dlebauer

[
  {
    "pecan_events_version": "0.1.0",
    "site_id": "02f8ecd6d492badc",
    "events": [
      {
        "event_type": "irrigation",
        "date": "2016-01-05",
        "amount_mm": 40,
        "method": "soil"

dlebauer

0	2004	  1	 0.0	0.02083	-6.260e+00	-6.891852	0.000000	 0.000000	 235.0	 264.344	 148.33	1	0.6
0	2004	  1	 0.5	0.02083	-6.400e+00	-6.892737	0.000000	 0.000000	 230.0	 264.034	 149.26	1	0.6
0	2004	  1	 1.0	0.02083	-6.490e+00	-6.893408	0.000000	 0.000000	 229.0	 264.579	 147.67	1	0.6
0	2004	  1	 1.5	0.02083	-6.640e+00	-6.893958	0.000000	 0.000000	 222.0	 262.528	 150.38	1	0.6
0	2004	  1	 2.0	0.02083	-6.770e+00	-6.894324	0.000000	 0.000000	 215.0	 260.710	 153.69	1	0.6
0	2004	  1	 2.5	0.02083	-6.720e+00	-6.894507	0.000000	 0.000000	 223.0	 264.893	 147.10	1	0.6
0	2004	  1	 3.0	0.02083	-6.790e+00	-6.894751	0.000000	 0.000000	 219.0	 263.478	 149.13	1	0.6
0	2004	  1	 3.5	0.02083	-6.820e+00	-6.894873	0.000000	 0.000000	 220.0	 264.593	 147.28	1	0.6
0	2004	  1	 4.0	0.02083	-6.760e+00	-6.894995	0.000000	 0.000000	 231.0	 270.481	 137.97	1	0.6
0	2004	  1	 4.5	0.02083	-6.930e+00	-6.895178	0.000000	 0.000000	 226.0	 270.428	 138.20	1	0.6

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.

dlebauer

#	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

dlebauer

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")
  

dlebauer

Equivalent Commands: Slurm vs SGE/OGS

1. Equivalent of seff (Job Efficiency Report)

Slurm:

seff <job_id>

SGE/OGS:

qacct -j 

dlebauer

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() |>

dlebauer

# 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

dlebauer

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) %>%

dlebauer

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;