Move optional dependencies from Imports to Suggests in PEcAn.data.land (#3599)

CHANGELOG.md

@@ -25,6 +25,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Sensitivity analysis and ensemble runs now generate separate input design matrices with appropriate dimensions, fixing dimension mismatch errors in multisite workflows. (#3708)
 - Generated runs are now stored in a `runs_manifest.csv` file in the output directory instead of modifying `samples.Rdata` (#3708)
 - SDA workflows now maintain joint input sampling, via internal calls to `generate_joint_ensemble_design()` (#3634).
+* `PEcAn.data.land`: Moved optional dependencies `doSNOW`, `dplR`, `httr`,
+  `MCMCpack`, `mvtnorm`, `neonUtilities`, `neonstore`, `PEcAn.benchmark`,
+  `PEcAn.visualization`, `rjags`, `sirt`, and `sp` from `Imports` to
+  `Suggests` (@omkarrr2533, #3599).
 
 
 

CITATION.cff

@@ -127,6 +127,9 @@ authors:
     affiliation: CMR Institute of Technology, Bengaluru
   - given-names: Aritra Dey
     affiliation: National Institute of Technology, Tiruchirappalli
+  - given-names: Om Kapale
+    affiliation: Chatrapati Shahu Maharaj CSCOE, Maharashtra
+
 
 preferred-citation:
   type: article

docker/depends/pecan_package_dependencies.csv

@@ -45,9 +45,9 @@
 "doSNOW","*","base/utils","Suggests",FALSE
 "doSNOW","*","modules/assim.sequential","Suggests",FALSE
 "doSNOW","*","modules/data.atmosphere","Suggests",FALSE
-"doSNOW","*","modules/data.land","Imports",FALSE
+"doSNOW","*","modules/data.land","Suggests",FALSE
 "doSNOW","*","modules/data.remote","Suggests",FALSE
-"dplR","*","modules/data.land","Imports",FALSE
+"dplR","*","modules/data.land","Suggests",FALSE
 "dplyr","*","base/qaqc","Imports",FALSE
 "dplyr","*","base/remote","Imports",FALSE
 "dplyr","*","base/utils","Imports",FALSE
@@ -127,7 +127,7 @@
 "here","*","base/db","Suggests",FALSE
 "httr","*","base/remote","Imports",FALSE
 "httr","*","modules/data.atmosphere","Imports",FALSE
-"httr","*","modules/data.land","Imports",FALSE
+"httr","*","modules/data.land","Suggests",FALSE
 "httr","*","modules/data.remote","Suggests",FALSE
 "IDPmisc","*","modules/assim.batch","Imports",FALSE
 "itertools","*","modules/assim.sequential","Suggests",FALSE
@@ -201,7 +201,7 @@
 "mclust","*","modules/rtm","Suggests",FALSE
 "MCMCpack","*","modules/allometry","Imports",FALSE
 "MCMCpack","*","modules/assim.batch","Imports",FALSE
-"MCMCpack","*","modules/data.land","Imports",FALSE
+"MCMCpack","*","modules/data.land","Suggests",FALSE
 "MCMCpack","*","modules/emulator","Imports",FALSE
 "methods","*","base/db","Imports",FALSE
 "methods","*","base/settings","Depends",FALSE
@@ -229,7 +229,7 @@
 "mvtnorm","*","modules/allometry","Imports",FALSE
 "mvtnorm","*","modules/assim.batch","Imports",FALSE
 "mvtnorm","*","modules/assim.sequential","Suggests",FALSE
-"mvtnorm","*","modules/data.land","Imports",FALSE
+"mvtnorm","*","modules/data.land","Suggests",FALSE
 "mvtnorm","*","modules/emulator","Imports",FALSE
 "ncdf4","*","base/db","Imports",FALSE
 "ncdf4","*","models/basgra","Imports",FALSE
@@ -258,8 +258,8 @@
 "ncdf4",">= 1.15","modules/benchmark","Imports",FALSE
 "ncdf4",">= 1.15","modules/data.atmosphere","Imports",FALSE
 "ncdf4",">= 1.15","modules/data.land","Imports",FALSE
-"neonstore","*","modules/data.land","Imports",FALSE
-"neonUtilities","*","modules/data.land","Imports",FALSE
+"neonstore","*","modules/data.land","Suggests",FALSE
+"neonUtilities","*","modules/data.land","Suggests",FALSE
 "nimble","*","modules/assim.sequential","Imports",FALSE
 "nneo","*","modules/data.atmosphere","Imports",FALSE
 "optparse","*","base/settings","Imports",FALSE
@@ -272,7 +272,7 @@
 "PEcAn.benchmark","*","base/all","Depends",TRUE
 "PEcAn.benchmark","*","modules/assim.batch","Imports",TRUE
 "PEcAn.benchmark","*","modules/assim.sequential","Suggests",TRUE
-"PEcAn.benchmark","*","modules/data.land","Imports",TRUE
+"PEcAn.benchmark","*","modules/data.land","Suggests",TRUE
 "PEcAn.BIOCRO","*","base/all","Suggests",TRUE
 "PEcAn.BIOCRO","*","base/qaqc","Suggests",TRUE
 "PEcAn.DALEC","*","base/all","Suggests",TRUE
@@ -439,7 +439,7 @@
 "PEcAn.utils",">= 1.4.8","models/template","Imports",TRUE
 "PEcAn.utils",">= 1.8.0","models/rothc","Imports",TRUE
 "PEcAn.visualization","*","modules/assim.sequential","Suggests",TRUE
-"PEcAn.visualization","*","modules/data.land","Imports",TRUE
+"PEcAn.visualization","*","modules/data.land","Suggests",TRUE
 "PEcAn.visualization","*","modules/priors","Suggests",TRUE
 "PEcAn.workflow","*","base/all","Depends",TRUE
 "PEcAn.workflow","*","modules/assim.batch","Imports",TRUE
@@ -491,7 +491,7 @@
 "reticulate","*","modules/data.remote","Imports",FALSE
 "rjags","*","base/utils","Suggests",FALSE
 "rjags","*","modules/assim.batch","Imports",FALSE
-"rjags","*","modules/data.land","Imports",FALSE
+"rjags","*","modules/data.land","Suggests",FALSE
 "rjags","*","modules/meta.analysis","Imports",FALSE
 "rjags","*","modules/photosynthesis","Depends",FALSE
 "rjags","*","modules/priors","Suggests",FALSE
@@ -576,11 +576,11 @@
 "sf","*","modules/data.land","Imports",FALSE
 "sf","*","modules/data.remote","Suggests",FALSE
 "SimilarityMeasures","*","modules/benchmark","Imports",FALSE
-"sirt","*","modules/data.land","Imports",FALSE
+"sirt","*","modules/data.land","Suggests",FALSE
 "sp","*","base/visualization","Suggests",FALSE
 "sp","*","modules/assim.sequential","Suggests",FALSE
 "sp","*","modules/data.atmosphere","Imports",FALSE
-"sp","*","modules/data.land","Imports",FALSE
+"sp","*","modules/data.land","Suggests",FALSE
 "sp","*","modules/data.remote","Imports",FALSE
 "stats","*","base/qaqc","Imports",FALSE
 "stats","*","models/rothc","Imports",FALSE

