NetCDF4 and CWatM support (#27)

Implements proper NetCDF support for MET Nordic downloads and includes the capability to convert them to CWatM compatible files. 

Also:

- reduced import dependencies, moved most non-critical to "Suggests"
- removed `ncdf` and `continue` parameter specific code from `get_metno_reanalysis3()`
- moved SWAT+ specific functions to own .R file
- moved  `get_metno_reanalysis3()` support functions to bottom of .R file
- updated documentation
- updated vignette for MET Nordic usage.

Author: moritzshore

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: miljotools
 Title: An R package hosting a variety of useful functions for
     environmental data handling and anaylsis
-Version: 0.5.0
+Version: 0.6.0
 Author: Moritz Shore
 Maintainer: Moritz Shore <[email protected]>
 Description: A few useful functions for environemental data processing and
@@ -16,32 +16,34 @@ Imports:
     abind,
     crayon,
     dplyr,
-    fs,
-    ggplot2,
-    ggrepel,
-    ggtern,
     lubridate,
     mapview,
     ncdf4,
-    plotly,
     purrr,
-    RColorBrewer,
     readr,
-    readxl,
     sf,
     stringr,
+    terra,
     tibble,
-    utils,
-    vroom,
-    writexl
+    vroom
 Suggests:
     devtools,
+    doParallel,
     euptf2,
+    fs,
+    ggplot2,
+    ggrepel,
+    ggtern,
     knitr,
+    lattice,
+    plotly,
+    RColorBrewer,
     Rdpack,
+    readxl,
     rmarkdown,
     roxygen2,
-    SWATprepR
+    SWATprepR,
+    writexl
 VignetteBuilder: 
     knitr
 Remotes: 

NAMESPACE

@@ -1,14 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
 export(classify_soil)
-export(convert_to_cwatm)
-export(cwatm_hourly_to_daily_ncdf4)
+export(cwatm_convert_nc)
 export(get_metno_reanalysis3)
+export(metnordic_aggregate)
+export(metnordic_buildquery)
+export(metnordic_coordwindow)
+export(metnordic_download)
+export(metnordic_merge)
+export(metnordic_reproject)
+export(mt_print)
 export(reanalysis3_daily)
 export(reanalysis3_swatinput)
 export(swat_weather_input_chain)
 export(thermopluviogram)
-importFrom(RColorBrewer,brewer.pal)
+import(ncdf4)
 importFrom(abind,abind)
 importFrom(crayon,bgBlue)
 importFrom(crayon,bgCyan)
@@ -21,15 +27,14 @@ importFrom(crayon,bold)
 importFrom(crayon,cyan)
 importFrom(crayon,green)
 importFrom(crayon,italic)
-importFrom(crayon,magenta)
-importFrom(crayon,red)
 importFrom(crayon,underline)
 importFrom(crayon,white)
 importFrom(crayon,yellow)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,filter)
+importFrom(dplyr,first)
 importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
 importFrom(dplyr,last)
@@ -39,11 +44,6 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tibble)
-importFrom(fs,dir_ls)
-importFrom(ggplot2,aes)
-importFrom(ggrepel,geom_label_repel)
-importFrom(ggtern,ggtern)
-importFrom(grDevices,colorRampPalette)
 importFrom(lubridate,as_datetime)
 importFrom(lubridate,date)
 importFrom(lubridate,day)
@@ -52,21 +52,12 @@ importFrom(lubridate,month)
 importFrom(lubridate,year)
 importFrom(mapview,mapview)
 importFrom(ncdf4,nc_close)
-importFrom(ncdf4,nc_create)
 importFrom(ncdf4,nc_open)
 importFrom(ncdf4,ncatt_get)
-importFrom(ncdf4,ncdim_def)
-importFrom(ncdf4,ncvar_add)
-importFrom(ncdf4,ncvar_def)
 importFrom(ncdf4,ncvar_get)
-importFrom(ncdf4,ncvar_put)
-importFrom(plotly,layout)
-importFrom(plotly,plot_ly)
 importFrom(purrr,map)
-importFrom(purrr,map2)
 importFrom(readr,read_csv)
 importFrom(readr,write_csv)
-importFrom(readxl,read_excel)
 importFrom(sf,read_sf)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
@@ -76,15 +67,12 @@ importFrom(sf,st_crs)
 importFrom(sf,st_intersects)
 importFrom(sf,st_transform)
 importFrom(sf,st_zm)
-importFrom(stats,reorder)
 importFrom(stringr,str_pad)
 importFrom(stringr,str_remove)
-importFrom(stringr,str_remove_all)
+importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_split)
-importFrom(tibble,tibble)
-importFrom(utils,packageVersion)
-importFrom(utils,read.table)
-importFrom(utils,write.csv)
-importFrom(vroom,vroom)
-importFrom(writexl,write_xlsx)
+importFrom(terra,crs)
+importFrom(terra,project)
+importFrom(terra,rast)
+importFrom(terra,writeCDF)

