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Updated FATES output time variable to fix issue #1939. #1953

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Jun 1, 2018
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Updated FATES output time variable to fix issue #1939. #1953

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f51ef6e
Updated FATES output time variable to fix issue #1939. Current fix is…
May 31, 2018
2b60089
Updated CHANGELOG.md
May 31, 2018
3d1f82b
Merge branch 'develop' into fix_fates_output_dates
May 31, 2018
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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9 changes: 5 additions & 4 deletions models/fates/R/model2netcdf.FATES.R
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Expand Up @@ -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)) {
Expand Down Expand Up @@ -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
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