fixes for new check errors in R >= 4.4.0 (modules edition)

Makefile.depends

@@ -35,6 +35,6 @@ $(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger
 $(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark
 $(call depends,modules/data.remote): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
 $(call depends,modules/meta.analysis): | .install/base/db .install/base/logger .install/base/settings .install/base/utils
-$(call depends,modules/priors): | .install/base/logger .install/base/visualization .install/modules/meta.analysis
+$(call depends,modules/priors): | .install/base/logger .install/base/utils .install/base/visualization .install/modules/meta.analysis
 $(call depends,modules/rtm): | .install/base/logger .install/base/utils .install/models/ed .install/modules/assim.batch
 $(call depends,modules/uncertainty): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/emulator .install/modules/priors

base/utils/NAMESPACE

@@ -60,6 +60,7 @@ export(ud_convert)
 export(unit_is_parseable)
 export(units_are_equivalent)
 export(vecpaste)
+export(zero.bounded.density)
 export(zero.truncate)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)

base/utils/NEWS.md

@@ -1,5 +1,7 @@
 # PEcAn.utils 1.8.0.9000
 
+## Added
+* utility function `zero.bounded.density` is now exported.
 
 
 # PEcAn.utils 1.8.0

base/utils/R/utils.R

@@ -186,6 +186,7 @@ get.run.id <- function(run.type, index, trait = NULL, pft.name = NULL, site.id=N
 ##' @return data frame with back-transformed log density estimate
 ##' @author \href{https://stats.stackexchange.com/q/6588/2750}{Rob Hyndman}
 ##' @references M. P. Wand, J. S. Marron and D. Ruppert, 1991. Transformations in Density Estimation. Journal of the American Statistical Association. 86(414):343-353 \url{http://www.jstor.org/stable/2290569}
+##' @export
 zero.bounded.density <- function(x, bw = "SJ", n = 1001) {
   y     <- log(x)
   g     <- stats::density(y, bw = bw, n = n)

docker/depends/pecan_package_dependencies.csv

@@ -56,6 +56,7 @@
 "dplyr","*","modules/benchmark","Imports",FALSE
 "dplyr","*","modules/data.land","Imports",FALSE
 "dplyr","*","modules/data.remote","Suggests",FALSE
+"dplyr","*","modules/priors","Suggests",FALSE
 "dplyr","*","modules/uncertainty","Imports",FALSE
 "dplyr",">= 0.8.1","modules/data.atmosphere","Imports",FALSE
 "dplyr",">= 1.1.2","base/db","Imports",FALSE
@@ -124,6 +125,7 @@
 "jsonlite","*","modules/data.remote","Suggests",FALSE
 "knitr","*","base/visualization","Suggests",FALSE
 "knitr","*","modules/data.atmosphere","Suggests",FALSE
+"knitr","*","modules/priors","Suggests",FALSE
 "knitr",">= 1.42","base/db","Suggests",FALSE
 "knitr",">= 1.42","base/qaqc","Suggests",FALSE
 "knitr",">= 1.42","modules/allometry","Suggests",FALSE
@@ -407,6 +409,7 @@
 "PEcAn.utils","*","modules/data.land","Imports",TRUE
 "PEcAn.utils","*","modules/data.remote","Imports",TRUE
 "PEcAn.utils","*","modules/meta.analysis","Imports",TRUE
+"PEcAn.utils","*","modules/priors","Imports",TRUE
 "PEcAn.utils","*","modules/rtm","Suggests",TRUE
 "PEcAn.utils","*","modules/uncertainty","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/basgra","Imports",TRUE
@@ -468,6 +471,7 @@
 "rjags","*","modules/data.land","Imports",FALSE
 "rjags","*","modules/meta.analysis","Imports",FALSE
 "rjags","*","modules/photosynthesis","Depends",FALSE
+"rjags","*","modules/priors","Suggests",FALSE
 "rjson","*","models/dvmdostem","Imports",FALSE
 "rlang","*","base/db","Imports",FALSE
 "rlang","*","base/qaqc","Imports",FALSE

modules/allometry/vignettes/AllomVignette.Rmd

@@ -2,7 +2,7 @@
 title: "PEcAn.allometry Vignette"
 author: "Mike Dietze"
 date: "April 23, 2015"
-output: html_document
+output: html_vignette
 vignette: >
   %\VignetteIndexEntry{PEcAn.allometry Vignette}
   %\VignetteEngine{knitr::rmarkdown}

