PEcAn.ED2 check warnings

Makefile.depends

@@ -28,7 +28,7 @@ $(call depends,models/cable): | .install/base/logger .install/base/utils
 $(call depends,models/clm45): | .install/base/logger .install/base/utils
 $(call depends,models/dalec): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/dvmdostem): | .install/base/logger .install/base/utils
-$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,models/fates): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/gday): | .install/base/utils .install/base/logger .install/base/remote
 $(call depends,models/jules): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils

models/ed/.Rbuildignore

@@ -4,3 +4,4 @@
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+vignettes/ed_run_data/

models/ed/DESCRIPTION

@@ -44,6 +44,7 @@ Imports:
     ncdf4 (>= 1.15),
     PEcAn.data.atmosphere,
     PEcAn.data.land,
+    PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.settings,

models/ed/R/create_veg.R

@@ -70,6 +70,6 @@ create_site <- function(input, check = TRUE) {
 #' @return Modified `data.frame`
 modify_df <- function(input, base) {
   col_names <- colnames(base)
-  out_list <- modifyList(as.list(base), as.list(input))
+  out_list <- utils::modifyList(as.list(base), as.list(input))
   as.data.frame(out_list)[col_names]
 }

models/ed/R/download_edi.R

@@ -14,6 +14,6 @@ download_edi <- function(directory) {
   download_link <- "https://files.osf.io/v1/resources/b6umf/providers/osfstorage/5a948ea691b689000fa2a588/?zip="
   target_file <- paste0(directory, ".zip")
   PEcAn.utils::download_file(download_link, target_file)
-  unzip(target_file, exdir = directory)
+  utils::unzip(target_file, exdir = directory)
   invisible(TRUE)
 }

models/ed/R/ed_varlookup.R

@@ -1,5 +1,6 @@
 #' Lookup function for translating commonly used ED variables
 #' returns out list, readvar variables to read from file, expr if any derivation is needed
+#' @param varname character; variable name to read from file
 #' @export
 ed.var <- function(varname) {
   if(varname == "AGB") {

models/ed/R/met2model.ED2.R

@@ -21,9 +21,12 @@
 #' @param start_date the start date of the data to be downloaded (will only use the year part of the date)
 #' @param end_date the end date of the data to be downloaded (will only use the year part of the date)
 #' @param lst timezone offset to GMT in hours
+#' @param lat latitude; if not provide the function will attempt to discover it in input files
+#' @param lon longitude; if not provide the function will attempt to discover it in input files
 #' @param overwrite should existing files be overwritten
 #' @param verbose should the function be very verbose
 #' @param leap_year Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.
+#' @param ... currently unused
 met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0, lat = NA,
                           lon = NA, overwrite = FALSE, verbose = FALSE, leap_year = TRUE, ...) {
 

models/ed/R/model2netcdf.ED2.R

@@ -783,7 +783,7 @@ put_T_values <-
   model_timestep_s <- length(output_date_vector) / length(out[[1]])
   iter_per_day <- round(1 / model_timestep_s) ## e.g. 48
   ## Create a timesteps vector (e.g. 0.00000000 0.02083333 0.04166667 0.06250000 0.08333333 0.10416667 ...)
-  timesteps <- head(seq(0, 1, by = 1 / iter_per_day), -1)
+  timesteps <- utils::head(seq(0, 1, by = 1 / iter_per_day), -1)
   ## Create a new date vector where each day is repeated by iter_per_day 
   ## (e.g. "2001-07-15" "2001-07-15" "2001-07-15" "2001-07-15" "2001-07-15" ...)
   sub_dates <- rep(output_date_vector, each = iter_per_day)

models/ed/R/modify_ed2in.R

@@ -89,7 +89,7 @@ modify_ed2in <- function(ed2in, ...,
   if (is.null(.dots)) {
     .dots <- list()
   }
-  dots <- modifyList(.dots, list(...))
+  dots <- utils::modifyList(.dots, list(...))
   is_upper <- names(dots) == toupper(names(dots))
   lower_args <- names(dots)[!is_upper]
   if (length(lower_args) > 0) {
@@ -211,7 +211,7 @@ modify_ed2in <- function(ed2in, ...,
     # 3 for HDF5 output, 0 for no output
     on_types <- (valid_types %in% output_types) * 3
     names(on_types) <- names(valid_types)
-    ed2in <- modifyList(ed2in, as.list(on_types))
+    ed2in <- utils::modifyList(ed2in, as.list(on_types))
   }
 
   if (!is.null(output_dir)) {
@@ -249,6 +249,6 @@ modify_ed2in <- function(ed2in, ...,
       )
     }
   }
-  ed2in <- modifyList(ed2in, namelist_args)
+  ed2in <- utils::modifyList(ed2in, namelist_args)
   ed2in
 }

