Merge pull request #1953 from serbinsh/fix_fates_output_dates

Updated FATES output time variable to fix issue #1939.

CHANGELOG.md

@@ -9,6 +9,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ## [Unreleased]
 
 ### Fixes
+- Fixed issue #1939 which corrects output time vector for FATES output
 - Update to read.output to look for and read only PEcAn formatted .nc output based on the pecan standard filename format of YYYY.nc.  Solves issues with models such as FATES and dvm-dos-tem where the original model output is also in .nc file format and was not ignored by read.output, causing errors with output parsing and plotting with Shiny. Removed deprecated function convert.outputs
 - PEcAn.data.atmosphere: 
     - download.Geostreams is pickier about formatting start/end datess, for fewer surprises in result timestamps

models/fates/R/model2netcdf.FATES.R

@@ -53,6 +53,7 @@ model2netcdf.FATES <- function(outdir) {
     files <- dir(outdir, "*clm2.h0.*.nc", full.names = TRUE)
     file.dates <- as.Date(sub(".nc", "", sub(".*clm2.h0.", "", files)))
     years <- lubridate::year(file.dates)
+    init_year <- unique(years)[1]
 
     ## Loop over years
     for (year in unique(years)) {
@@ -84,11 +85,11 @@ model2netcdf.FATES <- function(outdir) {
         sitelat <- ncdf4::ncvar_get(ncin,"lat")
         sitelon <- ncdf4::ncvar_get(ncin,"lon")
         ## time variable based on internal calc, nc$dim$time is the FATES output time
-        t <- ncdim_def(name = "time", units = paste0("days since ", year, "-01-01 00:00:00"),
-                       vals = as.vector(time), calendar = "standard", 
+        t <- ncdf4::ncdim_def(name = "time", units = paste0("days since ", init_year, "-01-01 00:00:00"),
+                       vals = as.vector(time), calendar = "noleap", 
                        unlim = TRUE)  # a direct analog of internal FATES output dim "time"
-        lat <- ncdim_def("lat", "degrees_north", vals = as.numeric(sitelat), longname = "coordinate_latitude")
-        lon <- ncdim_def("lon", "degrees_east", vals = as.numeric(sitelon), longname = "coordinate_longitude")
+        lat <- ncdf4::ncdim_def("lat", "degrees_north", vals = as.numeric(sitelat), longname = "coordinate_latitude")
+        lon <- ncdf4::ncdim_def("lon", "degrees_east", vals = as.numeric(sitelon), longname = "coordinate_longitude")
         xyt <- list(lon, lat, t)
 
         ### build netCDF data