if values are between 0.15 to 0.85, with values outside of this range
being considered a bad fit. Across all models 16.67 percent of
models are considered a bad fit. This is composed of 11
preferred models and 32 community models.
The third key value is the C-hat overdispersion
value, where models are deemed to not have any overdispersion
in detections if values are between 0.95 and 1.3. Across all
models 100 percent of models contain remaining overdispersion of
detections not accounted for in the detection formula. This is
composed of 0 preferred models and 0 community models.
The fourth value is the direction of the SIV based on our
hypotheses, where top-down models should have a significant
negative relationship and bottom-up models should have a significant
positive relationship. As a reminder, top-down models are when large
carnivores are the dominant species and bottom-up models are where large
carnivores are the subordinate species. For the preferred top-down
models, 2 models meet these conditions. For the preferred bottom-up
models, 14 models meet these conditions. For the community top-down
models, 14 models meet these conditions. For the community bottom-up
models, 26 models meet these conditions.
Unsupported results
In combining these different diagnostic tools, we can determine
different levels of support for our results. Models that had unsuitable
parameter convergence or Bayes p-values and remaining over-dispersion
are likely due to insufficient data or excessive residual noise from
weakly interacting species (Fig. S2,
unsupported_wrong_direction). Models that had unclear
SIVs are likely due to the inclusion of covariates in the model being
more informative than species interactions (Fig. S2,
unsupported_unclear_SIV). Models with clear SIVs in the
opposite direction as we hypothesized are likely due to shared responses
to unexplained variation in covariates not included in the model, such
as both predator and prey responding negatively to hunting in bottom-up
models, or both species responding positively to fruit availability in
top-down models (Fig. S2, unsupported_poor_fit).
Finally, when a model meets all of the previous criteria, then we can
determine the model as supported. Top-down and bottom-up models may fail
for different reasons, so unsupported species-pairs are simply
unsupported, while models can be classified into the described levels.
The results from each level are provided below:
There were a total of 68 unsupported_poor_fit models. This is
composed of 18 preferred models and 50 community models.
There were a total of 90 unsupported_unclear_SIV models. This is
composed of 20 preferred models and 70 community models.
There were a total of 55 unsupported_wrong_direction models. This
is composed of 12 preferred models and 43 community models.
There were a total of 45 supported models. This is composed of 14
preferred models and 31 community models.
In interpreting our supported results, we can split them between
top-down and bottom-up results:
Supported top-down results
- For the supported top-down results, we had a total of 16
models. This is composed of 2 preferred models and 14 community
models.
- Tigers showed 1 top-down relationships with their
preferred prey and 8 top-down relationships with the overall community.
In terms of distinct species-pairs, tigers exhibited top-down regulation
in 1 preferred species-pairs and 8 in community pairs.
- Leopards showed 1 top-down relationships with their
preferred prey and 2 top-down relationships with the overall community.
In terms of distinct species-pairs, leopards exhibited top-down
regulation in 1 preferred species-pairs and 2 in community pairs.
- Dholes showed 0 top-down relationships with their
preferred prey and 4 top-down relationships with the overall community.
In terms of distinct species-pairs, dholes exhibited top-down regulation
in 0 preferred species-pairs and 4 in community pairs.
- Clouded leopards showed 0 top-down relationships
with their preferred prey and 0 top-down relationships with the overall
community. In terms of distinct species-pairs, clouded leopards
exhibited top-down regulation in 0 preferred species-pairs and 1 in
community pairs.
Supported bottom-up results
- For the supported bottom-up results, we had a total of 29
models. This is composed of 12 preferred models and 17 community
models.
- Tigers showed 2 bottom-up relationships with their
preferred prey and 3 bottom-up relationships with the overall community.
In terms of distinct species-pairs, tigers exhibited bottom-up
regulation in 2 preferred species-pairs and 3 in community pairs.
- Leopards showed 2 bottom-up relationships with
their preferred prey and 4 bottom-up relationships with the overall
community. In terms of distinct species-pairs, leopards exhibited
bottom-up regulation in 2 preferred species-pairs and 4 in community
pairs.
- Dholes showed 1 bottom-up relationships with their
preferred prey and 4 bottom-up relationships with the overall community.
In terms of distinct species-pairs, dholes exhibited bottom-up
regulation in 1 preferred species-pairs and 4 in community pairs.
- Clouded leopards showed 7 bottom-up relationships
with their preferred prey and 6 bottom-up relationships with the overall
community. In terms of distinct species-pairs, clouded leopards
exhibited bottom-up regulation in 7 preferred species-pairs and 6 in
community pairs.
Specific results per large carnivore
- Tigers preferred bottom-up relationships were with
the following species: Rusa_unicolor, & Sus_scrofa, and the
preferred top-down relationships were with the
following species: Muntiacus_genus.
