pm4mp

The aim of the pm4mp package is to support and accelerate the phylogenetic-based prioritisation of species with underexplored medicinal potential. The new methods implemented in the package propose features to extend and improve the use of the “hot nodes” approach in bioprospecting. New functionalities have been introduced that allow new potentially medicinal species to be prioritised by assigning each a score based on its medicinal potential. These novel methodologies are presented, tested and discussed in Zecca et al. (2026).

The functions included allow to:

• download lists of medicinal plants from CMAUP v1.0 & v2.0 public database (Xian et al. 2019; Dongyue et al. 2024);
• check and match taxa names against a reference phylogeny provided by the user;
• prepare input files for subsequent analyses;
• call an external executable of the software Phylocom (Webb et al.2008) to perform multiple replicates of the ‘nodsigl’ analysis;
• import, process and summarise the outputs obtained from multiple replicates of the ‘nodsigl’ analysis according to predefined criteria and identify the ‘hot trees’ for the studied disease;
• compute the Hot Ancestry Score for all species present in the identified ‘hot trees’;
• compute the (relative) probability of being a medicinal species for all the taxa present in the provided (hot) tree(s) (i.e., for all ‘hot species’);
• show the results graphically.

NOTE:The Phylocom application, which is required to perform the ‘nodesigl’ analysis, is not included in this package and must be downloaded separately by the user from the author’s site.

Not all functions of the package require the presence of Phylocom to be used. In particular the following functions can be used without Phylocom being present:

• clean_and_match()
• dnu_CMAUPv1()
• dnu_CMAUPv2()
• hmpp()
• pr2d_CMAUPv1()
• pr2d_CMAUPv2()
• sample4nodesigl()
• tree4nodesigl()
• visual_comp()

Conversely, the following function depends directly on Phylocom being present for it to work:

• nodesiglR()

Finally, the following functions, although not directly dependent on the presence of Phylocom, directly or indirectly use the results of its ‘nodesigl’ analysis:

• nodesigle_harvesteR()(direct use)
• has()(indirect use: it needs the ouput of functionnodesigle_harvesteR())
• hot_tree_painteR()(indirect use:it needs the ouput of functionnodesigle_harvesteR())

Installation

You can install the last version of pm4mp from GitHub with:

# install.packages("devtools")
devtools::install_github("gzecca/pm4mp")

Load & attach

You can load and attach the installed version of pm4mp with:

library(pm4mp)

Getting help

You can use the help() function and the ? help operator to access the documentation pages for pm4mp functions.

# load and attach
library(pm4mp)

# access the documentation page of the function has()
help("has")

# access the documentation page of the function hmpp()
?hmpp

About examples in the documetation pages

• Currently, to illustrate how the package works, the examples in the documentation pages are built from scratch, without relying on pre-existing data. This should make the format of the files used and the workflow clearer. However, we recognise that this is not optimal for several reasons. We therefore plan to provide a vignette and example datasets in the near future.

• Since nearly all of the functions in the package generate output files, all of the examples presented in the documentation pages write files to the user’s tempdir() during their execution. At the end of each example, the code needed to clean up the user’s temp folder is provided.

Reference and credits

If you use the pm4mppackage, please cite:

• Zecca, G., Toini, E., Labra, M., & Grassi, F. (2026). Accelerating the prioritisation of plant species with underexplored medicinal potential: The pm4mp (Phylogenetic Methods for Medicinal Plants) R package. Plants, People, Planet, 1–19. https://doi.org/10.1002/ppp3.70189

For a first application of some of the functions described in the package (mainly thenodesigle_harvesteR() method) see:

• Lambiase, A., Spandri, G., Moukham, H., Toini, E., D’Urzo, A., Zecca, G., Commisso, M., Guzzo, F., Santoro, V., Piccinelli, A. L., Calleri, E., Salerno, S., Rinaldi, F., Negri, S., Santambrogio, C., Brioschi, M., Solana-Manrique, C., Labra, M., Grassi, F., Paricio, N., … Coccetti, P. (2026). Acteoside exerts neuroprotective effects by preventing α-synuclein aggregation and oxidative stress in models of Parkinson’s disease. Neurotherapeutics, 23(1), e00825. https://doi.org/10.1016/j.neurot.2025.e00825

If you use thePhylocomsoftware, please cite:

• Webb, C. O.; Ackerly, D. D. & Kembel, S. W. (2008) Phylocom: software for the analysis of community structure and trait evolution. Bioinformatics, 24: 2098-2100.

If you use the CMAUPdatabases, please cite:

• Dongyue Hou, Hanbo Lin, Yuhan Feng, et al. CMAUP database update 2024: extended functional and association information of useful plants for biomedical research. Nucleic Acids Research, DOI:doi.org/10.1093/nar/gkad921

• Xian Zeng, Peng Zhang, Yali Wang, et al. CMAUP: a database of collective molecular activities of useful plants. Nucleic Acids Research, 47(D1): D1118-D1127; DOI:doi.org/10.1093/nar/gky965

If you use the phylogeny published by Zanne et al.(2014), please cite:

• Zanne, A. E., Tank, D. C., Cornwell, W. K., Eastman, J. M., Smith, S. A., FitzJohn, R. G., McGlinn, D. J., O’Meara, B. C., Moles, A. T., Reich, P. B., Royer, D. L., Soltis, D. E., Stevens, P. F., Westoby, M., Wright, I. J., Aarssen, L., Bertin, R. I., Calaminus, A., Govaerts, R., … Beaulieu, J. M. (2014). Three keys to the radiation of angiosperms into freezing environments. Nature, 506, 89–92. https://doi.org/10.1038/nature12872