modules/data.land/R/IC_BADM_Utilities.R

@@ -181,6 +181,7 @@ entries <- entries[-which(ind),]
 #' @param long numeric longitude
 #' @param siteid site id as a string
 #' @param outdir output dir which you want to store the IC netcdf file
+#' @param ens ensemble members, passed on to `pool_ic_list2netcdf`
 #'
 #' @return a dataframe with file, host, mimetype, formatname, startdate, enddate and dbfile.name columns
 #' @export

modules/data.land/R/InventoryGrowthFusion.R

@@ -1,18 +1,47 @@
-##' @name InventoryGrowthFusion
-##' @title InventoryGrowthFusion
-##' @description this code fuses forest inventory data with tree growth data (tree ring or dendrometer band)
-##' for the same plots. Code is a rewrite of Clark et al 2007 Ecol Appl into JAGS
-##' 
-##' @param data  list of data inputs
-##' @param random = whether or not to include random effects
-##' @param n.chunk number of MCMC steps to evaluate at a time. Will only return LAST. If restarting, second number in vector is chunk to start from
-##' @param n.burn  number of steps to automatically discard as burn-in
-##' @param save.state whether or not to include inferred DBH in output (can be large). Enter numeric value to save.state periodically (in terms of n.chunk)
-##' @param restart  final mcmc.list from previous execution. NULL for new run. TRUE to save final state for new run.
-##' @note Requires JAGS
-##' @return an mcmc.list object
-##' @export
-InventoryGrowthFusion <- function(data, cov.data=NULL, time_data = NULL, n.iter=5000, n.chunk = n.iter, n.burn = min(n.chunk, 2000), random = NULL, fixed = NULL,time_varying=NULL, burnin_plot = FALSE, save.jags = "IGF.txt", z0 = NULL, save.state=TRUE,restart = NULL) {
+#' InventoryGrowthFusion
+#'
+#' this code fuses forest inventory data with tree growth data (tree ring or
+#' dendrometer band) for the same plots. Code is a rewrite of Clark et al 2007
+#' Ecol Appl into JAGS
+#' 
+#' @note Requires JAGS
+#'
+#' @param data list of data inputs
+#' @param cov.data covariate data
+#' @param time_data required if time_varying is provided
+#' @param n.iter total number of iterations across all chunks
+#' @param n.chunk number of MCMC steps to evaluate at a time. Will only return
+#'  LAST. If restarting, second number in vector is chunk to start from
+#' @param n.burn number of steps to automatically discard as burn-in
+#' @param random whether or not to include random effects
+#' @param fixed formula for fixed effects
+#' @param time_varying formula for time-varying effects
+#' @param burnin_plot logical: display a plot of the burnin steps?
+#' @param save.jags logical: Save the generated JAGS script?
+#' @param z0 initial conditions for state variable
+#' @param save.state whether or not to include inferred DBH in output (can be
+#'  large). Enter numeric value to save.state periodically (in terms of
+#'  n.chunk)
+#' @param restart final mcmc.list from previous execution. NULL for new run.
+#'  TRUE to save final state for new run.
+#'
+#' @return an mcmc.list object
+#' @export
+InventoryGrowthFusion <- function(
+                                  data,
+                                  cov.data = NULL,
+                                  time_data = NULL,
+                                  n.iter = 5000,
+                                  n.chunk = n.iter,
+                                  n.burn = min(n.chunk, 2000),
+                                  random = NULL,
+                                  fixed = NULL,
+                                  time_varying = NULL,
+                                  burnin_plot = FALSE,
+                                  save.jags = "IGF.txt",
+                                  z0 = NULL,
+                                  save.state = TRUE,
+                                  restart = NULL) {
 
   # baseline variables to monitor
   burnin.variables <- c("tau_add", "tau_dbh", "tau_inc", "mu") # process variability, dbh and tree-ring observation error, intercept

modules/data.land/R/Read_Tuscon.R

@@ -1,7 +1,9 @@
-##' @title Clean_Tucson
-##' @name Clean_Tucson
-##' @description  tree core QAQC
-##' @export
+#' Clean_Tucson
+#'
+#' tree core QAQC
+#'
+#' @param file WinDendro output
+#' @export
 Clean_Tucson <- function(file) {
   lines <- scan(file, character(), sep = "\n")
   split <- strsplit(lines, " ")
@@ -36,12 +38,16 @@ Clean_Tucson <- function(file) {
   return(newfile)
 } # Clean_Tucson
 