models/ed/R/other.helpers.ED2.R

@@ -17,8 +17,11 @@ list.files.nodir <- function(path, ...) {
 
 
 #' Function translating pecan vars to ED vars
+#' @param varnames character; variable names to translate
+#' @export
+#' @examples
 #' var.names <- c("DBH", "AGB", "AbvGrndWood")
-#' @export 
+#' translate_vars_ed(var.names)
 translate_vars_ed <- function(varnames) {
 
   var.list <- add.list <- list()

models/ed/R/read_ed_metheader.R

@@ -83,10 +83,10 @@ read_ed_metheader <- function(filename, check = TRUE, check_files = TRUE) {
         PEcAn.logger::logger.warn(msg)
       }
     }
-    metadata <- unlist(read.table(text = sub_file[2]))
+    metadata <- unlist(utils::read.table(text = sub_file[2]))
     names(metadata) <- c("nlon", "nlat", "dx", "dy", "xmin", "ymin")
     nvars <- as.numeric(sub_file[3])
-    variables_raw <- read.table(text = sub_file[4:6], header = TRUE)
+    variables_raw <- utils::read.table(text = sub_file[4:6], header = TRUE)
     variables_raw$value_type <- c("update_frequency", "flag")
     variables_table <- variables_raw %>%
       tidyr::gather("variable", "value", -.data$value_type) %>%

models/ed/R/read_ed_veg.R

@@ -93,7 +93,7 @@ get_latlon <- function(filepath, latlon) {
 #' @return `data.frame` containing
 #' @export
 read_css <- function(filepath, check = TRUE, ...) {
-  css <- read.table(filepath, header = TRUE)
+  css <- utils::read.table(filepath, header = TRUE)
   if (check) {
     check_css(css, ...)
   }
@@ -103,7 +103,7 @@ read_css <- function(filepath, check = TRUE, ...) {
 #' @rdname read_css
 #' @export
 read_pss <- function(filepath, check = TRUE) {
-  pss <- read.table(filepath, header = TRUE)
+  pss <- utils::read.table(filepath, header = TRUE)
   if (check) {
     check_pss(pss)
   }
@@ -116,7 +116,7 @@ read_site <- function(filepath, check = TRUE, ...) {
   top_line <- readLines(filepath, n = 1)
   nsite <- as.numeric(gsub(".*nsite +([[:digit:]]+).*", "\\1", top_line))
   file_format <- as.numeric(gsub(".*file_format +([[:digit:]]+).*", "\\1", top_line))
-  site <- read.table(filepath, header = TRUE, skip = 1)
+  site <- utils::read.table(filepath, header = TRUE, skip = 1)
   attr(site, "nsite") <- nsite
   attr(site, "file_format") <- file_format
   if (check) {

models/ed/R/read_restart.ED2.R

@@ -1,7 +1,12 @@
 #' @title State data assimilation read-restart for ED2
 #'
 #' @author Alexey Shiklomanov, Istem Fer
-#' @inheritParams PEcAn.ModelName::read_restart.ModelName
+#' @param outdir Output directory
+#' @param runid Run ID
+#' @param stop.time Year that is being read
+#' @param settings PEcAn settings object
+#' @param var.names Variable names to be extracted
+#' @param params Any parameters required for state calculations
 #' @examples
 #' \dontrun{
 #'   outdir <- "~/sda-hackathon/outputs"

models/ed/R/run_ed_singularity.R

@@ -21,7 +21,7 @@
 #' @param ed2in_path Path to ED2IN file.
 #' @param app Singularity "app" to run. Either "ED" or "EDR".
 #' @param singularity_args Additional arguments to be passed to `singularity run` (before)
-#' @param Additional arguments to [base::system2]
+#' @param ... Additional arguments to [base::system2]
 #' @export
 run_ed_singularity <- function(img_path, ed2in_path,
                                app = "ED",

models/ed/R/veg2model.ED2.R

@@ -163,7 +163,7 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source, ens
   css$time[is.na(css$time)]     <- start_year
   css$cohort[is.na(css$cohort)] <- 1:sum(is.na(css$cohort))
   css$dbh[is.na(css$dbh)]       <- 1  # assign nominal small dbh to missing
-  density.median                <- median(css$n[which(css$n > 0)])
+  density.median                <- stats::median(css$n[which(css$n > 0)])
   css$n[is.na(css$n) | css$n == 0]    <- density.median
   css$hite <- css$bdead <- css$balive <- css$lai <- 0
 
@@ -177,10 +177,10 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source, ens
   # Write files
 
   # css
-  write.table(css, filenames_full[1], quote = FALSE, row.names = FALSE)
+  utils::write.table(css, filenames_full[1], quote = FALSE, row.names = FALSE)
 
   # pss
-  write.table(pss, filenames_full[2], quote = FALSE, row.names = FALSE)
+  utils::write.table(pss, filenames_full[2], quote = FALSE, row.names = FALSE)
 