- The community bottom-up relationships were with the
following species: Arctictis_binturong, & Macaca_arctoides, &
Paguma_larvata, and the community top-down
relationships were with the following species:
Atherurus_macrourus & Lophura_nycthemera & Macaca_nemestrina
& Manis_javanica & Neofelis_genus & Trichys_fasciculata
& Viverra_megaspila & Viverra_zibetha.
- Leopards preferred bottom-up relationships were
with the following species: Muntiacus_genus, & Sus_scrofa, and the
preferred top-down relationships were with the
following species: Macaca_nemestrina.
- The community bottom-up relationships were with the
following species: Atherurus_macrourus, & Bos_gaurus, &
Rusa_unicolor, & Tapirus_indicus, and the community top-down
relationships were with the following species:
Catopuma_temminckii & Varanus_salvator.
- Dholes preferred bottom-up relationships were with
the following species: Rusa_unicolor, and the preferred top-down
relationships were with the following species: .
- The community bottom-up relationships were with the
following species: Arctictis_binturong, & Lophura_diardi, &
Paradoxurus_hermaphroditus, & Viverra_zibetha, and the
community top-down relationships were with the
following species: Arctonyx_collaris & Catopuma_temminckii &
Helarctos_malayanus & Macaca_fascicularis.
- Clouded leopards preferred bottom-up relationships
were with the following species: Arctictis_binturong, &
Arctonyx_collaris, & Capricornis_genus, & Muntiacus_genus, &
Sus_scrofa, & Viverra_tangalunga, & Viverra_zibetha, and the
preferred top-down relationships were with the
following species: .
- The community bottom-up relationships were with the
following species: Atherurus_macrourus, & Herpestes_brachyurus,
& Lophura_bulweri, & Paguma_larvata, & Tapirus_indicus,
& Trichys_fasciculata, and the community top-down
relationships were with the following species: .
Sensitivity test results
We implemented a total of 5 sensitivity tests that will be compared
with the original tests for a total of 6 tests. The key inference here
will be determining which species pairs agree across all possible tests,
noting that not every species pairing was able to be tested in every
way. Currently, all tests have been run with the MCMC setting
LONG. It is also important to note that while we ran counter
factual tests for all 64 preferred models, we also ran counter
factual tests for an additional 31 community models that generated
supported results in the original test.
- The first test, original_test, included a total of
64 preferred models and 31 community models. This equates to a total of
28 preferred species-pairs and 31 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 18 unsupported_poor_fit models, 20
unsupported_unclear_SIV models, 12 unsupported_wrong_direction models,
and 14 supported preferred models. This equates to 2
supported top-down preferred species-pairs & 12 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 0 unsupported_poor_fit models, 0
unsupported_unclear_SIV models, 0 unsupported_wrong_direction models,
and 31 supported community models. This equates to 14
supported top-down community species-pairs & 17 supported bottom-up
community species-pairs.
- The second test, isolate_extirpations, included a
total of 64 preferred models and 31 community models. This equates to a
total of 29 preferred species-pairs and 20 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 21 unsupported_poor_fit models, 18
unsupported_unclear_SIV models, 10 unsupported_wrong_direction models,
and 15 supported preferred models. This equates to 3
supported top-down preferred species-pairs & 12 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 6 unsupported_poor_fit models, 6
unsupported_unclear_SIV models, 0 unsupported_wrong_direction models,
and 19 supported community models. This equates to 7
supported top-down community species-pairs & 12 supported bottom-up
community species-pairs.
- The third test, site_matching_ThaiEFC, included a
total of 40 preferred models and 15 community models. This equates to a
total of 18 preferred species-pairs and 7 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 7 unsupported_poor_fit models, 11
unsupported_unclear_SIV models, 11 unsupported_wrong_direction models,
and 11 supported preferred models. This equates to 1
supported top-down preferred species-pairs & 10 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 1 unsupported_poor_fit models, 6
unsupported_unclear_SIV models, 1 unsupported_wrong_direction models,
and 7 supported community models. This equates to 3
supported top-down community species-pairs & 4 supported bottom-up
community species-pairs.
- The fourth test, isolate_altitude, included a total
of 64 preferred models and 29 community models. This equates to a total
of 30 preferred species-pairs and 23 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 16 unsupported_poor_fit models, 21
unsupported_unclear_SIV models, 11 unsupported_wrong_direction models,
and 16 supported preferred models. This equates to 4
supported top-down preferred species-pairs & 12 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 4 unsupported_poor_fit models, 3
unsupported_unclear_SIV models, 0 unsupported_wrong_direction models,
and 22 supported community models. This equates to 12
supported top-down community species-pairs & 10 supported bottom-up
community species-pairs.
