diff --git a/.Rbuildignore b/.Rbuildignore index 8080423d..3912071b 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,3 @@ ^.*\.Rproj$ -^\.Rproj\.user$ \ No newline at end of file +^\.Rproj\.user$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 00000000..2d19fc76 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 00000000..17e8d41b --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,4 @@ +## Giving pull request review access to these users +* @rburghol +* @BrendanBrogan +* @COBrogan \ No newline at end of file diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 01450fe6..d58dbd3f 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -19,10 +19,10 @@ permissions: jobs: build: - runs-on: macos-latest + runs-on: windows-latest strategy: matrix: - r-version: ['3.6.3', '4.1.1'] + r-version: ['4.4.1'] steps: - uses: actions/checkout@v3 diff --git a/DESCRIPTION b/DESCRIPTION index c933f3cc..87bdea90 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,5 +25,6 @@ Imports: lubridate, plyr, RPostgres, + DBI, R6, sqldf diff --git a/NAMESPACE b/NAMESPACE index f9bd73ba..dee25efe 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -15,7 +15,10 @@ export(dHOMConstant) export(dHOMConsumptiveUseFractionsPWS) export(dHOMDataMatrix) export(dHOMEquation) +export(dHOMHydroImpoundment) +export(dHOMHydroImpoundmentSmall) export(dHOMObjectClass) +export(dHOMWaterSystemTieredFlowBy) export(dHOMbroadCastObject) export(dHOMtextField) export(dHVarAnnotation) diff --git a/R/RomDataSource.R b/R/RomDataSource.R index 64fb2788..e26a71b1 100644 --- a/R/RomDataSource.R +++ b/R/RomDataSource.R @@ -101,7 +101,7 @@ RomDataSource <- R6Class( if (self$connection_type == 'rest') { private$token <- om_vahydro_token(self$site, self$rest_uname, rest_pw) } else { - self$connection <- dbConnect( + self$connection <- DBI::dbConnect( bigint = "integer", RPostgres::Postgres(), dbname = self$dbname, @@ -587,6 +587,9 @@ RomDataSource <- R6Class( } } } + # have an post process export method + export[[thisobject$propname]] <- plugin$exportOpenMIpost(thisobject, + export[[thisobject$propname]]) return(export) } else { diff --git a/R/RomProperty.R b/R/RomProperty.R index e63ce9d4..21cda14a 100644 --- a/R/RomProperty.R +++ b/R/RomProperty.R @@ -428,12 +428,30 @@ RomProperty <- R6Class( } super$delete(delete_remote) }, - #' @param row_cols update the matrix - #' @return NULL + #'@description + #'Takes in a data frame where each column represents a row to store in the + #'data matrix of this object. This method tranposes that data frame while + #'trying to maintain data strcutures and types + #' @param row_cols A data frame of rows that will be transposed to meet final + #' model or property structure e.g. \code{data.frame(c(1,'foo'), c(2,'bar'), c(3,'bingo'))} + #' will be coerced to \code{data.frame(c(1,2,3), c('foo','bar','bingo'))} + #' @return Nothing, but will set the data_matrix field on RomProperty + #' instance set_matrix = function(row_cols) { # expects a set of rows like this: # data.frame(c(1,'foo'), c(2,'bar'), c(3,'bingo')) - row_cols <- data.frame(t(row_cols),row.names=NULL) + #Transpose each row and then combine into one data frame. Previously we + #had used t() on the entire data frame to do this all at once, but t() + #required conversion to matrix which can only hold one data type and was + #adding white space to vectors with both charaters and numerics as it + #tried to keep consistent numbers of character + row_cols <- mapply( + FUN = function(df,coli){t(df[,coli])}, + coli = 