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

/* required styles */

.leaflet-map-pane,
.leaflet-tile,
.leaflet-marker-icon,
.leaflet-marker-shadow,
.leaflet-tile-pane,
.leaflet-overlay-pane,
.leaflet-shadow-pane,
.leaflet-marker-pane,

dlebauer

Sorghum Lines for Whole-Genome Resequencing

accession	sample identifier	taxid	organism common name	subspecific genetic lineage rank	panel	subspecific genetic lineage name	ploidy	number of replicons	estimated size	source material identifiers	sample name
PI564163	BTx623	4558	sorghum	cultiva

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;

dlebauer

select
	site_id,
	sites.sitename,
	st_X(sites.geometry) as lon,
	st_y(sites.geometry) as lat,
	formats.name as format_name,
	dbfiles.file_path as file_path,
	inputs.name as filename,
	inputs.start_date,
	inputs.end_date,

dlebauer

"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

dlebauer

library(traits)
library(dplyr)
library(ggplot2)
options(betydb_url = 'https://www.betydb.org/',
        betydb_api_version = 'v1'
) 
yields <- betydb_search(result_type = 'yields', genus = 'Panicum', limit = 'none')

treatments <- betydb_query(table = 'treatments', limit = 'none') %>% 
  dplyr::mutate(treatment_id = id) %>%