-##' @title Read_Tucson
-##' @name Read_Tucson
-##' @export
-##' @description wrapper around read.tucson that loads a whole directory of tree ring files 
-##' and calls a 'clean' function that removes redundant records 
-##' (WinDendro can sometimes create duplicate records when editing)
+#' Read_Tucson
+#'
+#' wrapper around read.tucson that loads a whole directory of tree ring files 
+#' and calls a 'clean' function that removes redundant records 
+#' (WinDendro can sometimes create duplicate records when editing)
+#'
+#' @param folder path to read files from.
+#'  Will read all files at this path matching "TXT", "rwl", or "rw"
+#'
+#' @export
 Read_Tucson <- function(folder) {
 
   filenames <- dir(folder, pattern = "TXT", full.names = TRUE)

modules/data.land/R/dataone_download.R

@@ -2,7 +2,7 @@
 #'
 #' @param id "The identifier of a package, package metadata or other package member" -- dataone r
 #' @param filepath path to where files will be stored
-#' @param CNode 
+#' @param CNode character, passed to `dataone::CNode`
 #' @param lazyLoad "A logical value. If TRUE, then only package member system metadata is downloaded and not data. The default is FALSE." -- dataone R 
 #' @param quiet "A 'logical'. If TRUE (the default) then informational messages will not be printed." -- dataone R
 #' 

modules/data.land/R/extract.stringCode.R

@@ -1,13 +1,16 @@
-##' @name extract.stringCode
-##' @title extract.string.code
-##' @export
+#' extract.stringCode
+#'
+#' @param x string to decode
+#' @param extractor function to apply
+#'
+#' @export
 extract.stringCode <- function(x, extractor = from.TreeCode) {
   return(extractor(x))
 } # extract.stringCode
 
-##' @name from.TreeCode
-##' @title from.TreeCode
-##' @export
+#' from.TreeCode
+#' @param x string to decode
+#' @export
 from.TreeCode <- function(x) {
   SITE <- substr(x, 1, 1)
   PLOT <- substr(x, 2, 2)
@@ -16,9 +19,9 @@ from.TreeCode <- function(x) {
   return(data.frame(SITE, PLOT, SUBPLOT, TAG))
 } # from.TreeCode
 
-##' @name to.TreeCode
-##' @title to.TreeCode
-##' @export
+#' to.TreeCode
+#' @param SITE,PLOT,SUBPLOT,TAG strings (or coercible to)
+#' @export
 to.TreeCode <- function(SITE, PLOT, SUBPLOT, TAG = NULL) {
   SITE <- as.character(SITE)
   PLOT <- as.character(PLOT)
@@ -31,17 +34,18 @@ to.TreeCode <- function(SITE, PLOT, SUBPLOT, TAG = NULL) {
   return(x)
 } # to.TreeCode
 
-##' @name from.Tag
-##' @title from.Tag
-##' @export
+#' from.Tag
+#' @param x string to decode
+#' @export
 from.Tag <- function(x) {
   miss <- rep(NA, length(x))
   return(data.frame(SITE = miss, PLOT = miss, SUBPLOT = miss, TAG = x))
 } # from.Tag
 
-##' @name to.Tag
-##' @title to.Tag
-##' @export
+#' to.Tag
+#' @param SITE,PLOT,SUBPLOT ignored
+#' @param TAG string (or coercible to)
+#' @export
 to.Tag <- function(SITE, PLOT, SUBPLOT, TAG = NULL) {
   SITE <- as.character(SITE)
   PLOT <- as.character(PLOT)

modules/data.land/R/extract_soil_nc.R

@@ -213,12 +213,13 @@ extract_soil_gssurgo<-function(outdir, lat, lon, size=1, radius=500, depths=c(0.
 
 
 
-#' Extract soil data
+#' Extract soil data from the gridpoint closest to a location
 #'
-#' @param in.file 
-#' @param outdir 
-#' @param lat 
-#' @param lon 
+#' @param in.file path to netcdf file containing soil data
+#' @param outdir directory in which to write netcdf file of extracted data.
+#'  Output filename will be the same as input filename.
+#' @param lat,lon location in decimal degrees.
+#'  Data will be extracted from the point in `in.file` that is nearest this
 #'
 #' @return path to netCDF file containing extracted data
 #' @export
@@ -318,9 +319,40 @@ extract_soil_nc <- function(in.file,outdir,lat,lon){
 