- The fifth test, isolate_FLII, included a total of
64 preferred models and 31 community models. This equates to a total of
27 preferred species-pairs and 21 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 17 unsupported_poor_fit models, 19
unsupported_unclear_SIV models, 15 unsupported_wrong_direction models,
and 13 supported preferred models. This equates to 2
supported top-down preferred species-pairs & 11 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 4 unsupported_poor_fit models, 7
unsupported_unclear_SIV models, 0 unsupported_wrong_direction models,
and 20 supported community models. This equates to 11
supported top-down community species-pairs & 9 supported bottom-up
community species-pairs.
- The sixth test, isolate_HFP, included a total of 64
preferred models and 30 community models. This equates to a total of 29
preferred species-pairs and 20 community species-pairs.
- Based on the same criteria above for the original tests, the
preferred results contained 17 unsupported_poor_fit models, 23
unsupported_unclear_SIV models, 9 unsupported_wrong_direction models,
and 15 supported preferred models. This equates to 4
supported top-down preferred species-pairs & 11 supported bottom-up
preferred species-pairs.
- Based on the same criteria above for the original tests, the
community results contained 3 unsupported_poor_fit models, 8
unsupported_unclear_SIV models, 0 unsupported_wrong_direction models,
and 19 supported community models. This equates to 10
supported top-down community species-pairs & 9 supported bottom-up
community species-pairs.
Agreement across sensitivity tests
Finally, we assessed which species pairs agreed across the different
tests and this resulted in 2 preferred top-down model and 9 community
bottom-up models. This also resulted in 4 community top-down model and 5
community bottom-up models.
- The 2 preferred top-down models that agree across all
sensitivity tests are:
SUB-Macaca_nemestrina~DOM-Panthera_pardus,
SUB-Muntiacus_genus~DOM-Panthera_tigris.
- This equates to 2 species pairs composed of the following pairs:
Macaca_nemestrina-&-Panthera_pardus,
Muntiacus_genus-&-Panthera_tigris
- The 9 preferred bottom-up models that agree across all
sensitivity tests are: SUB-Cuon_alpinus~DOM-Rusa_unicolor,
SUB-Neofelis_genus~DOM-Arctictis_binturong,
SUB-Neofelis_genus~DOM-Arctonyx_collaris,
SUB-Neofelis_genus~DOM-Capricornis_genus,
SUB-Neofelis_genus~DOM-Sus_scrofa,
SUB-Neofelis_genus~DOM-Viverra_zibetha,
SUB-Panthera_pardus~DOM-Muntiacus_genus,
SUB-Panthera_tigris~DOM-Rusa_unicolor,
SUB-Panthera_tigris~DOM-Sus_scrofa.
- This equates to 9 species pairs composed of the following pairs:
Cuon_alpinus-&-Rusa_unicolor,
Arctictis_binturong-&-Neofelis_genus,
Arctonyx_collaris-&-Neofelis_genus,
Capricornis_genus-&-Neofelis_genus, Neofelis_genus-&-Sus_scrofa,
Neofelis_genus-&-Viverra_zibetha,
Muntiacus_genus-&-Panthera_pardus,
Panthera_tigris-&-Rusa_unicolor,
Panthera_tigris-&-Sus_scrofa
- The 4 community top-down models that agree across all
sensitivity tests are:
SUB-Catopuma_temminckii~DOM-Panthera_pardus,
SUB-Trichys_fasciculata~DOM-Panthera_tigris,
SUB-Varanus_salvator~DOM-Panthera_pardus,
SUB-Viverra_megaspila~DOM-Panthera_tigris.
- This equates to 4 species pairs composed of the following pairs:
Catopuma_temminckii-&-Panthera_pardus,
Panthera_tigris-&-Trichys_fasciculata,
Panthera_pardus-&-Varanus_salvator,
Panthera_tigris-&-Viverra_megaspila
- The 5 community bottom-up models that agree across all
sensitivity tests are:
SUB-Cuon_alpinus~DOM-Arctictis_binturong,
SUB-Cuon_alpinus~DOM-Viverra_zibetha,
SUB-Neofelis_genus~DOM-Paguma_larvata,
SUB-Neofelis_genus~DOM-Tapirus_indicus,
SUB-Panthera_tigris~DOM-Arctictis_binturong.
- This equates to 5 species pairs composed of the following pairs:
Arctictis_binturong-&-Cuon_alpinus,
Cuon_alpinus-&-Viverra_zibetha, Neofelis_genus-&-Paguma_larvata,
Neofelis_genus-&-Tapirus_indicus,
Arctictis_binturong-&-Panthera_tigris
Save results
Save these results to GitHub, in this file directory:
/results_final/step3_output_combined_results. It is
important to note that Tables S3 (full model performance and SIVs) and
S4 (supported counterfactual results) are generated from this script, so
make sure to include these in the manuscript!