1:ncol(row_cols), + MoreArgs = list(df = row_cols), + SIMPLIFY = FALSE) + #Convert to data frame, but remove column names: + row_cols <- as.data.frame(do.call(rbind,row_cols)) names(row_cols) <- NULL self$data_matrix = row_cols }, diff --git a/R/TNC_IHA_Ports.R b/R/TNC_IHA_Ports.R index ead2d5cd..9c0ddc52 100644 --- a/R/TNC_IHA_Ports.R +++ b/R/TNC_IHA_Ports.R @@ -132,6 +132,15 @@ water.year <- function (x) { #'@author jason.e.law@@gmail.com (imported to Hydrotools by Connor Brogan,connor.brogan@@deq.virginia.gov) #'@references #'\url{http://www.nature.org/initiatives/freshwater/conservationtools/art17004.html} +#' @examples +#'# #Get data for NF Shenandoah Mount Jackson +#'# flows <- dataRetrieval::readNWISdv("01633000",parameterCd = "00060") +#'# flows <- dataRetrieval::renameNWISColumns(flows) +#'# #Convert flows to zoo +#'# flows_zoo <- zoo::as.zoo(x = flows$Flow) +#'# zoo::index(flows_zoo) <- flows$Date +#'# #Use group 1 to get the minimum monthly flows: +#'# hydrotools::group1(flows_zoo,"water",FUN = min) #'@importFrom zoo index coredata is.zoo #'@importFrom lubridate year month #'@importFrom rapportools median @@ -193,6 +202,15 @@ group1 <- function ( #'@return a data frame with the group 2 statistics for each year #'@author jason.e.law@@gmail.com (imported to Hydrotools by Connor Brogan,connor.brogan@@deq.virginia.gov) #'@references \url{http://www.conservationgateway.org/Files/Pages/indicators-hydrologic-altaspx47.aspx} +#'@examples +#'# #Get data for NF Shenandoah Mount Jackson +#'# flows <- dataRetrieval::readNWISdv("01633000",parameterCd = "00060") +#'# flows <- dataRetrieval::renameNWISColumns(flows) +#'# #Convert flows to zoo +#'# flows_zoo <- zoo::as.zoo(x = flows$Flow) +#'# zoo::index(flows_zoo) <- flows$Date +#'# #Use group 2 to get critical period flows and stats: +#'# hydrotools::group2(flows_zoo,"water",mimic.tnc = TRUE) #'@importFrom plyr ddply '.' #'@importFrom zoo coredata index #'@importFrom lubridate year diff --git a/R/dHVariablePluginDefault.R b/R/dHVariablePluginDefault.R index 603d5fd6..ef34b310 100644 --- a/R/dHVariablePluginDefault.R +++ b/R/dHVariablePluginDefault.R @@ -24,7 +24,6 @@ dHVariablePluginDefault <- R6Class( #message("Created plugin") }, #' @param entity the local object to work on - #' @param load_remote automatically query REST data source for matches? #' @return an updated config if necessary or FALSE if it fails exportOpenMI = function(entity) { # creates an array that can later be serialized as json, xml, or whatever @@ -73,6 +72,12 @@ dHVariablePluginDefault <- R6Class( ) return(export) }, + #' @param entity the local object to work on + #' @param export list of properties and subproperties to export + exportOpenMIpost = function(entity, export){ + #Allows modification of exported property lists prior to JSON conversion + return(export) + }, #' @param om_list the open MI export array/list to work on #' @return a Rom importable config or FALSE if it fails fromOpenMIBase = function(om_list) { @@ -490,6 +495,79 @@ dHOMWaterSystemTieredFlowBy <- R6Class( ) ) + +#' VA Hydro model impoundment plugin +#' @title dHOMHydroImpoundment +#' @description Simple class to deal with hydro impoundment class model objects +#' @details Has standard methods for exporting impoundment properties and subproperties +#' @importFrom R6 R6Class +#' @param entity list or object with entity info +#' @return reference class of type openmi.om.base. +#' @seealso NA +#' @examples NA +#' @export dHOMHydroImpoundment +dHOMHydroImpoundment <- R6Class( + "dHOMHydroImpoundment", + inherit = dHOMDataMatrix, + public = list( + #' @field name what is it called + name = NA, + #' @field object_class model object type + object_class = 'hydroImpoundment', + #' @param entity the local object to work on + #' @return an updated config if necessary or FALSE if it fails + exportOpenMIBase = function(entity) { + #print(paste("Entity matrix:", entity$propname)) + export = super$exportOpenMIBase(entity) + + return(export) + } + ) +) + +#' hydroimp +#' @title dHOMHydroImpoundmentSmall +#' @description Simple class to hold tabular flow by values +#' @details Has standard methods for managing data and meta data +#' @importFrom R6 R6Class +#' @param entity list or object with entity info +#' @return reference class of type openmi.om.base. +#' @seealso NA +#' @examples NA +#' @export dHOMHydroImpoundmentSmall +dHOMHydroImpoundmentSmall <- R6Class( + "dHOMHydroImpoundmentSmall", + inherit = dHOMHydroImpoundment, + public = list( + #' @field name what is it called + name = NA, + #' @field object_class model object type + object_class = 'hydroImpSmall', + #' @param entity the local object to work on + #' @return an updated config if necessary or FALSE if it fails + exportOpenMIBase = function(entity) { + #print(paste("Entity matrix:", entity$propname)) + export = super$exportOpenMIBase(entity) + + return(export) + }, + #' @param entity the local object to work on + #' @param export current export object + #' @return Returns a modified list of property and children + exportOpenMIpost = function(entity, export = list()) { + #Copy the storage_stage_area matrix and properties over to a new list + #matrix that is expected in the php import to OM + message("Copying impoundment storage_stage_area to matrix") + export[['matrix']] <- export[['storage_stage_area']][['matrix']] + #Remove the original list + export[['storage_stage_area']] <- NULL + return(export) + } + ) +) + + + # 'This is here because there is no way to instantiate a dynamic class using # 'a string for a class name, so we have to have logic to expose allowed classes #' Retrieve Plugin object for a variable entity @@ -506,6 +584,10 @@ get_plugin_class <- function(plugin_name, entity) { plugin = dHVariablePluginDefault$new(entity) } else if (plugin_name == "dHOMConstant") { plugin = dHOMConstant$new(entity) + } else if (plugin_name == "dHOMHydroImpoundmentSmall") { + plugin = dHOMHydroImpoundmentSmall$new(entity) + } else if (plugin_name == "dHOMHydroImpoundment") { + plugin = dHOMHydroImpoundment$new(entity) } else if (plugin_name == "dHOMEquation") { plugin = dHOMEquation$new(entity) } else if (plugin_name == "dHOMAlphanumericConstant") { diff --git a/R/om_get_rundata.R b/R/om_get_rundata.R index 59fc1d3c..5bf3ad1e 100644 --- a/R/om_get_rundata.R +++ b/R/om_get_rundata.R @@ -1,19 +1,32 @@ -#' The base class for executable equation based meta-model components. +#' Get OM Model Data +#' @description Retrieve model results (run data) from the VA Hydro server for a +#' particular model and run ID (scenario ID). +#' @details A wrapper of \code{hydrotools::fn_get_runfile()}. This function +#' returns the results in a zoo (see zoo::zoo()) that has the timestamp as the +#' index. See \code{hydrotools::fn_get_runfile()} for more details. #' -#' @param elid integer OM model element id -#' @param runid integer run id -#' @param site URL of om server +#' @param elid integer OM element connection ID e.g. the original OM model ID +#' @param runid integer run id representing the scenario. Ask