David LeBauer dlebauer

Events format

This specification defines a model-agnostic intermediate format for events, analogous to the PEcAn met standard. It is intended to:

Consolidate events from diverse sources (e.g. RS, farmer surveys, literature)
Represent ensemble-reesolved realizations of events that can be used in modeling workflows.
Be consumed by a model specific event parser like parse.events.<model> that can be called by write.configs.<model>.

This format for events that is based on the format used in the fieldactivity nested within a geoJSON data structure[^1], but has been modified to be more generalized, and focused on aggregating data from many sources that have varied types of information.

#	Category / File	Symptom / Error (abridged)	Root Cause / Context	Fix applied (see commit/patch)
1	GitHub Pages deploy `.github/workflows/publish.yaml`	`deploy-pages` 404 – “Getting signed artifact URL failed”	Deploy job could not find a Pages‑type artifact	Switched to `actions/upload-artifact@v4` and named it `github-pages`, which `deploy-pages@v4` accepts
2	Actions tag mismatch	“Missing download info for actions/upload‑artifact@v3”	Referenced tag never existed	Bumped to `upl

Equivalent Commands: Slurm vs SGE/OGS

1. Equivalent of `seff` (Job Efficiency Report)

Slurm:

seff <job_id>

SGE/OGS:

qacct -j

	library(tidyverse)
	# system.time(load("~/ccmmf/LandIQ_data/crops_all_years.RData"))
	crops_all <- data.table::fread( # ~50% faster than load!
	"~/ccmmf/LandIQ_data/crops_all_years.csv"
	)
	dwr_2018 <- terra::vect(
	"~/ccmmf/LandIQ_data/LandIQ_shapefiles/i15_Crop_Mapping_2018_SHP/i15_Crop_Mapping_2018.shp"
	) \|>
	terra::project("epsg:3310")

	library(xml2)
	library(yaml)

	# note: does not handle XML attributes or namespaces.
	# should work for simple xml structure used by PEcAn

	# Convert XML to YAML
	xml2yml <- function(xml_string) {
	yaml_string <- xml_string \|>
	read_xml() \|>

	# to get the original version of the eCO2 file
	download.file('https://github.com/cran/SoilR/raw/1.1-23/data/eCO2.rda',
	'eCO2.rda')
	load('eCO2.rda')

	library(SoilR)
	library(rstan)
	totalC_t0 <- 7.7; # not included in data, so hard code here
	t0 <- 0;
	N_t <- 25; # calculated by inspection

	library(tidyverse)
	# x <- read_csv('C:/Users/David/Downloads/Untitled spreadsheet - Sheet1.csv')
	#
	# colnames(x)
	# dim(x)
	#
	# xx <- x %>%
	# rename(organ = `Plant tissue`,
	# soil = `Soil \n Concentration`,
	# bcf = BCF) %>%

	select extract(year from created_at) as year, container_type, count(*) as n from dbfiles where id between 1000000000 and 2000000000 group by container_type, year order by container_type, year;

	select created_user_id, container_type, count(*) as n from dbfiles where id between 1000000000 and 2000000000 group by container_type, created_user_id order by n desc;

	select * from dbfiles where created_user_id is not null;

	select extract(year from created_at) as year, created_user_id, container_type, count(*) as n from dbfiles where id between 9000000000 and 10000000000 group by container_type, created_user_id, year order by year, container_type, created_user_id;

	select null as year, created_user_id, container_type, count(*) as n from dbfiles where id between 9000000000 and 10000000000 group by container_type, created_user_id order by container_type, created_user_id;

	"site_id","sitename","lon","lat","format_name","file_path","filename","start_date","end_date","duration","created_at"
	"1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/only_co2/ED_driver/Ed_driver/","Cmip5_RCP8.5_Present_day_temp","1/1/2006 06:00:00","1/1/2100 05:59:00","93 years 11 mons 30 days 23:59:00","6/4/2022 18:19:38.277567"
	"1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/with_co2/ED_driver/","CMIP5_RCP8.5_with_Co2","1/1/2006 06:00:00","13/12/2100 05:59:00","94 years 11 mons 11 days 23:59:00","6/4/2022 18:17:08.145333"
	"1000026939","Moody AFB","-83.1753","30.984401","ed.met_driver_header files format","/projectnb/dietzelab/mccabete/test_pecan/cogongrass_projections/GFDL/moody_AFB/resampled_present_day/ED_driver","Cmip5_Present_day","1/1/2006 06:00:00","1/1/2100 05:59:00","93 y