Merge cv testing to main, to make consistent with 0.6.0 release

.Rbuildignore

@@ -14,8 +14,6 @@
 ^uncertainty_testing\.R$
 ^test_workflows_parallel\.R$
 ^test_workflows_parallel\.log$
-^uncertainty_analysis\.R$
-^extract_data_for_Gabe\.R$
 ^refCorrections\.xlsx$
 ^make_ref_corrections_data\.R$
 ^LICENSE\.md$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NEONiso
 Type: Package
 Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
-Version: 0.6.0.9000
+Version: 0.6.0
 Authors@R: c(person("Rich", "Fiorella", email = "rfiorella@lanl.gov",
                 role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0824-4777")))
 Maintainer: Rich Fiorella <rfiorella@lanl.gov>
@@ -11,11 +11,12 @@ Description: Functions for downloading,
     calibrating, and analyzing atmospheric isotope data bundled
     into the eddy covariance data products of the National Ecological
     Observatory Network (NEON) <https://www.neonscience.org>. 
-    In this version, calibration tools are provided for only the 
-    carbon isotope products. Tools for calibrating water isotope 
-    products are under development. More details are found in Fiorella et al. (2021)
+    Calibration tools are provided for carbon and water isotope products.
+    Carbon isotope calibration details are found in Fiorella et al. (2021)
     <doi:10.1029/2020JG005862>, and the readme 
-    file at <https://github.com/lanl/NEONiso>.
+    file at <https://github.com/lanl/NEONiso>. Tools for calibrating water 
+    isotope products have been added as of 0.6.0, but have known deficiencies
+    and should be considered very experimental currently.
 License: GPL-3
 BugReports: https://github.com/lanl/NEONiso/issues
 URL: https://github.com/lanl/NEONiso

README.md

@@ -59,6 +59,7 @@ There will be two major changes and a minor change coming to this package in the
 
 Several months of data on the NEON data portal have an issue where the Picarro time clock has diverged from the valve manifold time. A fix has been developed, but has not been propagated to the NEON data portal.
 
+
 ## Copyright notice:
 
 © 2022. Triad National Security, LLC. All rights reserved.

test_workflows.R

@@ -14,7 +14,7 @@
 # 8) calibrate_water_linreg_bysite works
 
 # where does uncalibrated data live?
-data.dir <- '~/airflow/data/01-DP4_00200_001/'
+data.dir <- '~/Desktop/DP4_00200_001/'
 
 # set test_date
 #test_date <- "2022-01-01"
@@ -27,22 +27,22 @@ devtools::load_all()
 dir.create(paste0('~/NEONcal/',test_date,"_tests"))
 
 # which tests to run?
-run_test1 <- TRUE
+run_test1 <- FALSE
 run_test2 <- FALSE
-run_test3 <- FALSE 
+run_test3 <- FALSE
 run_test4 <- FALSE
 run_test5 <- FALSE
 run_test6 <- FALSE  
 run_test7 <- FALSE
-run_test8 <- FALSE
+run_test8 <- TRUE
 rapid_test <- FALSE # if rapid, only run ~5% of possible site months.
 
 # load required packages: 
 library(rhdf5)
 library(dplyr)
 library(lubridate)
 
-#----------------------------- -----------------------
+#----------------------------------------------------
 # Carbon tests:
 #----------------------------------------------------
 # calibrate_carbon_bymonth tests:
@@ -78,7 +78,8 @@ if (run_test1 | run_test2 | run_test3 | run_test5) {
 }
 
 if (run_test4 | run_test6) {
-  csites <- c(NEONiso:::terrestrial_core_sites(), NEONiso:::terrestrial_relocatable_sites())
+  #csites <- c(NEONiso:::terrestrial_core_sites(), NEONiso:::terrestrial_relocatable_sites())
+  csites <- "ONAQ"
 }
 
 # water files
@@ -100,13 +101,14 @@ if (run_test7) {
 
   # get names only.
   wnames.lst <- strsplit(wnames,split="/")
-  wnames.tmp <- sapply(wnames.lst,'[[',7)
+  wnames.tmp <- sapply(wnames.lst,'[[',8)
 
   wnames.out <- gsub(".h5",".calibrated.h5",wnames.tmp)
 }
 
 if (run_test8) {
-  wsites <- NEONiso:::water_isotope_sites()
+ # wsites <- NEONiso:::water_isotope_sites()
+ wsites <- "ONAQ"
 }
 
 # if we're doing rapid testing!
@@ -187,7 +189,7 @@ if (run_test4) {
     fout <- list.files(paste0(data.dir,csites[i],'/'), pattern = '.h5', full.names=FALSE)
 
     calibrate_carbon(fin,
-                     paste0('~/NEONcal/',test_date,'_tests/04/',fout[1]),
+                     paste0('~/NEONcal/',test_date,'_tests/04/',fout[length(fout)]),
                      site=csites[i], r2_thres = 0.95,
                      calibration_half_width = 100000)
   }