the modeling team +#' for scenario IDs if you are unsure otherwise see the WSPA Shiny Dashboard +#' for more information +#' @param site URL of OM server, typically established in WSPA config files #' @param cached boolean - if TRUE will use recently stored local copy #' @param hydrowarmup boolean - if TRUE will trim beginning of model time frame -#' @return reference class of type openmi.om.equation -#' @seealso NA +#' to account for potential model warm up as water routes downstream from the +#' headwaters and operational rules engage +#' @param cleanup Logical. Should the function delete the log file create for +#' the cached argument? If this is TRUE, the .log files will be deleted after +#' download from OM server +#' @return data.frame of model results #' @export om_get_rundata -#' @examples NA -om_get_rundata <- function(elid, runid, site='http://deq2.bse.vt.edu', cached=FALSE, hydrowarmup=TRUE) { - +#' @examples #om_get_rundata(72446, 600, site=omsite) +om_get_rundata <- function(elid, runid, site='http://deq2.bse.vt.edu', + cached=FALSE, hydrowarmup=TRUE, + cleanup = FALSE) { # replace this with a single function that grabs # a hydro model for summarization and slims it down - dat <- fn_get_runfile(elid, runid, 37, site, cached = FALSE) + dat <- fn_get_runfile(elid, runid, 37, site, cached = FALSE, cleanup = cleanup, + outaszoo = outaszoo) syear = as.integer(min(dat$year)) eyear = as.integer(max(dat$year)) if ((hydrowarmup == TRUE) & (syear < (eyear - 2))) { @@ -33,9 +46,11 @@ om_get_rundata <- function(elid, runid, site='http://deq2.bse.vt.edu', cached=FA #ensure there are associated timezones sdate <- as.POSIXct(sdate,tz = "EST") edate <- as.POSIXct(edate,tz = "EST") + #Get the window of interest from the timeseries dat <- window(dat, start = sdate, end = edate); #Change mode of zoo to numeric e.g. Convert all fields to numeric mode(dat) <- 'numeric' + return(dat) } \ No newline at end of file diff --git a/R/utils.R b/R/utils.R index c87d057e..bf27a657 100644 --- a/R/utils.R +++ b/R/utils.R @@ -123,6 +123,10 @@ fn_get_runfile_info <- function( #' @param cached boolean - use local copy or force refresh #' @param outaszoo boolean return as a zoo timeseries if TRUE, or as data frame #' @param use_tz character pass in a custom timezone for zoo +#' @param cleanup Logical - Should the log file be deleted (TRUE) or written to +#' working directory (FALSE)? Note that the cached argument requires these log +#' files so setting cleanup to FALSE will prevent caching regardless of cached +#' argument #' @return reference class of type openmi.om.equation #' @seealso NA #' @export fn_get_runfile @@ -130,7 +134,8 @@ fn_get_runfile_info <- function( fn_get_runfile <- function( elementid = -1, runid = -1, scenid = 37, site = "http://deq2.bse.vt.edu", cached = TRUE, - outaszoo=TRUE, use_tz=FALSE + outaszoo=TRUE, use_tz=FALSE, + cleanup = FALSE ) { if (elementid == -1 ) { return(FALSE); @@ -222,6 +227,12 @@ fn_get_runfile <- function( f3 <- zoo::zoo(datv, order.by = datv$timestamp) } unlink('tempfile') + #If the user has provided a logical value for cleanup, check to see if user + #has requested the logfile be deleted. If cleanup is TRUE, delete the log file + if(is.logical(cleanup) && cleanup){ + unlink(filename) + } + #Return either the data frame or the zoo if(outaszoo){ return(f3) }else{ diff --git a/auth.private.example b/auth.private.example index d586ffca..e687ae8f 100644 --- a/auth.private.example +++ b/auth.private.example @@ -1,7 +1,10 @@ #VAHydro-1.0 Authentication -username <- "TRICKY_USERNAME" +username <- "old_USERNAME" hash <- "TRICKY_PASSWORD" #VAHydro-2.0 Admin REST Authentication -rest_uname <- 'TRICKY_USERNAME' +rest_uname <- 'rest_USERNAME' rest_pw <- 'TRICKY_PASSWORD' + +odbc_uname <- 'odbc_USERNAME' +odbc_pw <- 'TRICKY_PASSWORD' diff --git a/config.local.private.example b/config.local.private.example index b42daf68..6ac53039 100644 --- a/config.local.private.example +++ b/config.local.private.example @@ -1,2 +1,13 @@ -# WHERE ARE YOU LOCALLY STORING THE hydro-tools REPOSITORY -repo_location <- "C:\\Users\\nrf46657\\Desktop\\VAHydro Development\\GitHub\\" \ No newline at end of file +# set up a caching function for NWIS +Sys.setenv(USGS_cache_dir = "/media/model/usgs") +export_path <- '/Workspace/tmp/' + +hydro_tools <- 'https://raw.githubusercontent.com/HARPgroup/hydro-tools/master' +cbp6_location <- 'https://raw.githubusercontent.com/HARPgroup/cbp6/master' +hydro_tools_location <- hydro_tools +om_location <- "https://raw.githubusercontent.com/HARPgroup/om/master" +elfgen_location <- "https://raw.githubusercontent.com/HARPgroup/elfgen/master" +openmi_om_location <- "https://raw.githubusercontent.com/HARPgroup/openmi-om/master" +vahydro_location <- "https://github.com/HARPgroup/vahydro/blob/master" +github_location <- "C:/usr/local/home/git" +HARParchive_location <- paste0(github_location, "/HARParchive") diff --git a/data/test.csv b/data/test.csv deleted file mode 100644 index d7e79264..00000000 --- a/data/test.csv +++ /dev/null @@ -1,2 +0,0 @@ -hydroid,name -1,dummy \ No newline at end of file diff --git a/man/RomFeature.Rd b/man/RomFeature.Rd index f7bea27d..6741e15c 100644 --- a/man/RomFeature.Rd +++ b/man/RomFeature.Rd @@ -252,7 +252,7 @@ NULL \item{\code{inputs}}{criteria to search for (list key = value format)} -\item{\code{operator}}{what type of spatial function, default = st_contains. +\item{\code{operator}}{what type of spatial function,default = st_contains Other options are 'overlaps' or 'st_within'} \item{\code{return_geoms}}{FALSE will return a smaller dataframe} diff --git a/man/RomProperty.Rd b/man/RomProperty.Rd index 6b6f4a2d..72cb4f4b 100644 --- a/man/RomProperty.Rd +++ b/man/RomProperty.Rd @@ -285,6 +285,9 @@ NULL \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-RomProperty-set_matrix}{}}} \subsection{Method \code{set_matrix()}}{ +Takes in a data frame where each column represents a row to store in the +data matrix of this object. This method tranposes that data frame while +trying to maintain data strcutures and types \subsection{Usage}{ \if{html}{\out{
}}\preformatted{RomProperty$set_matrix(row_cols)}\if{html}{\out{
}} } @@ -292,12 +295,15 @@ NULL \subsection{Arguments}{ \if{html}{\out{
}} \describe{ -\item{\code{row_cols}}{update the matrix} +\item{\code{row_cols}}{A data frame of rows that will be transposed to meet final +model or property structure e.g. \code{data.frame(c(1,'foo'), c(2,'bar'), c(3,'bingo'))} +will be coerced to \code{data.frame(c(1,2,3), c('foo','bar','bingo'))}} } \if{html}{\out{
}} } \subsection{Returns}{ -NULL +Nothing, but will set the data_matrix field on RomProperty + instance } } \if{html}{\out{
}} diff --git a/man/dHOMAlphanumericConstant.Rd b/man/dHOMAlphanumericConstant.Rd index 8574ecf7..dd04b002 100644 --- a/man/dHOMAlphanumericConstant.Rd +++ b/man/dHOMAlphanumericConstant.Rd @@ -44,6 +44,7 @@ NA
Inherited methods diff --git a/man/dHOMConstant.Rd b/man/dHOMConstant.Rd index 090e6b77..7da3de40 100644 --- a/man/dHOMConstant.Rd +++ b/man/dHOMConstant.Rd @@ -44,6 +44,7 @@ NA
