{"id":32204136,"url":"https://github.com/ihsankhaliq/ascotracer","last_synced_at":"2025-10-22T04:51:23.596Z","repository":{"id":45328003,"uuid":"311562210","full_name":"IhsanKhaliq/ascotraceR","owner":"IhsanKhaliq","description":"A mechanistic model to simulate the spread of Ascochyta blight in a chickpea field","archived":false,"fork":false,"pushed_at":"2022-10-19T05:52:25.000Z","size":7448,"stargazers_count":3,"open_issues_count":6,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-15T12:39:09.836Z","etag":null,"topics":["ascochyta-blight","ascochyta-rabiei","chickpea","in-paddock-spread","mechanistic-models","quantitative-epidemiology","r","simulation-model","splash-dispersal","spread-model","weather-driven-model"],"latest_commit_sha":null,"homepage":"https://ihsankhaliq.github.io/ascotraceR/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/IhsanKhaliq.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-11-10T06:06:42.000Z","updated_at":"2025-03-22T08:13:45.000Z","dependencies_parsed_at":"2022-08-19T03:20:47.315Z","dependency_job_id":null,"html_url":"https://github.com/IhsanKhaliq/ascotraceR","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/IhsanKhaliq/ascotraceR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IhsanKhaliq%2FascotraceR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IhsanKhaliq%2FascotraceR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IhsanKhaliq%2FascotraceR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IhsanKhaliq%2FascotraceR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IhsanKhaliq","download_url":"https://codeload.github.com/IhsanKhaliq/ascotraceR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IhsanKhaliq%2FascotraceR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280382978,"owners_count":26321423,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-22T02:00:06.515Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ascochyta-blight","ascochyta-rabiei","chickpea","in-paddock-spread","mechanistic-models","quantitative-epidemiology","r","simulation-model","splash-dispersal","spread-model","weather-driven-model"],"created_at":"2025-10-22T04:51:19.954Z","updated_at":"2025-10-22T04:51:23.588Z","avatar_url":"https://github.com/IhsanKhaliq.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"README\"\noutput: github_document\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n\n\u003c!-- badges: start --\u003e\n[![tic](https://github.com/IhsanKhaliq/ascotraceR/workflows/tic/badge.svg?branch=master)](https://github.com/IhsanKhaliq/ascotraceR/actions)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![DOI](https://zenodo.org/badge/311562210.svg)](https://zenodo.org/badge/latestdoi/311562210)\n\u003c!-- badges: end --\u003e\n\n# ascotraceR: An R package resource to simulate the spatiotemporal spread of Ascochyta blight in a chickpea field over a growing season \n\nThe goal of of _ascotraceR_ is to develop a weather driven model to simulate the spread of Ascochyta blight disease in a chickpea field over a growing season.\n\nThis model is adapted from a model developed by [(Diggle *et al.* 2002)](https://doi.org/10.1094/PHYTO.2002.92.10.1110) for simulating the spread of anthracnose in a lupin field. The model is run using local weather data.\nThe _ascotraceR_ model simulates the pathogen related processes of conidial production, dispersal, successful deposition and infection on chickpea plants.\nHost related processes of growth are simulated in terms of development of growing points.\nThe model divides the paddock into 1 square metre cells (observation quadrats/units) and simulates chickpea growth and _A. rabiei_ activities in each cell.\nInitially, there is one growing point per sown seed when seed are sown.\nChickpea growth is then described in terms of increase in the number of growing points.\nConidia are dispersed from infested stubble by rain splash or wind driven rain when rainfall threshold is reached.