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# 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

"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) %>% 

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

library(PEcAn.DB)


# given PFT name but no model name???
# 
#    if select count(*) from pfts where name= <PFT name> > 1 then
#       select modeltype_id from pfts where name = <PFT name>
#           if > 1 modeltype_id 
#              select name from modeltypes where id = modeltype_id 
#              return these model names as messsage asking which one user wants

dlebauer

"ensemble","npp","site","mort2","growth_resp_factor","leaf_turnover_rate","leaf_width","nonlocal_dispersal","fineroot2leaf","root_turnover_rate","seedling_mortality","stomatal_slope","quantum_efficiency","Vcmax","r_fract","cuticular_cond","root_respiration_rate","Vm_low_temp","SLA","mean_annual_temp","mean_diurnal_range","isothermality","temp_seasonality","max_temp_warmest month","min_temp_coldest_month","temp_annual_range","mean_temp_wettest_quarter","mean_temp_driest_quarter","mean_temp_warmest_quarter","mean_temp_coldest_quarter","mean_annual_precip","precip_wettest_month","precip_driest_month","precip_seasonality","precip_wettest_quarter","precip_driest_quarter","precip_warmest_quarter","precip_coldest_quarter"
"1",3.28794455528259,"WL",13.4941024361116,0.199588976581073,5.22541143636259,4.54482864260038,0.160406564989664,2.80249135407987,0.158750654546649,0.964989573638797,3.78549864797161,0.0563503122493127,20.7691338359971,0.230258975287167,20938.2246204727,7.90012049814983,10.8950676841584,39.22618746

dlebauer

{
  "dimensions": {
    "wavelength": 939
  },
  "variables": {
    "wavelength": {
      "shape": ["wavelength"],
      "type": "double",
      "attributes": {
        "long_name": "Hyperspectral Wavelength",

dlebauer