Package: hagis 3.1.12
Adam H. Sparks
hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer and Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis.
Authors:
hagis_3.1.12.tar.gz
hagis_3.1.12.zip(r-4.5)hagis_3.1.12.zip(r-4.4)hagis_3.1.12.zip(r-4.3)
hagis_3.1.12.tgz(r-4.4-any)hagis_3.1.12.tgz(r-4.3-any)
hagis_3.1.12.tar.gz(r-4.5-noble)hagis_3.1.12.tar.gz(r-4.4-noble)
hagis_3.1.12.tgz(r-4.4-emscripten)hagis_3.1.12.tgz(r-4.3-emscripten)
hagis.pdf |hagis.html✨
hagis/json (API)
NEWS
| # Install 'hagis' in R: |
| install.packages('hagis', repos = c('https://openplantpathology.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/openplantpathology/hagis/issues
- P_sojae_survey - _Phytophthora sojae_ Survey Example Data
- sample_meta - _Phytophthora sojae_ Survey Example Metadata
plant-pathologypathotypepathogen-surveyvirulence analysisdifferential setassessment scalepathotype-complexitiesplant-diseasepopulation-diversities
Last updated 1 months agofrom:344ff123dd. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 11 2024 |
| R-4.5-win | NOTE | Nov 11 2024 |
| R-4.5-linux | NOTE | Nov 11 2024 |
| R-4.4-win | OK | Nov 11 2024 |
| R-4.4-mac | OK | Nov 11 2024 |
| R-4.3-win | OK | Nov 11 2024 |
| R-4.3-mac | OK | Nov 11 2024 |
Exports:autoplotcalculate_complexitiescalculate_diversitiescreate_binary_matrixdiversities_tableindividual_pathotypessummarize_gene
Dependencies:clicolorspacedata.tabledigestfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepanderpillarpkgconfigR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Beta-diversity Analysis with hagis
Rendered frombetadiversity.Rmdusingknitr::rmarkdownon Nov 11 2024.Last update: 2024-05-16
Started: 2020-10-06
hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
Rendered fromhagis.Rmdusingknitr::rmarkdownon Nov 11 2024.Last update: 2024-05-16
Started: 2019-01-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot hagis Complexities Objects | autoplot.hagis.complexities |
| Plot hagis Summary Objects | autoplot.hagis.gene.summary |
| Calculate Distribution of Complexities by Sample | calculate_complexities |
| Calculate Diversities Indices | calculate_diversities |
| Create Binary Data Matrix From Pathotype Data | create_binary_matrix |
| Custom Print for hagis Diversities Tables | diversities_table |
| Prints Individual Pathotypes for Each Sample | individual_pathotypes |
| _Phytophthora sojae_ Survey Example Data | P_sojae_survey |
| _Phytophthora sojae_ Survey Example Metadata | sample_meta |
| Calculate and Summarize Distribution of Susceptibilities by Gene | summarize_gene |
