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dlebauer / season_4_irrigation.sql
Last active May 27, 2022 16:47
irrigation zones https://github.com/terraref/computing-pipeline/issues/400
begin;
rollback;
insert into sites (sitename, geometry) VALUES ('MAC Field Scanner Season 4 Irrigation Zone 1',
(select st_union(geometry) as geometry
from sites
where sitename ~ 'Column (1|2|3|4)$'
and sitename like 'MAC Field Scanner Season 4%'));
/*Zone 2*/
insert into sites (sitename, geometry) VALUES
@dlebauer
dlebauer / map.geojson
Last active May 27, 2022 16:22
TERRA REF Season 4 irrigation treatments
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@dlebauer
dlebauer / all_s4_6_traits.sql
Last active May 4, 2022 16:07
two approaches to retrieving canopy height + canopy cover data
\copy (select raw_date, sitename, cultivar, trait, method, mean
from traits_and_yields_view_private
sitename like '%Season 4%' and sitename ~ 'Range (20|30)$')
to ~/season4traits.csv delimiter ',' csv header;
\copy (select raw_date, sitename, cultivar, trait, method, mean
from traits_and_yields_view_private
sitename like '%Season 6%' and sitename ~ 'Range (20|30)$')
to ~/season6traits.csv delimiter ',' csv header;
@dlebauer
dlebauer / srer_priors.tsv
Created March 30, 2022 23:34
pft variable phylogeny distn parama paramb n citation
forb_priors mort2 plants gamma 1.47 0.0578 0 LeBauer 2010 Expert Prior
forb_priors growth_resp_factor grass beta 2.63 6.52 0 LeBauer 2010 Expert Prior
forb_priors fineroot2leaf grass lnorm 0.811 0.843 0 Chapin 2002 Principles of Terrestrial Ecosystem Ecology
forb_priors root_turnover_rate grass weibull 1.67 0.657 66 Gill 2000 Global patterns of root turnover for terrestrial ecosystems
forb_priors seedling_mortality monocots beta 3.61 0.433 0 LeBauer 2010 Expert Prior
forb_priors Vcmax lnorm 4.51 0.64 19 Wullschleger 1993 Biochemical Limitations to Carbon Assimilation in C3 Plants: A Retrospective Analysis of the A/Ci Curves from 109 Species
forb_priors root_respiration_rate angiosperm gamma 4.95 0.762 36 George 2003 Fine-root respiration in a loblolly pine and sweetgum forest growing in elevated CO2
forb_priors r_fract plants beta 2 4 0 LeBauer 2010 Expert Prior
forb_priors c2n_leaf grass gamma 4.18 0.13 95 Wright 2004 The world-wide leaf economics spectr
@dlebauer
dlebauer / README.md
Last active March 18, 2022 21:16
UA Drone Day 2022 flight plan

flight_plan_sm

@dlebauer
dlebauer / model_output_munging.R
Created September 15, 2021 21:44
exploring more robust alternatives to https://github.com/az-digitalag/state_organic_ag/pull/5/files#diff-1fb0826bac1b44806443765a86931b5c4b9ed8a35d16d8083f80906ef8fd7d49
sum_out <- broom.mixed::tidyMCMC(coda_out, conf.int = TRUE, conf.level = 0.95) %>%
rename(mean = estimate, sd = std.error, pc2.5 = conf.low, pc97.5 = conf.high) %>%
mutate(sig = if_else(pc2.5 * pc97.5 > 0, TRUE, FALSE)) # test if UCL and LCL both have the same sign
years <- data.frame(year_index = 1:length(unique(x$year)), year = unique(x$year))
states <- data.frame(state_index = 1:length(unique(x$state)), state = unique(x$state))
sum_rep <- broom.mixed::tidyMCMC(coda_rep, conf.int = TRUE, conf.level = 0.95) %>%
rename(mean = estimate, sd = std.error, pc2.5 = conf.low, pc97.5 = conf.high) %>%
separate(term, sep = '\\[|\\]|,', into = c('term', 'i', 'j', 'other'), convert = TRUE) %>%
@dlebauer
dlebauer / organic_ag_data_nass_quickstats.R
Created July 27, 2021 18:24
start to wrangle NASS quickstats organic survey data
#CSV downloaded from https://quickstats.nass.usda.gov/results/12827E57-2B20-368C-A91F-1B97FF8F7B35#E2E0BF24-9F88-35DB-8526-8E47D941FDBF
library(dplyr)
library(tidyr)
nass_data <- readr::read_csv("raw_data/E2E0BF24-9F88-35DB-8526-8E47D941FDBF.csv",na = '(D)',
skip = 1,
col_names = c(
"program", "period", "week_ending", "geo_level", "state", "state_ansi",
"ag_district", "ag_district_code", "county", "county_ansi", "zip_code",
"region", "watershed_code", "watershed", "commodity", "data_item",
@dlebauer
dlebauer / download_terraref_from_dryad.R
Created July 27, 2021 18:21
code to download and unzip trait data from Dryad and then plot it
library(ggplot2)
library(dplyr)
download.file(url = 'https://datadryad.org/stash/downloads/file_stream/624637', destfile = 'trait_data.zip', mode = 'wb')
unzip(zipfile = 'trait_data.zip', unzip = 'unzip')
s6heights <- readr::read_csv('traits/season_6_traits/season_6_canopy_height_sensor.csv')
s4heights <- readr::read_csv('traits/season_4_traits/season_4_canopy_height_sensor.csv')
heights <- bind_rows(s4heights, s6heights)
@dlebauer
dlebauer / species2plants.R
Created February 23, 2016 21:55
restore species to usda plants: code for https://github.com/USDA/USDA-APIs/issues/7#issuecomment-187791953
library(data.table)
species <- fread('species.csv')
## identify and remove records that were present when we imported the table
usdaplants <- species[!is.na(NativeStatus) ]
## data table method of renaming columns
setnames(usdaplants,
old = c('id', 'genus', 'species', 'scientificname', 'commonname'),
new = c('betydb.species.id', 'Genus', 'Species', 'ScientificName', 'CommonName'))
@dlebauer
dlebauer / after.sql
Last active April 15, 2021 04:55
refactoring brapi queries https://github.com/az-digitalag/organization/issues/438
select
t.treatment_id :: text as treatmentDbId,
t.site_id :: text as observationUnitDbId,
t.variable_id :: text as observationVariableDbId,
v.name as observationVariableName,
t.id :: text as observationDbId,
t.mean :: text as value,
t.date as observationTimeStamp,
s.sitename as observationUnitName,
t.cultivar_id :: text as germplasmDbId,