From aa91c82b0641fda13db8c4f49686735d4025d3ab Mon Sep 17 00:00:00 2001 From: sujal Date: Sun, 26 Apr 2026 13:24:14 +0530 Subject: [PATCH 1/2] Improve PEcAn.SIPNET README and documentation structure --- models/sipnet/README.md | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/models/sipnet/README.md b/models/sipnet/README.md index 2c94137f57..759167e6c5 100644 --- a/models/sipnet/README.md +++ b/models/sipnet/README.md @@ -1,5 +1,7 @@ # PEcAn.SIPNET +PEcAn.SIPNET is the PEcAn interface package for running the SIPNET ecosystem model within the PEcAn workflow. It handles input/output translation, model execution, and integration with PEcAn tools such as data assimilation and ensemble analysis. + [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) @@ -11,7 +13,9 @@ The SIPNET v1 (**S**implified PnET (**P**hotosynthesis** and **E**vapo**t**ranspiration)) model is a lightweight ecosystem model designed to simulate ecosystem carbon and water dynamics. -SIPNET v2 added a nitrogen cycle, trace greenhouse-gas (N₂O, CH₄) fluxes, and support for cropland and ecosystem management. As of PEcAn v1.10, support for SIPNET v2 is partially implemented and under active development. +SIPNET is a process-based ecosystem model that simulates carbon, water, and nutrient dynamics at sub-daily time steps. It includes modules for photosynthesis, respiration, soil processes, and vegetation dynamics. + +For full model details, see the SIPNET documentation. **Key Features:** - Simulates photosynthesis, respiration, allocation, soil water, soil temperature, and nitrogen cycling @@ -20,7 +24,7 @@ SIPNET v2 added a nitrogen cycle, trace greenhouse-gas (N₂O, CH₄) fluxes, an - Event-based management for agricultural processes (planting, harvest, tillage, irrigation) - Clean, modular, BSD-licensed codebase suitable for research and production -For comprehensive SIPNET documentation, see the [SIPNET project website](https://pecanproject.github.io/sipnet). +For full model details, see the [SIPNET documentation](https://pecanproject.github.io/sipnet). ## Using SIPNET via PEcAn @@ -34,11 +38,21 @@ PEcAn.SIPNET is the PEcAn interface package that enables SIPNET integration with - [Demo 1: Basic PEcAn Run](https://pecanproject.github.io/pecan-documentation/develop/rendered-demo-notebooks/run_pecan.html) - [SIPNET in the PEcAn Book](https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html) + +## Documentation Structure + +- This README provides an overview of using SIPNET within PEcAn. +- Detailed model documentation is available in the [SIPNET documentation](https://pecanproject.github.io/sipnet). +- The PEcAn documentation provides workflow-level guidance and examples. + +Users are encouraged to refer to the SIPNET documentation for model-specific details and to the PEcAn documentation for workflow integration. + + ## Installation ### Install PEcAn.SIPNET Package -You can install the development version of `PEcAn.SIPNET` from r-universe: +Install the PEcAn.SIPNET package from r-universe: ```r # Enable repository from pecanproject @@ -63,7 +77,7 @@ To use PEcAn.SIPNET, you also need the SIPNET model executable installed on your ## Documentation - **PEcAn.SIPNET Package Docs:** https://pecanproject.github.io/package-documentation/develop/PEcAn.SIPNET/ -- **SIPNET Model Docs:** https://pecanproject.github.io/sipnet +- **SIPNET Model Docs:** [SIPNET documentation](https://pecanproject.github.io/sipnet) - **PEcAn Book - SIPNET Chapter:** https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html - **Source Code:** https://github.com/PecanProject/pecan/tree/develop/models/sipnet From 9e13955fa864ed8813c8f40558abca0bc601b75b Mon Sep 17 00:00:00 2001 From: sujal Date: Mon, 27 Apr 2026 21:18:30 +0530 Subject: [PATCH 2/2] removed duplicate content --- models/sipnet/README.md | 73 ----------------------------------------- 1 file changed, 73 deletions(-) diff --git a/models/sipnet/README.md b/models/sipnet/README.md index 759167e6c5..b6733c932d 100644 --- a/models/sipnet/README.md +++ b/models/sipnet/README.md @@ -1,42 +1,6 @@ -# PEcAn.SIPNET -PEcAn.SIPNET is the PEcAn interface package for running the SIPNET ecosystem model within the PEcAn workflow. It handles input/output translation, model execution, and integration with PEcAn tools such as data assimilation and ensemble analysis. - -[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![PEcAn.SIPNET status badge](https://pecanproject.r-universe.dev/badges/PEcAn.SIPNET)](https://pecanproject.r-universe.dev/PEcAn.SIPNET) - - - -## What is SIPNET? - -The SIPNET v1 (**S**implified PnET (**P**hotosynthesis** and **E**vapo**t**ranspiration)) model is a lightweight ecosystem model designed to simulate ecosystem carbon and water dynamics. - -SIPNET is a process-based ecosystem model that simulates carbon, water, and nutrient dynamics at sub-daily time steps. It includes modules for photosynthesis, respiration, soil processes, and vegetation dynamics. - -For full model details, see the SIPNET documentation. - -**Key Features:** -- Simulates photosynthesis, respiration, allocation, soil water, soil temperature, and nitrogen cycling -- Operates on sub-daily time steps -- Tracks vegetation, litter, soil, and mineral-N pools -- Event-based management for agricultural processes (planting, harvest, tillage, irrigation) -- Clean, modular, BSD-licensed codebase suitable for research and production - -For full model details, see the [SIPNET documentation](https://pecanproject.github.io/sipnet). - -## Using SIPNET via PEcAn - -PEcAn.SIPNET is the PEcAn interface package that enables SIPNET integration with the PEcAn workflow system. This package: -- Converts PEcAn-standard inputs to SIPNET format -- Manages SIPNET model configuration and execution -- Converts SIPNET outputs to netCDF in PEcAn standard format -- Enables data assimilation, sensitivity analysis, and ensemble runs within the PEcAn modeling framework - -**Getting Started:** -- [Demo 1: Basic PEcAn Run](https://pecanproject.github.io/pecan-documentation/develop/rendered-demo-notebooks/run_pecan.html) -- [SIPNET in the PEcAn Book](https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html) ## Documentation Structure @@ -48,41 +12,4 @@ PEcAn.SIPNET is the PEcAn interface package that enables SIPNET integration with Users are encouraged to refer to the SIPNET documentation for model-specific details and to the PEcAn documentation for workflow integration. -## Installation - -### Install PEcAn.SIPNET Package - -Install the PEcAn.SIPNET package from r-universe: - -```r -# Enable repository from pecanproject -options(repos = c( - pecanproject = 'https://pecanproject.r-universe.dev', - CRAN = 'https://cloud.r-project.org')) -# Download and install PEcAn.SIPNET in R -install.packages('PEcAn.SIPNET') -``` - -Or install directly from GitHub: - -```r -library(remotes) -install_github('pecanproject/pecan', subdir = "models/sipnet") -``` - -### Install SIPNET Model - -To use PEcAn.SIPNET, you also need the SIPNET model executable installed on your system. You can download precompiled versions from the SIPNET [releases page](https://github.com/PecanProject/sipnet/releases), or [download the code](https://github.com/PecanProject/sipnet) from Github and compile it yourself following the official [instructions](https://github.com/PecanProject/sipnet/blob/master/docs/user-guide/getting-started.md). - -## Documentation - -- **PEcAn.SIPNET Package Docs:** https://pecanproject.github.io/package-documentation/develop/PEcAn.SIPNET/ -- **SIPNET Model Docs:** [SIPNET documentation](https://pecanproject.github.io/sipnet) -- **PEcAn Book - SIPNET Chapter:** https://pecanproject.github.io/pecan-documentation/develop/models-sipnet.html -- **Source Code:** https://github.com/PecanProject/pecan/tree/develop/models/sipnet - -## Learn More -- **PEcAn Project:** https://pecanproject.github.io -- **Tutorials:** https://pecanproject.github.io/tutorials/ -- **SIPNET Repository:** https://github.com/PecanProject/sipnet