From 8bb9a9d668bc0299c26cbddca4b52276fe170eb7 Mon Sep 17 00:00:00 2001
From: Fabian Bernhard <10245680+fabern@users.noreply.github.com>
Date: Mon, 8 Jul 2024 16:30:42 +0200
Subject: [PATCH] Formalize pkg structure

---
 DESCRIPTION                   |  7 ++++---
 NAMESPACE                     | 20 ++++++++++++++++++++
 R/df_to_grid.R                |  9 +++++----
 R/extract_nc.R                |  1 +
 R/gc_rsofun_driver_era5.R     |  4 ++--
 R/nc_to_df.R                  |  2 +-
 R/plot_map4.R                 |  7 +++++--
 vignettes/event_detection.Rmd |  2 +-
 8 files changed, 39 insertions(+), 13 deletions(-)
 create mode 100644 NAMESPACE

diff --git a/DESCRIPTION b/DESCRIPTION
index 5742046..559eeb0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,8 +18,8 @@ Authors@R: c(
                 role = c("cph", "fnd"))
            )
 Description: A collection of diverse functions to serve data wrangling and visualisations for research by the research group for Geocomputation and Earth Observation (GECO). 
-URL: https://github.com/geco-bern/GECOr
-BugReports: https://github.com/geco-bern/GECOr/issues
+URL: https://github.com/geco-bern/rgeco
+BugReports: https://github.com/geco-bern/rgeco/issues
 Depends:
     R (>= 4.2)
 Imports:
@@ -41,7 +41,8 @@ Suggests:
     covr,
     testthat
 License: AGPL-3
+Encoding: UTF-8
 LazyData: true
 ByteCompile: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..5a80896
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,20 @@
+# Generated by roxygen2: do not edit by hand
+
+export(align_events)
+export(calc_patm)
+export(calc_vp)
+export(calc_vp_inst)
+export(calc_vpd)
+export(calc_vpd_inst)
+export(collect_drivers_sofun)
+export(df_to_grid)
+export(extract_nc)
+export(gc_era5_request)
+export(gc_rsofun_driver_era5)
+export(get_consecutive)
+export(nc_to_df)
+export(plot_map4)
+export(prepare_setup_sofun)
+export(read_nc_onefile)
+export(write_nc2)
+importFrom(magrittr,"%>%")
diff --git a/R/df_to_grid.R b/R/df_to_grid.R
index b8e7db4..49259c3 100644
--- a/R/df_to_grid.R
+++ b/R/df_to_grid.R
@@ -8,8 +8,9 @@
 #' @param varnam A character string specifying the variable name in the data frame.
 #' @param lonnam A character string specifying the column name containing longitude
 #' values. Defaults to \code{"lon}.
-#' @param latnam A character string specifying the column name containing longitude
+#' @param latnam A character string specifying the column name containing latitude
 #' values. Defaults to \code{"lat}.
+#'
 #' @return A 2D matrix
 #' @export
 #'
@@ -17,14 +18,14 @@ df_to_grid <- function(df, varnam, lonnam = "lon", latnam = "lat"){
 
   lonvals <- unique(df[[lonnam]])
   latvals <- unique(df[[latnam]])
-  
+
   ## make sure no gaps
   lonvals2 <- seq(min(lonvals), max(lonvals), by = min(abs(lonvals[2:(length(lonvals))] - lonvals[1:(length(lonvals)-1)])))
   latvals2 <- seq(min(latvals), max(latvals), by = min(abs(latvals[2:(length(latvals))] - latvals[1:(length(latvals)-1)])))
-  
+
   # ## Expand to all gridcells
   # # grid <- paste0(dir, "s1_fapar3g_v3_global.fland.nc")
-  # 
+  #
   # if (grid=="halfdeg"){
   #   out <- list(
   #     lon = seq(from = -179.75, to = 179.75, by = 0.5),
diff --git a/R/extract_nc.R b/R/extract_nc.R
index b306ce6..7c416ae 100644
--- a/R/extract_nc.R
+++ b/R/extract_nc.R
@@ -7,6 +7,7 @@
 #' to be extracted (points organised by rows).
 #' @param filn A character string specifying the path to a raster file that can be read with
 #' \code{raster::brick} or \code{raster::raster}.
+#' @param get_time A boolean specifying whether to extract time from the raster file.
 #' @return A data frame of the same number of rows as \code{df} with extracted data
 #' nested in column \code{data}.
 #' @export
diff --git a/R/gc_rsofun_driver_era5.R b/R/gc_rsofun_driver_era5.R
index 2f9b78a..27dd059 100644
--- a/R/gc_rsofun_driver_era5.R
+++ b/R/gc_rsofun_driver_era5.R
@@ -1,4 +1,4 @@
-#' Format an ERA5 based {rsofun} driver
+#' Format an ERA5 based \code{rsofun} driver
 #'
 #' Uses the ECMWF CDS workflow API to summarize rsofun driver files
 #' on a daily time step.
@@ -7,7 +7,7 @@
 #' @param site_info site info data frame including a site name, location, and
 #'  other ancillary variables
 #'
-#' @return ERA5 based {rsofun} drivers for a point location specified in the
+#' @return ERA5 based \code{rsofun} drivers for a point location specified in the
 #'  site_info parameter
 #' @export
 