modules/data.land/DESCRIPTION

@@ -27,33 +27,21 @@ Depends: R (>= 4.1.0)
 Imports:
     coda,
     curl,
-    doSNOW,
     dplyr,
-    dplR,
     foreach,
     fs,
     future,
     furrr,
-    httr,
     lubridate,
     magrittr,
-    MCMCpack,
-    mvtnorm,
     ncdf4 (>= 1.15),
-    neonUtilities,
-    neonstore,
-    PEcAn.benchmark,
     PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.utils,
-    PEcAn.visualization,
     purrr,
-    rjags,
     rlang,
     sf,
-    sirt,
-    sp,
     stringr,
     terra,
     tidyr,
@@ -62,18 +50,30 @@ Imports:
 Suggests:
     dataone,
     datapack,
-    jsonlite,
-    jsonvalidate,
+    doSNOW,
+    dplR,
     getPass,
     glue,
+    httr,
+    jsonlite,
+    jsonvalidate,
+    MASS,
+    MCMCpack,
+    mvtnorm,
+    neonUtilities,
+    neonstore,
+    PEcAn.benchmark,
     PEcAn.settings,
-    redland,
+    PEcAn.visualization,
     raster,
+    redland,
     reticulate,
+    rjags,
+    sirt,
+    sp,
     testthat (>= 3.1.0),
     traits,
-    withr,
-    MASS
+    withr
 Remotes:
     github::ropensci/traits
 License: BSD_3_clause + file LICENSE

modules/data.land/NEWS.md

@@ -14,7 +14,10 @@
 ## Changed
 
 * Package `traits`, used by `match_pft()` and `match_species_id()` only when no database connection is provided, is now suggested rather than required.
-
+* Packages `doSNOW`, `dplR`, `httr`, `MCMCpack`, `mvtnorm`, `neonUtilities`,
+  `neonstore`, `PEcAn.benchmark`, `PEcAn.visualization`, `rjags`, `sirt`, and
+  `sp` are now suggested rather than required. They are only needed for
+  specific optional functionality. (#3599)
 
