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use src and out paths set in config #1

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2 changes: 1 addition & 1 deletion inversion/config.r
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

# ~~~~~~~~~~~~~~ Necessary paths ~~~~~~~~~~~~~~#

# paths to inversion directories
# paths to inversion directories - must include trailing '/'
src_path <- "src/"
out_path <- "out/"

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40 changes: 20 additions & 20 deletions inversion/run_all.r
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ if(!is.na(lonlat_outer_file) & !dir.exists("H_outer/"))
if(!dir.exists("HQ/"))
dir.create("HQ/")

if(!dir.exists("out/"))
dir.create("out/")
if(!dir.exists(out_path))
dir.create(out_path)


if (clear_H) {
Expand Down Expand Up @@ -56,119 +56,119 @@ invisible(sapply(out_files[iFiles], FUN = function(x) system(paste("rm", x))))
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_receptors.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_receptors.r")
source(paste0(src_path, "make_receptors.r"))

# 2. make sprior (prior emissions vector)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_sprior.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_sprior.r")
source(paste0(src_path, "make_sprior.r"))

if (include_outer) {
# 3. make outer (outer-domain emissions vector)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_outer.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_outer.r")
source(paste0(src_path, "make_outer.r"))
}

# 4. make sigma (prior uncertainty vector)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_sigma.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_sigma.r")
source(paste0(src_path, "make_sigma.r"))

if (include_bio) {
# 5. make sbio - biogenic flux vector
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_sbio.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_sbio.r")
source(paste0(src_path, "make_sbio.r"))
}

if (clear_H) {
# 6. make H (footprint matrices)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running Hsplit.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/Hsplit.r")
source(paste0(src_path, "Hsplit.r"))
}

if (include_outer | include_bio) {
# 7. derive biogenic and outer-domain additions to bkgd
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_Hs_bkgd.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_Hs_bkgd.r")
source(paste0(src_path, "make_Hs_bkgd.r"))
}

# 8. make spatial covariance matrix
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_sp_cov.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_sp_cov.r")
source(paste0(src_path, "make_sp_cov.r"))

# 9. make temporal covariance matrix
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_tmp_cov.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_tmp_cov.r")
source(paste0(src_path, "make_tmp_cov.r"))

# 10. make HQ
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_HQ.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_HQ.r")
source(paste0(src_path, "make_HQ.r"))

# 11. make bkgd
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_bg.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_bg.r")
source(paste0(src_path, "make_bg.r"))

# 12. make z (anthropogenic enhancement values)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_z.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_z.r")
source(paste0(src_path, "make_z.r"))

# 13. make R (model data mismatch)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_R.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_R.r")
source(paste0(src_path, "make_R.r"))

# 14. make z - Hsp
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_zHsp.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_zHsp.r")
source(paste0(src_path, "make_zHsp.r"))

# 15. make s_hat (optimized emissions vector)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running inversion.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/inversion.r")
source(paste0(src_path, "inversion.r"))

# 16. make_Vshat (posterior uncertainty - technically makes Vshat-bar, which is
# the grid-scale aggregated uncertainty)
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running make_Vshat.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/make_Vshat.r")
source(paste0(src_path, "make_Vshat.r"))

# 17. convert posterior emissions/uncertainty into netcdf format for interpreting results
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("saving results to netcdf")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/post_proc.r")
source(paste0(src_path, "post_proc.r"))

if (compute_chi_sq) {
# 18. calculate Chi-squared
print("~~~~~~~~~~~~~~~~~~~~~~~~")
print("running chi_sq.r")
print("~~~~~~~~~~~~~~~~~~~~~~~~")
source("src/chi_sq.r")
source(paste0(src_path, "chi_sq.r"))
}


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2 changes: 1 addition & 1 deletion inversion/src/post_proc.r
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ library(ncdf4)

# run dependent scripts
source("config.r")
source("src/post_uncert_func.r") #function to extract posterior gridded uncertainty
source(paste0(src_path, "post_uncert_func.r")) #function to extract posterior gridded uncertainty

# specify start/end from config.r variables
flux_times <- seq(from = flux_start_POSIX, to = flux_end_POSIX-1, by = flux_t_res) #flux_t_res defined in config.r
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