R/cwatm_convert_nc.R

@@ -0,0 +1,79 @@
+#' Convert MET Nordic Files to CWatM Meteo Input
+#'
+#' This function converts a projected MET Nordic file (from
+#' `metnordic_reproject()`) to be compatible with CWatm. This function mainly
+#' just changes the dimension names from easting and northing to x and y and
+#' swapes variable order but has a crap load of boiler plate because... well..
+#' ncdf4.
+#'
+#' Code largely adapted from this handy guide:
+#' ([link](https://pjbartlein.github.io/REarthSysSci/netCDF.html#create-and-write-a-projected-netcdf-file))
+#' from Pat Bartlein, [email protected]
+#'
+#' @seealso [metnordic_reproject()]
+#'
+#' @author Moritz Shore
+#'
+#' @param infile String: path to projected MET Nordic .nc file as created by `metnordic_reproject()`
+#' @param outfile String: path and file name to desired output file
+#'
+#' @returns Path to outfile
+#' @export
+#'
+#' @examples
+#' #TODO
+#' @import ncdf4
+cwatm_convert_nc <- function(infile, outfile){
+  ### Re-reading it and changing attributes to x and y (This is only needed for CWATM.. TODO: seperate function?)
+  to_reform <- nc_open(infile)
+  main_var <- to_reform$var %>% names() %>% nth(1)
+
+  ## getting data
+
+  met_var <- ncvar_get(to_reform, main_var)
+  met_var_att <- ncatt_get(to_reform, main_var)
+  easting <- ncvar_get(to_reform,"easting")
+  easting_att <- ncatt_get(to_reform, "easting")
+  northing <- ncvar_get(to_reform,"northing")
+  northing_att <- ncatt_get(to_reform, "northing")
+  time <- ncvar_get(to_reform, "time")
+  time_att <- ncatt_get(to_reform, "time")
+  crs <- ncvar_get(to_reform, "crs")
+  crs_att <- ncatt_get(to_reform, "crs")
+
+  ## Dim Definitions
+  xdef <- ncdf4::ncdim_def(name = "x", units = "meters", vals =  easting, longname = "x", )
+  ydef <- ncdf4::ncdim_def(name = "y", units = "meters", vals =  northing, longname = "y")
+  timedef <- ncdf4::ncdim_def(name = "time", units = time_att$units, vals = time, calendar = time_att$calendar, longname = time_att$long_name)
+
+  ## Var Definitions
+  fillvalue <- 1e32
+  main_var_def <- ncvar_def(name = main_var, units = met_var_att$units, dim = list(xdef,ydef,timedef), missval = met_var_att$`_FillValue`, prec = "float")
+  crs_def <- ncvar_def(name = "crs", units = "", dim = list(), prec = "integer")
+
+  # Creating the new ncfile
+  proj_nc <- nc_create(filename = outfile, vars = list(crs_def, main_var_def), force_v4 = T) # the order of this might be important
+
+  # Adding data
+  ncvar_put(nc = proj_nc, varid = main_var, vals = met_var)
+
+  # Adding Attributes
+  ncatt_put(proj_nc, varid = main_var, attname = "grid_mapping", "crs")
+
+  ncatt_put(proj_nc, varid = "crs", attname = "crs_wkt", crs_att$crs_wkt)
+  ncatt_put(proj_nc, varid = "crs", attname = "spatial_ref", crs_att$spatial_ref)
+  ncatt_put(proj_nc, varid = "crs", attname = "proj4", crs_att$proj4)
+  ncatt_put(proj_nc, varid = "crs", attname = "geotransform", crs_att$geotransform)
+
+  ncatt_put(nc = proj_nc, varid = 0 ,attname = "Conventions", attval = ncatt_get(to_reform, 0, "Conventions")[[2]])
+  ncatt_put(nc = proj_nc, varid = 0 ,attname = "created_by", attval = ncatt_get(to_reform, 0, "created_by")[[2]])
+  ncatt_put(nc = proj_nc, varid = 0 ,attname = "date", attval = ncatt_get(to_reform, 0, "date")[[2]])
+  ncatt_put(nc = proj_nc, varid = 0 ,attname = "institution", attval = ncatt_get(to_reform, 0, "institution")[[2]])
+  ncatt_put(nc = proj_nc, varid = 0 ,attname = "history", attval = ncatt_get(to_reform, 0, "history")[[2]])
+
+  # Saving
+  nc_close(to_reform)
+  nc_close(proj_nc)
+
+  return(outfile)
+}

R/globals.R

@@ -1,2 +1,2 @@
-# bandaid
+# bandaid (metnorenal3.R "metnorenal3.R --> rename(max_temp = air_temperature_2m)"
 utils::globalVariables(c("daily", "air_temperature_2m"))