Fixing roxygen docs for several functions that were incompletely docu…

…mented/not exported
ncss-tech · Jun 10, 2022 · 65343a5 · 65343a5
1 parent 1b23c8e
commit 65343a5
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Showing 26 changed files with 134 additions and 34 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,6 +5,7 @@ export(KSSL_VG_model)
 export(NASIS)
 export(NASISDomainsAsFactor)
 export(OSDquery)
+export(ROSETTA)
 export(SCAN_sensor_metadata)
 export(SCAN_site_metadata)
 export(SDA_query)
@@ -38,14 +39,18 @@ export(fetchVegdata)
 export(filter_geochem)
 export(format_SQL_in_statement)
 export(getHzErrorsNASIS)
+export(getHzErrorsPedonPC)
 export(get_EDIT_ecoclass_by_geoUnit)
 export(get_NASIS_fkey_by_name)
 export(get_NASIS_pkey_by_name)
 export(get_NASIS_pkeyref_by_name)
+export(get_NASIS_table_key_by_name)
 export(get_NASIS_table_name_by_purpose)
 export(get_NOAA_GHCND)
 export(get_NOAA_stations_nearXY)
 export(get_OSD)
+export(get_RMF_from_NASIS_db)
+export(get_SDA_coecoclass)
 export(get_SDA_cosurfmorph)
 export(get_SDA_hydric)
 export(get_SDA_interpretation)
@@ -66,29 +71,37 @@ export(get_component_correlation_data_from_NASIS_db)
 export(get_component_data_from_NASIS_db)
 export(get_component_diaghz_from_NASIS_db)
 export(get_component_esd_data_from_NASIS_db)
+export(get_component_from_GDB)
 export(get_component_from_SDA)
 export(get_component_horizon_data_from_NASIS_db)
 export(get_component_otherveg_data_from_NASIS_db)
 export(get_component_restrictions_from_NASIS_db)
+export(get_concentrations_from_NASIS_db)
 export(get_copedon_from_NASIS_db)
 export(get_cosoilmoist_from_NASIS)
+export(get_cosoilmoist_from_NASISWebReport)
+export(get_cosoilmoist_from_SDA)
 export(get_cotext_from_NASIS_db)
 export(get_extended_data_from_NASIS_db)
 export(get_extended_data_from_pedon_db)
 export(get_hz_data_from_NASIS_db)
 export(get_hz_data_from_pedon_db)
 export(get_lablayer_data_from_NASIS_db)
 export(get_labpedon_data_from_NASIS_db)
+export(get_legend_from_GDB)
 export(get_legend_from_NASIS)
 export(get_legend_from_SDA)
 export(get_lmuaoverlap_from_NASIS)
 export(get_lmuaoverlap_from_SDA)
+export(get_mapunit_from_GDB)
 export(get_mapunit_from_NASIS)
 export(get_mapunit_from_SDA)
 export(get_mutext_from_NASIS_db)
+export(get_phfmp_from_NASIS_db)
 export(get_projectmapunit_from_NASIS)
 export(get_site_data_from_NASIS_db)
 export(get_site_data_from_pedon_db)
+export(get_sitesoilmoist_from_NASISWebReport)
 export(get_soilseries_from_NASIS)
 export(get_text_notes_from_NASIS_db)
 export(get_veg_data_from_NASIS_db)
@@ -119,6 +132,7 @@ export(simplifyArtifactData)
 export(simplifyColorData)
 export(simplifyFragmentData)
 export(summarizeSoilTemperature)
+export(taxaExtent)
 export(uncode)
 export(waterDayYear)
 importClassesFrom(aqp,SoilProfileCollection)

diff --git a/R/ROSETTA.R b/R/ROSETTA.R
@@ -86,7 +86,14 @@
   return(vg.data)
 }
 
+# 2020-11-19:
+# * NA are handled safely by the API now
+# * model selection is automatic when model code = 0
+# * work with Todd to determin the optimal request / record count trade-off
 
+# 2021-01-06
+# * best model (0) is always used, API no longer accepts `model` as a parameter
+# * versions 1,2,3 supported
 
 
 #' @title Query USDA-ARS ROSETTA Model API
@@ -164,17 +171,7 @@
 #'
 #' Zhang, Y., and M.G. Schaap. 2017. Weighted recalibration of the Rosetta pedotransfer model with improved estimates of hydraulic parameter distributions and summary statistics (Rosetta3). Journal of Hydrology 547: 39-53. doi: \doi{10.1016/j.jhydrol.2017.01.004}.
 #'
-#'
-
-# 2020-11-19:
-# * NA are handled safely by the API now
-# * model selection is automatic when model code = 0
-# * work with Todd to determin the optimal request / record count trade-off
-
-# 2021-01-06
-# * best model (0) is always used, API no longer accepts `model` as a parameter
-# * versions 1,2,3 supported
-
+#' @export
 ROSETTA <- function(x, vars, v = c('1', '2', '3'), include.sd = FALSE, chunkSize = 10000, conf = NULL) {
 
