Docs add intro pages

book_source/01_introduction/00_introduction.Rmd

@@ -1,3 +1,5 @@
 # (PART) Introduction {-}
 
-Welcome to the PEcAn Book! Here you'll learn about the PEcAn project, our community values, and how to use this book. Whether you're just starting out or you already know your way around, you'll find what you need here.
+This part introduces the PEcAn framework, its overall architecture, and
+the core concepts needed to understand how PEcAn supports ecosystem
+modeling workflows.

book_source/02_demos_tutorials_workflows/00_tutorials_demos_workflows.Rmd

@@ -1,3 +1,5 @@
 # (PART) Tutorials, Demos and How To's {-}
 
-This section contains step-by-step tutorials, example workflows, and demonstrations designed to help users get started with PEcAn and learn common usage patterns through practical examples.
+This section contains step-by-step tutorials, example workflows,
+and demonstrations designed to help users get started with PEcAn and learn
+common usage patterns through practical examples.

book_source/03_topical_pages/00_topicalpages.Rmd

@@ -1,3 +1,6 @@
 # (PART) Topical Pages {-}
 
-This section provides reference documentation on core PEcAn concepts, data formats, models, and system components. These chapters are intended to provide deeper understanding of individual modules in support of both using PEcAn for science and development of the PEcAn toolbox.
+This section provides reference documentation on core PEcAn concepts, data formats,
+models, and system components.
+These chapters are intended to provide deeper understanding of individual modules in
+support of both using PEcAn for science and development of the PEcAn toolbox.

book_source/03_topical_pages/02_pecan_standards.Rmd

@@ -23,6 +23,7 @@ To aid in the conversion between PEcAn internal ISO_8601 standard and CF convent
 
 ### Meteorology Standards 
 
+
 #### Dimensions
 
 

book_source/03_topical_pages/03_pecan_xml.Rmd

@@ -435,22 +435,65 @@ The following are the most common types of inputs, along with their correspondin
 
 ##### `met`: Meteorological inputs {#xml-run-inputs-met}
 
--(Under construction. See the
--[`PEcAn.data.atmosphere` package documentation](https://pecanproject.github.io/package-documentation/develop/PEcAn.data.atmosphere/)
+See the `PEcAn.data.atmosphere` package documentation for more details.
+In particular, users working with meteorological inputs should focus on
+the data download functions and the `met2CF` conversion utilities, which
+handle retrieval of raw meteorological products and conversion to
+CF-compliant NetCDF files used by PEcAn.
 
 
-##### (Experimental) `soil`: Soil inputs {#xml-run-inputs-soil}
+##### `soil`: Soil inputs {#xml-run-inputs-soil}
 
-(Under construction. See the `PEcAn.data.land` package, located in `modules/data.land`, for more details).
+Soil inputs are handled through the `PEcAn.data.land` module.
+For full technical details, see the
+[PEcAn.data.land package documentation](https://pecan.ncsa.illinois.edu/pkgdocs/PEcAn.data.land/).
 
-##### (Experimental) `veg`: Vegetation initial conditions {#xml-run-inputs-veg}
+In practice, most PEcAn workflows do not rely on automated soil data
+processing at runtime. Instead, users typically preprocess soil data
+and provide standardized `soil.nc` files that are referenced directly
+in `pecan.xml`.
+
+Although automated soil processing is supported in principle, there are
+currently only two soil data products commonly used in PEcAn workflows:
+gSSURGO and SoilGrids.
+
+The `<soil>` element in `pecan.xml` is primarily used to specify paths to
+preprocessed soil inputs rather than to trigger on-the-fly data
+processing.
+
+Note that some models reference soil inputs using the `<soil>` tag,
+while others use `<soilphysics>`. This inconsistency is historical and
+can cause confusion; a future harmonization of these tags would be
+beneficial.
+
+
+##### `veg`: Vegetation initial conditions {#xml-run-inputs-veg}
 
 ##### `poolinitcond`: initial condition inputs {#xml-run-inputs-poolinitcond}
 * `source`: Data source of initial condition .rd veg files ex: NEON_veg, FIA.
 * `output`: This tag can only must match the cooresponding tag in the modeltypes_formats table that matches with your model type ex for SIPNET model tag is poolinitcond.
 * `ensemble`: Number of initial conditions ensemble member files ex: 30.
 
-(Under construction. Follow developments in the `PEcAn.data.land` package, located in `modules/data.land` in the source code).
+###### `phenology`
+
+Defines the timing of vegetation growth and dormancy, such as leaf-out and
+senescence. Phenology information allows PEcAn to determine when vegetation
+is actively growing and interacting with climate drivers.
+
+Phenology inputs are typically derived from external datasets and help align
+model simulations with observed seasonal behavior.
+
+###### `management`
+
+Specifies management activities applied to vegetation, such as planting,
+harvesting, fertilization, or irrigation. Management inputs allow PEcAn to
+represent human interventions that affect ecosystem processes.
+
+Management information may vary over time and is commonly linked to site- or
+crop-specific datasets.
+
+
+ (Follow developments in the `PEcAn.data.land` package, located in `modules/data.land` in the source code).
 