\nRainfall threshold refers to the minimum amount of rainfall required to disperse conidia from pycnidia and to provide sufficient duration of moisture for conidia to germinate and penetrate into the host tissues.\nAfter penetrating host tissues, conidia produce infected growing points.\nInfected growing points become sporulating lesions after completion of a latent period.\nThe length of the latent period is a function of temperature, and the number of conidia produced per sporulating growing point depends on the level of resistance of the chickpea cultivar.\nAs the model runs, it keeps a continuous track of non-infected, latent, infected and sporulating growing points (lesions).\nThe _ascotraceR_’s minimum input requirements are location specific weather data and a list of input variables.\n\n## Quick start\n\n_ascotraceR_ is available on CRAN.\nTo install the latest release, just run\n\n```r\ninstall.packages(\"ascotraceR\")\n```\n\nAlternatively, you may install the development version from GitHub this way.\n\n```r\nif (!require(\"remotes\"))\n  install.packages(\"remotes\")\nremotes::install_github(\"IhsanKhaliq/ascotraceR\",\n                        build_vignettes = TRUE\n)\n```\n\nOnce installed you can simulate disease spread in a chickpea paddock.\n\nLoad the library.\n\n```{r, load-libs, message=FALSE}\nlibrary(\"ascotraceR\")\nlibrary(\"data.table\")\nlibrary(\"lubridate\")\n\nset.seed(3)\n```\n\nImport the weather data.\n\n```{r load-weather}\n# weather data\nBilla_Billa \u003c- fread(\n  system.file(\n    \"extdata\",\n    \"2020_Billa_Billa_weather_data_ozforecast.csv\",\n    package = \"ascotraceR\"\n  )\n)\n\n# format time column\nBilla_Billa[, local_time := dmy_hm(local_time)]\n\n# specify the station coordinates of the Billa Billa weather station\nBilla_Billa[, c(\"lat\", \"lon\") := .(-28.1011505, 150.3307084)]\n\nhead(Billa_Billa)\n```\n\n### Wrangle weather data \n\nA function, `format_weather()`, is provided to convert raw weather data into the format appropriate for the model.\nIt is mandatory to use this function to ensure weather data is properly formatted before running the model.\n\n```{r format-weather}\nBilla_Billa \u003c- format_weather(\n  x = Billa_Billa,\n  POSIXct_time = \"local_time\",\n  temp = \"mean_daily_temp\",\n  ws = \"ws\",\n  wd_sd = \"wd_sd\",\n  rain = \"rain_mm\",\n  wd = \"wd\",\n  station = \"location\",\n  time_zone = \"Australia/Brisbane\",\n  lon = \"lon\",\n  lat = \"lat\"\n)\n```\n\n### Simulate Ascochyta blight spread\n\nA function, `trace_asco()`, is provided to simulate the spread of Ascochyta blight in a chickpea field over a growing season.\n\n```{r trace-asco}\n# Predict Ascochyta blight spread for the year 2020 at Billa Billa\ntraced \u003c- trace_asco(\n  weather = Billa_Billa,\n  paddock_length = 20,\n  paddock_width = 20,\n  initial_infection = \"2020-07-17\",\n  sowing_date = \"2020-06-04\",\n  harvest_date = \"2020-10-27\",\n  time_zone = \"Australia/Brisbane\",\n  seeding_rate = 40,\n  gp_rr = 0.0065,\n  spores_per_gp_per_wet_hour = 0.6,\n  latent_period_cdd = 150,\n  primary_inoculum_intensity = 100,\n  primary_infection_foci = \"centre\"\n)\n```\n\n### Summarise the output\n\nYou can easily get summary statistics for the whole paddock over the simulated season and area under the disease progress curve, AUDPC, using `summarise_trace()`.\n\n```{r summarise}\nsummarise_trace(traced)\n```\n\n## Code of Conduct\n\nPlease note that the ascotraceR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).\nBy contributing to this project, you agree to abide by its terms.\n\n## Reference\n\n\u003e Diggle AJ, Salam MU, Thomas GJ, Yang H, O'connell M, Sweetingham M, 2002. AnthracnoseTracer: a spatiotemporal model for simulating the spread of anthracnose in a lupin field. Phytopathology 92, 1110-21.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fihsankhaliq%2Fascotracer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fihsankhaliq%2Fascotracer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fihsankhaliq%2Fascotracer/lists"}