diff --git a/R/nc_to_df.R b/R/nc_to_df.R
index 4e93fc2..0ce0372 100644
--- a/R/nc_to_df.R
+++ b/R/nc_to_df.R
@@ -4,7 +4,7 @@
 #' information
 #'
 #' @param obj Either character string specifying the NetCDF file path to be read or a
-#' object returned by function \link{GECOr::read_nc_onefile()} or \link{GECOr::nc_to_df()}.
+#' object returned by function \link{rgeco::read_nc_onefile()} or \link{rgeco::nc_to_df()}.
 #' @param varnam A character string specifying the variable name in the NetCDF file.
 #' @param lon A numeric vector specifying longitude values. Defaults to \code{NA}.
 #' @param lat A numeric vector specifying latitude values. Defaults to \code{NA}.
diff --git a/R/plot_map4.R b/R/plot_map4.R
index 74fd47b..b54584f 100644
--- a/R/plot_map4.R
+++ b/R/plot_map4.R
@@ -3,7 +3,7 @@
 #' Returns a cowplot object for a global map plot.
 #'
 #' @param obj An object, either a \code{SpatRaster} (returned from a \code{terra::rast()} function call),
-#' or a list returned from a \code{GECOr::read_nc_onefile()} function call.
+#' or a list returned from a \code{rgeco::read_nc_onefile()} function call.
 #' @param varnam A charachter string specifying the variable name. Optional and
 #' used only if \code{obj} is a \code{SpatRaster} with multiple variables. If
 #' \code{obj} is a rbeni-nc object (returned by \code{read_nc_onefile()}),
@@ -44,7 +44,10 @@
 #' @param is_boolean A logical specifying whether the raster contains boolean values (either \code{TRUE} or \code{FALSE}). Defaults to \code{FALSE}.
 #' @param combine A boolean specifying whether the map and the colorscale should be combined using cowplot.
 #' Defaults to \code{TRUE}. If \code{FALSE}, a list of elements are retruned, where elements are the ggplot2 plot object
-#' and the coloscale object returned by the call to \link{plot_discrete_cbar}.
+#' and the coloscale object returned by the call to \code{plot_discrete_cbar}.
+#' @param ... ...
+#' @importFrom grDevices colorRampPalette
+#' @importFrom methods as
 #'
 #' @return A ggplot object for a global map plot.
 #' @export
diff --git a/vignettes/event_detection.Rmd b/vignettes/event_detection.Rmd
index 69aed54..ddde2a1 100644
--- a/vignettes/event_detection.Rmd
+++ b/vignettes/event_detection.Rmd
@@ -19,7 +19,7 @@ library(ggplot2)
 library(rgeco)
 ```
 
-An event is defined here as consecutive time steps where a certain condition is fulfilled - yielding a vector of a logical (boolean) variable. This vignette demonstrates how such events are derived from the boolean vector using the GECOr function `get_consecutive()`, and a time series data frame re-arranged and labelled with sequential time steps into a given event (`eventstep`), using the GECOr function `align_events()`. 
+An event is defined here as consecutive time steps where a certain condition is fulfilled - yielding a vector of a logical (boolean) variable. This vignette demonstrates how such events are derived from the boolean vector using the rgeco function `get_consecutive()`, and a time series data frame re-arranged and labelled with sequential time steps into a given event (`eventstep`), using the rgeco function `align_events()`. 
 
 ## Prepare data