 ##### `pft.site` Multi-site site / PFT mapping
 

book_source/03_topical_pages/06_data/01_meteorology.Rmd

@@ -1,6 +1,8 @@
 # Available Meteorological Drivers {#met-drivers}
 
-Meteorological (met) drivers provide the climate forcing data required by ecosystem models in PEcAn. Available drivers include site-level observations, regional and global reanalysis products, and climate model projections.
+Meteorological (met) drivers provide the climate forcing data required by
+ecosystem models in PEcAn. Available drivers include site-level observations,
+regional and global reanalysis products, and climate model projections.
 
 ### How to choose a meteorological driver {-}
 
@@ -9,10 +11,17 @@ location, and time period of interest.
 
 General guidance:
 
-- **Site-level analyses** should use flux tower–based datasets (e.g. Ameriflux, Fluxnet, ICOS) when their goal is to precisely match observations from that tower and they are prepared to make analysis-specific choices on how to handle gaps or inconsistencies in the data. Site-level analyses where completeness and timeseries consistency is more important than matching specific days may prefer to use a gridded product.
-- **Regional analyses** commonly use gridded reanalysis or model outputs (such as NARR or NLDAS) whose coverage matches the scale of the analysis.
-- **Global or long-term analyses** typically rely on products with broad spatial and temporal coverage like CRUNCEP, ERA5, or GLDAS.
-- **Future simulations** require climate model outputs (e.g. CMIP5).
+- Site-level analyses should use flux tower–based datasets (e.g. Ameriflux,
+  Fluxnet, ICOS) when their goal is to precisely match observations from that
+  tower and they are prepared to make analysis-specific choices on how to handle
+  gaps or inconsistencies in the data.
+- Site-level analyses where completeness and timeseries consistency is more
+  important than matching specific days may prefer to use a gridded product.
+- Regional analyses commonly use gridded reanalysis or model outputs (such as
+  NARR or NLDAS) whose coverage matches the scale of the analysis.
+- Global or long-term analyses typically rely on products with broad spatial and
+  temporal coverage like CRUNCEP, ERA5, or GLDAS.
+- Future simulations require climate model outputs (e.g. CMIP5).
 
 ### Summary of available drivers {-}
 

book_source/03_topical_pages/12_troubleshooting-pecan.Rmd

@@ -1,9 +1,14 @@
 # Troubleshooting and Debugging PEcAn
 
-This chapter provides guidance for diagnosing and resolving common issues encountered when installing, configuring, and running PEcAn workflows. Problems may arise from web interface configuration, file system paths, model integration, or internal workflow execution.
-The sections below document frequently encountered errors as well as general debugging techniques that can help identify the source of a problem.
+This chapter provides guidance for diagnosing and resolving common
+issues encountered when running PEcAn workflows. Problems may arise
+from configuration errors, data availability issues, model failures,
+or system-level dependencies.
 
-### General troubleshooting approach {-}
+Start with the general troubleshooting guidance below, then refer to
+specific sections for detailed solutions.
+
+## General troubleshooting approach {-}
 
 When troubleshooting PEcAn issues:
 
@@ -13,13 +18,14 @@ When troubleshooting PEcAn issues:
 - Reproduce the issue with a minimal workflow.
 - Use R debugging tools such as `debug()`, `traceback()`, and `browser()`.
 
-### Common issues covered in this chapter {-}
 
-- [Cookies and PEcAn web pages](#cookies-and-pecan-web-pages)
-- [`mkdir()` warnings](#warning-mkdir-function.mkdir-no-such-file-or-directory)
-- [PFT mapping issues in ED models](#after-creating-a-new-pft-the-tag-for-pft-not-passed-to-config.xml-in-ed)
+## Common topics
+- [Workflow failures](#workflow-failures)
+- [Database issues](#database-issues)
+- [Model errors](#model-errors)
+- [Docker-related problems](#docker-issues)
 - [Debugging](#debugging)
-- [Useful scripts](#useful-scripts)
+
 
 ## Cookies and pecan web pages
 

book_source/03_topical_pages/93_installation/00_installation_index.Rmd

@@ -1,3 +1,8 @@
 # Installation details
 
+This page describes advanced installation options and system
+requirements for running PEcAn outside of Docker-based setups.
+Most users should follow the standard installation guide unless
+custom configurations are required.
+
 This chapter contains details about installing and maintaining the uncontainerized version of PEcAn on a virtual machine or a server. If you are running PEcAn inside of Docker, many of the particulars will be different and you should refer to the [docker](developer-workflows/docker-index.html) chapter instead of this one.