The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

phylopred

Predicting species interactions from phylogenetic distance under presence-only data.

phylopred models the probability that two species share a parasite (or other interaction) as a function of their phylogenetic distance, and predicts new hosts for a parasite from its known hosts:

• Pairwise host-sharing logistic models, parasite-cluster bootstrap, and formal slope comparison between clades (generalist vs specialist).
• Presence-only performance metrics: threshold efficiency f_gamma = a / (gamma * b + c) and a phylogenetic partial ROC (sensitivity vs fraction of the phylogeny predicted suitable).
• Positive-unlabeled (PU) host prediction with xplus on phylogenetic features.
• Leave-hosts-out validation of predictive performance.

Installation

remotes::install_github("alrobles/phylopred")

Documentation site: https://alrobles.github.io/phylopred/

Example

library(phylopred)

pairs <- prepare_pair_data(beetleTreeInteractions, phy_dist)
fit <- fit_phylopred_model(pairs)
summary(fit)

parasite <- names(sort(table(pairs$parasite), decreasing = TRUE))[1]
one <- pairs[pairs$parasite == parasite, ]
one$pred <- predict(fit$fit, newdata = one, type = "response")
m <- host_threshold_metric(one$pred, one$suscept)
plot(m)
roc <- phylo_partial_roc(one$pred, one$suscept, error_rate = 0.95)
plot(roc)

See the vignette caligus-vs-lepeophtheirus for a complete real-data case study with the cofid copepod-fish interaction database and the Fish Tree of Life.

Manuscript

The manuscript, supplementary material, and archived analysis results are maintained separately in the phylopred-paper repository.

References

• Robles-Fernandez, A. L. & Lira-Noriega, A. (2017). Combining phylogenetic and occurrence information for risk assessment of pest and pathogen interactions with host plants. Frontiers in Applied Mathematics and Statistics, 3:17. doi:10.3389/fams.2017.00017
• Peterson, A. T., Papes, M. & Soberon, J. (2008). Rethinking receiver operating characteristic analysis applications in ecological niche modeling. Ecological Modelling, 213, 63-72.
• Rabosky, D. L. and colleagues (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559, 392-395.
• Morales-Serna, F. N. (2025). Global patterns of modularity and narrow host use in fish-parasitic copepods (Crustacea). Biodiversity Data Journal, 13, e163693. https://doi.org/10.3897/BDJ.13.e163693 — basis of the cofid database (https://github.com/alrobles/cofid)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.