   # check for required packages

diff --git a/R/fetchNASISWebReport.R b/R/fetchNASISWebReport.R
@@ -29,6 +29,10 @@
 #' @param droplevels logical: indicating whether to drop unused levels in
 #' classifying factors. This is useful when a class has large number of unused
 #' classes, which can waste space in tables and figures.
+#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` for
+#' categorical data, or the "RV" for numeric data or `201` cm if the "RV" is also
+#' `NULL` (default: `TRUE`)
+#' @param usiteid character: User Site IDs
 #' @return A data.frame or list with the results.
 #' @author Stephen Roecker
 #' @keywords manip

diff --git a/R/fetchPedonPC.R b/R/fetchPedonPC.R
@@ -7,6 +7,7 @@
 #' Fetch commonly used site/horizon data from a version 5.x PedonPC database, return as a SoilProfileCollection object.
 #' @aliases fetchPedonPC getHzErrorsPedonPC
 #' @param dsn The path to a PedonPC version 6.x database
+#' @param strict Use "strict" horizon error checking? Default: `TRUE`
 #' @return a SoilProfileCollection class object
 #' @note This function attempts to do most of the boilerplate work when
 #' extracting site/horizon data from a PedonPC or local NASIS database. Pedons

diff --git a/R/filter_KSSL.R b/R/filter_KSSL.R
@@ -7,7 +7,7 @@
 #' @param prep_code Character vector of prep code(s) to include in result.
 #' @param major_element_method Character vector of major element method(s) to include in result.
 #' @param trace_element_method Character vector of trace element method(s) to include in result.
-#' @return A data.frame, subsetted according to the constraints specified in arguments.
+#' @return A data.frame, subset according to the constraints specified in arguments.
 #' @author Andrew G. Brown.
 #' @rdname filter_geochem
 #' @export filter_geochem

diff --git a/R/getHzErrorsNASIS.R b/R/getHzErrorsNASIS.R
@@ -1,5 +1,5 @@
 
-#' Get logic errors in NASIS Pedon Horizon  
+#' Get Logic Errors in NASIS/PedonPC Pedon Horizon  
 #' @param strict how strict should horizon boundaries be checked for
 #' consistency: TRUE=more | FALSE=less
 #' @param SS fetch data from the currently loaded selected set in NASIS or from
@@ -8,7 +8,7 @@
 #' table structure; default: NULL
 #' @return A data.frame containing problematic records with columns:
 #' 'peiid','pedon_id','hzdept','hzdepb','hzname'
-#' @export getHzErrorsNASIS
+#' @export 
 getHzErrorsNASIS <- function(strict = TRUE, SS = TRUE, dsn = NULL) {
 
   if (!local_NASIS_defined(dsn))

diff --git a/R/getHzErrorsPedonPC.R b/R/getHzErrorsPedonPC.R
@@ -1,12 +1,14 @@
 ## TODO: this isn't really needed any more
+#' @export 
+#' @rdname fetchPedonPC
 getHzErrorsPedonPC <- function(dsn, strict=TRUE) {
 
 	# get data
 	site_data <- get_site_data_from_pedon_db(dsn)
 	hz_data <- get_hz_data_from_pedon_db(dsn)
 
 	# combine pieces
-  f <- merge(hz_data, site_data, by='peiid', all.x = TRUE, sort = FALSE)
+	f <- merge(hz_data, site_data, by = 'peiid', all.x = TRUE, sort = FALSE)
 
 	f.test <- aqp::checkHzDepthLogic(f, hzdepths = c('hzdept', 'hzdepb'),
 	                                 idname = 'pedon_id', fast = TRUE)

diff --git a/R/get_NASIS_table_key_by_name.R b/R/get_NASIS_table_key_by_name.R
@@ -8,7 +8,8 @@
 #' @examples
 #' \dontrun{
 #' get_NASIS_table_key_by_name(c("site","phorizon_View_1","not_a_table"))
-#' }
+#' }#' 
+#' @export 
 get_NASIS_table_key_by_name <- function(tables, 
                                          keycol = c("all", "fkey", "pkeyref", "pkey")) {
 

diff --git a/R/get_RMF_from_NASIS_db.R b/R/get_RMF_from_NASIS_db.R
@@ -1,3 +1,5 @@
+#' @export 
+#' @rdname fetchNASIS
 get_RMF_from_NASIS_db <- function(SS=TRUE, dsn = NULL) {
 