 # PEcAn.data.land 1.9.0
 

modules/data.land/R/IC_BADM_Utilities.R

@@ -315,7 +315,11 @@ EPA_ecoregion_finder <- function(Lat, Lon, folder.path = NULL){
   U.S.SB.sp <-
     data.frame(Lati = Lat %>% as.numeric(),
                Long = Lon %>% as.numeric())
-
+  if (!requireNamespace("sp", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'sp' is required for spatial data processing but is not installed.",
+      "Please install it with: install.packages('sp')")
+  }
   sp::coordinates(U.S.SB.sp) <- ~ Long + Lati
   # L1 layer
   L1 <-

modules/data.land/R/InventoryGrowthFusion.R

@@ -454,8 +454,12 @@ model{
 
 
   PEcAn.logger::logger.info("COMPILE JAGS MODEL")
+  if (!requireNamespace("rjags", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'rjags' is required for JAGS model fitting but is not installed.",
+      "Please install it with: install.packages('rjags')")
+  }
   j.model <- rjags::jags.model(file = textConnection(TreeDataFusionMV), data = data, inits = init, n.chains = 3)
-
   if(n.burn > 0){
     PEcAn.logger::logger.info("BURN IN")
     jags.out <- rjags::coda.samples(model = j.model, 

modules/data.land/R/InventoryGrowthFusionDiagnostics.R

@@ -5,8 +5,12 @@
 ##' @author Michael Dietze
 ##' @export 
 InventoryGrowthFusionDiagnostics <- function(jags.out, combined=NULL) {
-
-  out      <- as.matrix(jags.out)
+  if (!requireNamespace("PEcAn.visualization", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'PEcAn.visualization' is required for diagnostic plots but is not installed.",
+      "Please install it via the PEcAn project: https://github.com/PecanProject/pecan")
+  }
+  out <- as.matrix(jags.out)
   x.cols   <- which(substr(colnames(out), 1, 1) == "x")
   if(length(x.cols) > 0){
     ci       <- apply(out[, x.cols], 2, stats::quantile, c(0.025, 0.5, 0.975))

modules/data.land/R/Read_Tuscon.R

@@ -57,10 +57,15 @@ Read_Tucson <- function(folder) {
   if (length(corrected) > 0) {
     filenames <- filenames[-corrected]
   }
+  if (!requireNamespace("dplR", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'dplR' is required for reading Tucson format files but is not installed.",
+      "Please install it with: install.packages('dplR')")
+  }
   filedata <- list()
   for (file in filenames) {
     file <- Clean_Tucson(file)
-    filedata[[file]] <- dplR::read.tucson(file, header = FALSE)
+     filedata[[file]] <- dplR::read.tucson(file, header = FALSE)
   }
 
   return(filedata)

modules/data.land/R/download_NEON_soilmoisture.R

@@ -37,7 +37,12 @@ download_NEON_soilmoist <- function(site, avg = "all", var = "all",
                                     outdir) {
 
 
-  #################### Data Download from NEON #################### 
+  if (!requireNamespace("neonUtilities", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'neonUtilities' is required for downloading NEON soil moisture data but is not installed.",
+      "Please install it with: install.packages('neonUtilities')")
+  }
+   #################### Data Download from NEON #################### 
   soil.raw = neonUtilities::loadByProduct(dpID = "DP1.00094.001", site = site, avg = avg, startdate = startdate, enddate = enddate, check.size = FALSE)
 
   # Export into new folder in outdir

modules/data.land/R/extract_NEON_veg.R

@@ -20,7 +20,11 @@
 #' start_date = as.Date("2020-01-01") 
 #' end_date = as.Date("2021-09-01")
 extract_NEON_veg <- function(lon, lat, start_date, end_date, store_dir, neonsites = NULL, ...){
-
+  if (!requireNamespace("neonstore", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'neonstore' is required for extracting NEON vegetation data but is not installed.",
+      "Please install it with: install.packages('neonstore')")
+  }
   #Function to grab the first measurements for each plot between start and end date.
   Grab_First_Measurements_of_Each_Plot <- function(temp_data){
     Plot_Year <- paste0(temp_data$plot, temp_data$year)

modules/data.land/R/extract_SM_CDS.R

@@ -19,6 +19,11 @@ extract_SM_CDS <- function(site_info,
                            out.path = NULL, 
                            allow.download = TRUE,
                            search_window = 10){
+  if (!requireNamespace("sp", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'sp' is required for spatial data processing but is not installed.",
+      "Please install it with: install.packages('sp')")
+  }
   #find downloaded files and the corresponding dates.
   ncfiles <- base::list.files(in.path, full.names = T)
   available.dates <- ncfiles %>% purrr::map(function(file){

