Scope | Constructing a curve | Reading before assigning | Describing stored partitions | Optional model-assisted interpretation | Reproducibility record | Current limits
Package: AMDconfigurations 0.4.0
AMDconfigurations: Geometric Analysis of Configurations in High-Dimensional Spaces
Computes Average Membership Degree (AMD) from soft-membership matrices and constructs AMD curves across candidate configuration counts. The current curve backend uses repeated fuzzy c-means fits while keeping the AMD definition, membership estimation, curve construction, and final assignment as separate operations. Fitted memberships, convergence diagnostics, preprocessing transformations, seeds, row maps, and process-level reproducibility links are retained. The package reports numerical curve features but leaves their scientific interpretation to an explicitly justified analysis. The method was introduced by Mendoza and Araújo (2022) <doi:10.1111/ecog.06289>.
Authors:
AMDconfigurations_0.4.0.tar.gz
AMDconfigurations_0.4.0.zip(r-4.7-any)AMDconfigurations_0.4.0.zip(r-4.6-any)AMDconfigurations_0.4.0.zip(r-4.5-any)
AMDconfigurations_0.4.0.tgz(r-4.6-any)AMDconfigurations_0.4.0.tgz(r-4.5-any)
AMDconfigurations_0.4.0.tar.gz(r-4.7-any)AMDconfigurations_0.4.0.tar.gz(r-4.6-any)
AMDconfigurations_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AMDconfigurations/json (API)
| # Install 'AMDconfigurations' in R: |
| install.packages('AMDconfigurations', repos = c('https://mmendoza1967.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mmendoza1967/amdconfigurations/issues
Pkgdown/docs site:https://mmendoza1967.github.io
Datasets:
- Fulldata - Ecological dataset used in the example
- Transcdata_small - Reduced transcriptomic dataset
Last updated from:0b036fc2bb. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 107 | ||
| source / vignettes | OK | 301 | ||
| linux-release | OK | 103 | ||
| macos-release | OK | 205 | ||
| macos-oldrel | OK | 132 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 96 | ||
| windows-oldrel | OK | 77 | ||
| wasm-release | OK | 94 |
Exports:amd_reproducibility_manifestamd_scoreassign_configurationscompute_amd_curvediagnose_amdload_amd_predictorplot_AMDpredict_amd
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Record the reproducibility environment for an AMD process | amd_reproducibility_manifest |
| Compute Average Membership Degree from soft memberships | amd_score |
| Assign observations to a user-selected number of configurations | assign_configurations |
| Compute an Average Membership Degree (AMD) curve | compute_amd_curve |
| Describe an AMD curve and its stored partitions | diagnose_amd |
| Ecological dataset used in the example | Fulldata |
| Load the optional drop-37 AMD reader | load_amd_predictor |
| Plot an AMD curve | plot_AMD |
| Plot method for AMD curve objects | plot.amd_curve |
| Plot an optional AMD reader result | plot.amd_prediction |
| Propose a modal resolution from an AMD analysis | predict_amd |
| Print an AMD curve object | print.amd_curve |
| Print descriptive AMD diagnostics | print.amd_diagnostics |
| Print an optional AMD reader result | print.amd_prediction |
| Summarise an AMD curve object | summary.amd_curve |
| Summarise an optional AMD reader result | summary.amd_prediction |
| Reduced transcriptomic dataset (1000 variables) | Transcdata_small |