Update NEE and LE gap-fill functions by Amedieus · Pull Request #3883 · PecanProject/pecan

Amedieus · 2026-03-19T03:32:21Z

Description

Motivation and Context

Review Time Estimate

Immediately
Within one week
When possible

Types of changes

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

My change requires a change to the documentation.
My name is in the list of CITATION.cff
I agree that PEcAn Project may distribute my contribution under any or all of
- the same license as the existing code,
- and/or the BSD 3-clause license.
I have updated the CHANGELOG.md.
I have updated the documentation accordingly.
I have read the CONTRIBUTING document.
I have added tests to cover my changes.
All new and existing tests passed.

mdietze · 2026-04-03T21:52:47Z

@@ -0,0 +1,589 @@
+utils::globalVariables(c(


I'd strongly recommend agains setting global variables

mdietze · 2026-04-03T21:53:29Z

+#'
+#' @param site.dir character: path to the site information table.
+#' @param n_sites numeric: number of sites to keep from the site table,
+#' the total number of sites is 241.


I'd drop this specific number, as it's likely to change in the future

mdietze · 2026-04-03T21:55:05Z

+#' @return character vector of selected site IDs. Example: 'Site ID' CA-ARB
+#'
+#' @author Yang Gu
+read_site_ids <- function(site.dir, n_sites = 40) {


Remember that this code is becoming part of the overall PEcAn codebase, and in that context site_id means something different. I'd recommend a slight renaming to include fluxnet in the function name

mdietze · 2026-04-03T21:55:59Z

+#' @return data.frame containing filtered predictor/flux data.
+#'
+#' @author Yang Gu
+read_pred_data <- function(pred.var.dir, site_ids) {


similar request to make the function name more specific, such as read_flux_gapfill_covariates

mdietze · 2026-04-03T23:18:12Z

+#' }
+#'
+#' @author Yang Gu
+build_sitecov_df <- function(resimet.df,


Suggested change

build_sitecov_df <- function(resimet.df,

build_fluxnet_sitecov_df <- function(resimet.df,

Co-authored-by: Michael Dietze <dietze@bu.edu>

mdietze · 2026-04-30T19:28:00Z

+#' @export
+#' @author Shawn Serbin, Michael Dietze
+model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date, delete.raw = FALSE, revision = NULL, prefix = "sipnet.out",
+                                overwrite = TRUE, conflict = FALSE) {


If this is a local debugging change I'd exclude it from a PR. Probably better to change this through the settings, not through a hard-coded change in the default.

mdietze · 2026-04-30T19:28:04Z

@@ -0,0 +1,158 @@
+# loading libraries


This creates a new high-level folder called "local" without group discussion or a clear definition for what should go in such a folder. I'd recommend git mving this to the SDA inst/ folder for now.d

mdietze · 2026-04-30T19:29:01Z

@@ -93,31 +121,91 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
  timestep.s <- 86400 / out_day




you probably want to avoid committing random whitespace changes unless there's an actual reason for them

mdietze · 2026-04-30T19:30:12Z

+      output[["litter_N"]] <- sub.sipnet.output$litterN
    }
    if ("n2o" %in% names(sub.sipnet.output)) {
-      output[["N2O_flux"]] <- PEcAn.utils::ud_convert(sub.sipnet.output$n2o, "g/m2", "kg/m2") / timestep.s


could you explain the proposed changes in file conflict handling?

mdietze · 2026-04-30T19:30:53Z

    if ("mineral_N" %in% names(output)) {
      nc_var[["mineral_N"]] <- ncdf4::ncvar_def("mineral_N", units = "kg N m-2",
-        dim = list(lon, lat, t), missval = -999, longname = "Soil mineral nitrogen")
+                                                dim = list(lon, lat, t), missval = -999, longname = "Soil mineral nitrogen")


please revert whitespace change so as to avoid long lines

mdietze · 2026-04-30T19:33:27Z

+                                                                    runid), start.year = lubridate::year(stop.time), end.year = lubridate::year(stop.time), 
+                                  variables = c(state.vars, "time_bounds"))
+
+  # 4) 若关键变量缺失，直接给出可读的报错信息（避免在 ud_convert 里才崩）


please limit code comments to English

mdietze · 2026-04-30T19:34:02Z

+  last <- which(as.Date(real_time) == as.Date(stop.time))[length(which(as.Date(real_time) == 
+                                                                         as.Date(stop.time)))]
+
+  # print("breakpoint3")


I'd recommend against committing debugging info

mdietze · 2026-04-30T19:35:58Z

+      )
+    }
  }
+  ## Delete this


mdietze · 2026-04-30T19:36:26Z

-    for(i in 1:block$constant$YN) {
-      valueInCompiledNimbleFunction(Cmcmc$samplerFunctions[[samplerNumberOffset+i]], 'toggle', 0)
-    }
+  ## Revise 2: Delete this


mdietze · 2026-04-30T19:37:43Z

    if (all(names.sampler %in% names.site.input)) {
      input_design <- PEcAn.uncertainty::generate_joint_ensemble_design(settings = settings[[i]], 
-                                                                        ensemble_samples = ensemble.samples, 
+


not clear why this line was removed

Upload NEE and LE gap-fill functions

77f3c93

github-actions Bot added the modules label Mar 19, 2026

yanggu added 3 commits March 19, 2026 14:25

make roxygen files fot gap-filling scripts

6198171

commit rosxygen files for read_site_ids

2dce279

update description

dd53678

github-actions Bot added the dockerfile label Mar 19, 2026

yanggu added 3 commits March 19, 2026 17:47

update Rd

7c5a76b

Fix NSE notes in xgb_gapfill

5e0c31e

put packages into Suggests

42d8f0c

Amedieus requested a review from mdietze March 20, 2026 00:14

mdietze requested review from DongchenZ and ankurdesai March 20, 2026 17:51

mdietze requested changes Apr 3, 2026

View reviewed changes

Amedieus and others added 8 commits April 8, 2026 07:29

Merge branch 'develop' into develop

ae1390a

Merge branch 'PecanProject:develop' into develop

c660cfd

Merge branch 'develop' into develop

ad314c5

data prep for downscaling and bcm code

b6bdea5

Merge branch 'develop' of https://github.com/Amedieus/PEcAn into develop

3de4e1e

Merge branch 'PecanProject:develop' into develop

ea206ad

Update modules/data.land/R/SIPNET_flux_gapfill.R

a8b9dc9

Co-authored-by: Michael Dietze <dietze@bu.edu>

upload the revised version to repo

706252a

github-actions Bot added the models label Apr 28, 2026

multi chain MCMC config & fix NEE unit

5367eb8

mdietze reviewed Apr 30, 2026

View reviewed changes

yanggu added 2 commits May 12, 2026 14:13

update bf byproduct

14b4ff4

monthly sipnet available

8e2c97d

github-actions Bot added the base label May 12, 2026

	build_sitecov_df <- function(resimet.df,
	build_fluxnet_sitecov_df <- function(resimet.df,

		@@ -93,31 +121,91 @@ model2netcdf.SIPNET <- function(outdir, sitelat, sitelon, start_date, end_date,
		timestep.s <- 86400 / out_day

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Amedieus commented Mar 19, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Amedieus commented Mar 19, 2026 •

edited

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