   # RMF

diff --git a/R/get_SDA_coecoclass.R b/R/get_SDA_coecoclass.R
@@ -14,6 +14,7 @@
 #' @param not_rated_value Default: `"Not assigned"`
 #' @param miscellaneous_areas Include miscellaneous areas (non-soil components)?
 #' @param dsn Path to local SQLite database or a DBIConnection object. If `NULL` (default) use Soil Data Access API via `SDA_query()`.
+#' @export 
 get_SDA_coecoclass <- function(method = "None",
                                areasymbols = NULL, mukeys = NULL, WHERE = NULL,
                                query_string = FALSE, 

diff --git a/R/get_component_from_GDB.R b/R/get_component_from_GDB.R
@@ -1,3 +1,5 @@
+#' @export 
+#' @rdname fetchGDB
 get_component_from_GDB <- function(dsn = "gNATSGO_CONUS.gdb", WHERE = NULL, childs = FALSE, droplevels = TRUE, stringsAsFactors = NULL) {
 
   # check
@@ -61,8 +63,9 @@ get_component_from_GDB <- function(dsn = "gNATSGO_CONUS.gdb", WHERE = NULL, chil
   return(co)
 }
 
-
-
+#' @export 
+#' @rdname fetchGDB
+#' @param stats Return statistics (number of mapunit keys per legend; number of components, major components per mapunit, total and hydric component percentage)? Default: `FALSE`
 get_legend_from_GDB <- function(dsn = "gNATSGO_CONUS.gdb", WHERE = NULL, droplevels = TRUE, stringsAsFactors = NULL, stats = FALSE) {
 
   if (!is.null(WHERE)) {
@@ -106,8 +109,8 @@ get_legend_from_GDB <- function(dsn = "gNATSGO_CONUS.gdb", WHERE = NULL, droplev
 
 }
 
-
-
+#' @export 
+#' @rdname fetchGDB
 get_mapunit_from_GDB <- function(dsn = "gNATSGO_CONUS.gdb", WHERE = NULL, droplevels = TRUE, stringsAsFactors = NULL, stats = FALSE) {
 
   # tests

diff --git a/R/get_component_from_LIMS.R b/R/get_component_from_LIMS.R
diff --git a/R/get_concentrations_from_NASIS_db.R b/R/get_concentrations_from_NASIS_db.R
@@ -1,3 +1,5 @@
+#' @export 
+#' @rdname fetchNASIS
 get_concentrations_from_NASIS_db <- function(SS=TRUE, stringsAsFactors = NULL, dsn = NULL) {
 
   if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {

diff --git a/R/get_cosoilmoist_from_LIMS.R b/R/get_cosoilmoist_from_LIMS.R
@@ -1,3 +1,5 @@
+#' @export
+#' @rdname fetchNASISWebReport
 get_cosoilmoist_from_NASISWebReport <- function(projectname, impute = TRUE, stringsAsFactors = NULL) {
 
   if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
@@ -24,7 +26,8 @@ get_cosoilmoist_from_NASISWebReport <- function(projectname, impute = TRUE, stri
   return(d.cosoilmoist)
   }
 
-
+#' @export
+#' @rdname fetchNASISWebReport
 get_sitesoilmoist_from_NASISWebReport <- function(usiteid) {
 
   url <- "https://nasis.sc.egov.usda.gov/NasisReportsWebSite/limsreport.aspx?report_name=get_sitesoilmoist_from_NASISWebReport"

diff --git a/R/get_cosoilmoist_from_SDA.R b/R/get_cosoilmoist_from_SDA.R
@@ -1,3 +1,6 @@
+#' @export
+#' @rdname fetchSDA
+#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` forcategorical data, or the "RV" for numeric data or `201` cm if the "RV" is also`NULL` (default: `TRUE`)
 get_cosoilmoist_from_SDA <- function(WHERE = NULL, duplicates = FALSE, impute = TRUE,
                                      stringsAsFactors = NULL
                                      ) {

diff --git a/R/get_phfmp_from_NASIS_db.R b/R/get_phfmp_from_NASIS_db.R
@@ -1,3 +1,5 @@
+#' @export 
+#' @rdname fetchNASIS
 get_phfmp_from_NASIS_db <- function(SS = TRUE, stringsAsFactors = NULL, dsn = NULL) {
 
   if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {

diff --git a/R/taxaExtent.R b/R/taxaExtent.R
@@ -200,7 +200,7 @@
 #' }
 #' 
 #' }
-#' 
+#' @export
 taxaExtent <- function(x, level = c('order', 'suborder', 'greatgroup', 'subgroup'), formativeElement = FALSE, timeout = 60) {
 
   ## sanity checks

diff --git a/man/fetchGDB.Rd b/man/fetchGDB.Rd
diff --git a/man/fetchNASIS.Rd b/man/fetchNASIS.Rd
diff --git a/man/fetchNASISWebReport.Rd b/man/fetchNASISWebReport.Rd
diff --git a/man/fetchPedonPC.Rd b/man/fetchPedonPC.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -200,7 +200,7 @@ @@
     #' }
     #'
     #' }
-    #'
+    #' @export
     taxaExtent <- function(x, level = c('order', 'suborder', 'greatgroup', 'subgroup'), formativeElement = FALSE, timeout = 60) {
       ## sanity checks
@@ Expand Down @@