 #' Get standard units for a soil variable
 #'
-#' @param varname 
+#' Given SSURGO names for soil properties, looks up their standard units.
+#' Note that names must match exactly.
 #'
-#' @return character
+#' Supported variables are:
+#'  * `soil_depth`
+#'  * `soil_cec`
+#'  * `fraction_of_clay_in_soil`
+#'  * `fraction_of_sand_in_soil`
+#'  * `fraction_of_silt_in_soil`
+#'  * `fraction_of_gravel_in_soil`
+#'  * `volume_fraction_of_water_in_soil_at_saturation`
+#'  * `volume_fraction_of_water_in_soil_at_field_capacity`
+#'  * `volume_fraction_of_condensed_water_in_dry_soil`
+#'  * `volume_fraction_of_condensed_water_in_soil_at_wilting_point`
+#'  * `soilC`
+#'  * `soil_ph`
+#'  * `soil_bulk_density`
+#'  * `soil_type`
+#'  * `soil_hydraulic_b`
+#'  * `soil_water_potential_at_saturation`
+#'  * `soil_hydraulic_conductivity_at_saturation`
+#'  * `thcond0`
+#'  * `thcond1`
+#'  * `thcond2`
+#'  * `thcond3`
+#'  * `soil_thermal_conductivity`
+#'  * `soil_thermal_conductivity_at_saturation`
+#'  * `soil_thermal_capacity`
+#'  * `soil_albedo`
+#'
+#' @param varname character vector. See details
+#'
+#' @return character matrix with columns `var` and `unit`
+#' @md
 #' @export
 #'
 #' @examples

modules/data.land/R/fia2ED.R

@@ -7,13 +7,19 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 
-##' convert x into a table
-##'
-##' @title fia.to.psscss
-##' @param create pss/css files based on data in the fia database
-##' @return nothing
-##' @export
-##' @author Mike Dietze, Rob Kooper, Ryan Kelly
+#' Create pss/css files based on data in the fia database
+#'
+#' @param settings PEcAn settings object
+#' @param lat,lon site location in decimal degrees.
+#'  Defults to values passed in `settings`.
+#' @param year defaults to year of start date passed in settings
+#' @param gridres grid resolution in degrees
+#' @param min.year,max.year limits on years of FIA data to look for
+#' @param overwrite logical: regenerate files already in the database?
+#'
+#' @return modified settings, invisibly
+#' @export
+#' @author Mike Dietze, Rob Kooper, Ryan Kelly
 fia.to.psscss <- function(settings, 
                           lat = as.numeric(settings$run$site$lat),
                           lon = as.numeric(settings$run$site$lon),

modules/data.land/R/load_veg.R

@@ -1,8 +1,21 @@
-##' load_veg
-##'
-##' uses `PEcAn.benchmark::load_data()` to get veg data
-##' @export
-##' @author Istem Fer
+#' load_veg
+#'
+#' uses `PEcAn.benchmark::load_data()` to get veg data
+#'
+#' @param new_site list passed to `load_data`
+#' @param start_date,end_date date range to look up
+#' @param source_id input id to look up in DB
+#' @param source name of data source (used in file naming)
+#' @param icmeta metadata for initial conditions
+#' @param format_name file format to look for
+#' @param machine_host hostname of machine where the data lives
+#' @param dbparms parameters to use when opening connection to database
+#' @param outfolder path to write results
+#' @param overwrite Logical: replace existing files? NOTE: Currently ignored!
+#' @param ... Additional arguments, currently ignored
+#'
+#' @export
+#' @author Istem Fer
 load_veg <- function(new_site, start_date, end_date,
                      source_id, source, icmeta = NULL, format_name = NULL,
                      machine_host, dbparms, outfolder, overwrite = FALSE, ...){

modules/data.land/R/matchInventoryRings.R

@@ -1,5 +1,11 @@
-##' @name matchInventoryRings
-##' @title matchInventoryRings
+#' matchInventoryRings
+#'
+#' @param trees,rings codes from which to extract IDs
+#' @param extractor function to call, specified without its initial `to.`
+#'  e.g. "TreeCode" calls `to.TreeCode`
+#' @param nyears number of years to extract
+#' @param coredOnly logical: Only include trees with data from 2000?
+#'
 ##' @export
 matchInventoryRings <- function(trees, rings, extractor = "TreeCode", nyears = 30, coredOnly = TRUE) {
 

modules/data.land/R/match_species_id.R

@@ -14,6 +14,7 @@
 #' @param format_name Species code format name (see details)
 #' @param bety BETY connection object
 #' @param translation_table Data frame with custom translation table (see details).
+#' @param ... additional arguments, currently ignored
 #' @return \code{data.frame} containing the following columns:
 #' \describe{
 #'  \item{\code{input_code}}{Character provided as input}

modules/data.land/R/plot2AGB.R

@@ -14,7 +14,8 @@
 ##' 
 ##' @param combined   data frame merging plot inventory and tree ring data
 ##' @param out        MCMC samples for diameter (sample x tree)
-##' @param outfolder  output folder for graphs & data 
+##' @param outfolder  output folder for graphs & data
+##' @param allom.stats Allometry statistics computed by `AllomAve`
 ##' @param unit.conv  area conversion from sum(kg/tree) to kg/area
 ##' 
 ##' @author Mike Dietze \email{dietze@@bu.edu}