modules/data.land/R/extract_soil_nc.R

@@ -31,6 +31,11 @@
 #' @export
 #'  
 extract_soil_gssurgo <- function(outdir, lat, lon, size=1, grid_size=3, grid_spacing=100, depths=c(0.15,0.30,0.60)){
+  if (!requireNamespace("sirt", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'sirt' is required for Dirichlet distribution functions but is not installed.",
+      "Please install it with: install.packages('sirt')")
+  }
   # I keep all the ensembles here 
   all.soil.ens <-list()
 
@@ -250,13 +255,11 @@ extract_soil_gssurgo <- function(outdir, lat, lon, size=1, grid_size=3, grid_spa
       split(list(soilprop.new.grouped$DepthL, soilprop.new.grouped$mukey)) %>%
       purrr::map_df(function(DepthL.Data){
         tryCatch({
-          # I model the soil properties for this depth
-          dir.model <-DepthL.Data[,c(1:3)] %>%
+          dir.model <- DepthL.Data[,c(1:3)] %>%
             as.matrix() %>%
             sirt::dirichlet.mle(.)
-          # Monte Carlo sampling based on my dirichlet model
           alpha <- dir.model$alpha
-          alpha <- matrix(alpha, nrow= size, ncol=length(alpha), byrow=TRUE )
+          alpha <- matrix(alpha, nrow= size, ncol=length(alpha), byrow=TRUE)
           simulated.soil <- sirt::dirichlet.simul(alpha)
           # Validate SOC data before processing
           if (any(is.na(DepthL.Data$soil_organic_carbon_stock))) {

modules/data.land/R/gSSURGO_Query.R

@@ -82,6 +82,11 @@ gSSURGO.Query <- function(mukeys,
                </soap:Body>
                </soap:Envelope>')
 
+  if (!requireNamespace("httr", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'httr' is required for gSSURGO queries but is not installed.",
+      "Please install it with: install.packages('httr')")
+  }
   out <- httr::POST(
     url = "https://SDMDataAccess.nrcs.usda.gov/Tabular/SDMTabularService.asmx",
     config = list(

modules/data.land/R/load_veg.R

@@ -40,6 +40,11 @@ load_veg <- function(new_site, start_date, end_date,
   # query format info
   format     <- PEcAn.DB::query.format.vars(bety = con, input.id = source_id)
 
+  if (!requireNamespace("PEcAn.benchmark", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'PEcAn.benchmark' is required for loading vegetation data but is not installed.",
+      "Please install it with: install.packages('PEcAn.benchmark')")
+  }
   # load_data{benchmark}
   obs        <- PEcAn.benchmark::load_data(data.path = data_path, format, site = new_site)
 

modules/data.land/R/matchInventoryRings.R

@@ -8,7 +8,11 @@
 #'
 ##' @export
 matchInventoryRings <- function(trees, rings, extractor = "TreeCode", nyears = 30, coredOnly = TRUE) {
-
+  if (!requireNamespace("dplR", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'dplR' is required for tree ring processing but is not installed.",
+      "Please install it with: install.packages('dplR')")
+  }
   ## build tree codes
   id.build <- function(x) {
     do.call(paste0("to.", extractor), x)
@@ -19,7 +23,7 @@ matchInventoryRings <- function(trees, rings, extractor = "TreeCode", nyears = 3
   ## build tree ring codes
   if (is.list(rings)) {
     ring.file <- rep(names(rings), times = sapply(rings, ncol))
-    rings     <- dplR::combine.rwl(rings)
+    rings <- dplR::combine.rwl(rings)
   }
   ring.ID    <- names(rings)
   id.extract <- function(x) {

modules/data.land/R/plot2AGB.R

@@ -50,6 +50,11 @@ plot2AGB <- function(combined, out, outfolder, allom.stats, unit.conv = 0.02) {
   biomass_thoc2 <- array(NA, c(mplot, nrep, nt))
 
   ## sample over tree chronologies
+  if (!requireNamespace("mvtnorm", quietly = TRUE)) {
+    PEcAn.logger::logger.severe(
+      "Package 'mvtnorm' is required for multivariate normal sampling but is not installed.",
+      "Please install it with: install.packages('mvtnorm')")
+  }
   pb <- utils::txtProgressBar(min = 0, max = nrep, style = 3)
   for (g in seq_len(nrep)) {