   # site
   # hardcoded per fia2ED implemention

models/ed/R/write.configs.ed.R

@@ -137,7 +137,7 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   ## Edit ED2IN file for runs
   revision <- settings$model$revision
   if (is.null(revision)) {
-    model <- db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
+    model <- PEcAn.DB::db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
     revision <- model$revision
   }
   revision <- gsub("^r", "", revision)
@@ -255,7 +255,7 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
 
     # Overwrite defaults with values from settings$model$ed2in_tags list
     if(!is.null(settings$model$ed2in_tags)){
-      sda_tags <- modifyList(sda_tags, settings$model$ed2in_tags[names(sda_tags)])
+      sda_tags <- utils::modifyList(sda_tags, settings$model$ed2in_tags[names(sda_tags)])
     }
     ed2in.text <- modify_ed2in(ed2in.text, .dots = sda_tags, add_if_missing = TRUE, check_paths = check)
   }
@@ -520,12 +520,12 @@ write.config.xml.ED2 <- function(settings, trait.values, defaults = settings$con
       }
 
       if (grepl("soil", pft)) {
-        data(soil, package = "PEcAn.ED2", envir = environment())
+        utils::data(soil, package = "PEcAn.ED2", envir = environment())
         vals <- as.list(soil)
         names(vals) <- colnames(soil)
 
         converted.trait.values <- convert.samples.ED(trait.values[[i]])
-        vals <- modifyList(vals, converted.trait.values)
+        vals <- utils::modifyList(vals, converted.trait.values)
 
         decompositon.xml <- PEcAn.settings::listToXml(vals, "decomposition")
         xml <- XML::append.xmlNode(xml, decompositon.xml)
@@ -548,14 +548,14 @@ write.config.xml.ED2 <- function(settings, trait.values, defaults = settings$con
         converted.trait.values <- convert.samples.ED(trait.values[[i]])
 
         ## Selectively replace defaults with trait values
-        vals <- modifyList(vals, converted.trait.values)
+        vals <- utils::modifyList(vals, converted.trait.values)
 
         ## Convert settings constants to ED units
         converted.defaults <- convert.samples.ED(defaults[[pft]]$constants)
 
         ## Selectively replace defaults and trait values with constants from settings
         if (!is.null(converted.defaults)){
-          vals <- modifyList(vals, converted.defaults)
+          vals <- utils::modifyList(vals, converted.defaults)
         }
 
         ## Make sure that include_pft is set to 1

models/ed/R/write_ed_veg.R

@@ -39,15 +39,15 @@ write_ed_veg <- function(ed_veg, path_prefix) {
 #' @export
 write_css <- function(css, path_prefix, latitude = NULL, longitude = NULL) {
   css_fname <- prepare_ed_veg_filename(path_prefix, ".css", latitude, longitude)
-  write.table(css, css_fname, quote = FALSE, row.names = FALSE)
+  utils::write.table(css, css_fname, quote = FALSE, row.names = FALSE)
   invisible(css_fname)
 }
 
 #' @rdname write_css
 #' @export
 write_pss <- function(pss, path_prefix, latitude = NULL, longitude = NULL) {
   pss_fname <- prepare_ed_veg_filename(path_prefix, ".pss", latitude, longitude)
-  write.table(pss, pss_fname, quote = FALSE, row.names = FALSE)
+  utils::write.table(pss, pss_fname, quote = FALSE, row.names = FALSE)
   invisible(pss_fname)
 }
 
@@ -61,7 +61,7 @@ write_site <- function(site, path_prefix, latitude = NULL, longitude = NULL) {
     attr(site, "file_format")
   )
   writeLines(first_line, site_fname)
-  write.table(site, site_fname, quote = FALSE, row.names = FALSE, append = TRUE)
+  utils::write.table(site, site_fname, quote = FALSE, row.names = FALSE, append = TRUE)
   invisible(site_fname)
 }
 

models/ed/R/write_restart.ED2.R

@@ -1,7 +1,18 @@
 #' @title Write ED2 restart file from SDA results
 #' 
+#' @param outdir output directory
+#' @param runid run id
+#' @param start.time Time of current assimilation step
+#' @param stop.time Time of next assimilation step
+#' @param settings pecan settings list
+#' @param new.state Analysis state matrix returned by `sda.enkf`
+#' @param RENAME flag to either rename output file or not
+#' @param new.params optional, additional params to pass `write.configs` that
+#'   are deterministically related to the parameters updated by the analysis
+#' @param inputs new input paths updated by the SDA workflow, will be passed to
+#'   `write.configs`
+#'   
 #' @author Alexey Shiklomanov, Istem Fer
-#' @inheritParams PEcAn.ModelName::write_restart.ModelName
 #' @return TRUE if successful
 #' @export
 write_restart.ED2 <- function(outdir, runid, start.time, stop.time,