From 2e62f57485d1929093a04cc301ca31b01f4289af Mon Sep 17 00:00:00 2001
From: Fabian Bernhard <10245680+fabern@users.noreply.github.com>
Date: Thu, 19 Dec 2024 18:34:32 +0100
Subject: [PATCH] Add missing documentation *.Rd-files

---
 DESCRIPTION                  |  2 +-
 man/collect_drivers_sofun.Rd | 38 ++++++++++++++++++++++++++++++++++
 man/prepare_setup_sofun.Rd   | 40 ++++++++++++++++++++++++++++++++++++
 3 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 man/collect_drivers_sofun.Rd
 create mode 100644 man/prepare_setup_sofun.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 23b9b0e..eb2d09a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -46,7 +46,7 @@ Remotes:
     bczernecki/climate
 LazyData: true
 ByteCompile: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests:
     ggplot2,
     rmarkdown,
diff --git a/man/collect_drivers_sofun.Rd b/man/collect_drivers_sofun.Rd
new file mode 100644
index 0000000..bdb547f
--- /dev/null
+++ b/man/collect_drivers_sofun.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/collect_drivers_sofun.R
+\name{collect_drivers_sofun}
+\alias{collect_drivers_sofun}
+\title{Collect all drivers}
+\usage{
+collect_drivers_sofun(site_info, params_siml, meteo, fapar, co2, params_soil)
+}
+\arguments{
+\item{site_info}{A data frame containing site meta info (rows for sites). 
+Required columns are: \code{"sitename", "year_start", 
+"year_end", "lon", "lat", "elv"}. See \code{\link{prepare_setup_sofun}} for
+details.}
+
+\item{params_siml}{A nested data frame with rows for each site containing 
+simulation parameters for SOFUN. See \code{\link{run_pmodel_f_bysite}} or
+\code{\link{run_biomee_f_bysite}}.}
+
+\item{meteo}{A nested data frame with rows for each site and meteorological
+forcing data time series nested inside a column named \code{"data"}.}
+
+\item{fapar}{A nested data frame with rows for each site and fAPAR 
+forcing data time series nested inside a column named \code{"data"}.}
+
+\item{co2}{A nested data frame with rows for each site and CO2 
+forcing data time series nested inside a column named \code{"data"}.}
+
+\item{params_soil}{Soil texture data descriptor, a data frame with columns
+\code{"layer", "fsand", "fclay", "forg" } and \code{"fgravel"}.}
+}
+\value{
+A \code{rsofun} input data frame (see \link{p_model_drivers} for a detailed
+description of its structure and contents).
+}
+\description{
+Collect all drivers for site-level simulations 
+into a nested data frame with one row for each site.
+}
diff --git a/man/prepare_setup_sofun.Rd b/man/prepare_setup_sofun.Rd
new file mode 100644
index 0000000..97784b8
--- /dev/null
+++ b/man/prepare_setup_sofun.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prepare_setup_sofun.R
+\name{prepare_setup_sofun}
+\alias{prepare_setup_sofun}
+\title{Complements the setup settings}
+\usage{
+prepare_setup_sofun(site_info, params_siml)
+}
+\arguments{
+\item{site_info}{A character string specifying the path to the site meta 
+information file, or a data frame containing the site meta info. Required
+columns are:
+\describe{
+\item{\code{sitename}}{Name of the site, must be the first column of the file.}
+\item{\code{lon}}{Longitude of site.}
+\item{\code{lat}}{Latitude of site.}
+\item{\code{elv}}{Elevation of site, in m.}
+\item{\code{year_start, year_end}}{Years for which the simulation is to be done,
+corresponding to data availability from site.}
+}}
+
+\item{params_siml}{A named list containing the simulation parameters
+for SOFUN.}
+}
+\value{
+A data frame (tibble) containing the site meta information, 
+complemented by column \code{params_siml} which is a nested list 
+of complemented simulation parameters.
+}
+\description{
+Complements the settings based on the site meta info CSV file or data frame.
+}
+\examples{
+\dontrun{
+ setup <- prepare_setup_sofun(
+   site_info = site_info,
+   params_siml = params_siml
+  )
+}
+}