Inherited methods diff --git a/man/dHOMConsumptiveUseFractionsPWS.Rd b/man/dHOMConsumptiveUseFractionsPWS.Rd index 01c6f4ff..8b943650 100644 --- a/man/dHOMConsumptiveUseFractionsPWS.Rd +++ b/man/dHOMConsumptiveUseFractionsPWS.Rd @@ -43,6 +43,7 @@ NA
Inherited methods
  • hydrotools::dHVariablePluginDefault$exportOpenMI()
    • +
  • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
  • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
  • hydrotools::dHVariablePluginDefault$initialize()
  • hydrotools::dHOMDataMatrix$param_info()
    • diff --git a/man/dHOMDataMatrix.Rd b/man/dHOMDataMatrix.Rd index 5569b7aa..ea547c2b 100644 --- a/man/dHOMDataMatrix.Rd +++ b/man/dHOMDataMatrix.Rd @@ -46,6 +46,7 @@ NA
    Inherited methods diff --git a/man/dHOMEquation.Rd b/man/dHOMEquation.Rd index 52bea810..52651807 100644 --- a/man/dHOMEquation.Rd +++ b/man/dHOMEquation.Rd @@ -44,6 +44,7 @@ NA
    Inherited methods diff --git a/man/dHOMHydroImpoundment.Rd b/man/dHOMHydroImpoundment.Rd new file mode 100644 index 00000000..0db5aec5 --- /dev/null +++ b/man/dHOMHydroImpoundment.Rd @@ -0,0 +1,89 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dHVariablePluginDefault.R +\name{dHOMHydroImpoundment} +\alias{dHOMHydroImpoundment} +\title{dHOMHydroImpoundment} +\value{ +reference class of type openmi.om.base. +} +\description{ +Simple class to deal with hydro impoundment class model objects +} +\details{ +VA Hydro model impoundment plugin + +Has standard methods for exporting impoundment properties and subproperties +} +\examples{ +NA +} +\seealso{ +NA +} +\section{Super classes}{ +\code{\link[hydrotools:dHVariablePluginDefault]{hydrotools::dHVariablePluginDefault}} -> \code{\link[hydrotools:dHOMDataMatrix]{hydrotools::dHOMDataMatrix}} -> \code{dHOMHydroImpoundment} +} +\section{Public fields}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{name}}{what is it called} + +\item{\code{object_class}}{model object type} +} +\if{html}{\out{
    }} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-dHOMHydroImpoundment-exportOpenMIBase}{\code{dHOMHydroImpoundment$exportOpenMIBase()}} +\item \href{#method-dHOMHydroImpoundment-clone}{\code{dHOMHydroImpoundment$clone()}} +} +} +\if{html}{\out{ +
    Inherited methods + +
    +}} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMHydroImpoundment-exportOpenMIBase}{}}} +\subsection{Method \code{exportOpenMIBase()}}{ +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{dHOMHydroImpoundment$exportOpenMIBase(entity)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{entity}}{the local object to work on} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +an updated config if necessary or FALSE if it fails +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMHydroImpoundment-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{dHOMHydroImpoundment$clone(deep = FALSE)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
    }} +} +} +} diff --git a/man/dHOMHydroImpoundmentSmall.Rd b/man/dHOMHydroImpoundmentSmall.Rd new file mode 100644 index 00000000..2c55fa13 --- /dev/null +++ b/man/dHOMHydroImpoundmentSmall.Rd @@ -0,0 +1,110 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dHVariablePluginDefault.R +\name{dHOMHydroImpoundmentSmall} +\alias{dHOMHydroImpoundmentSmall} +\title{dHOMHydroImpoundmentSmall} +\value{ +reference class of type openmi.om.base. +} +\description{ +Simple class to hold tabular flow by values +} +\details{ +hydroimp + +Has standard methods for managing data and meta data +} +\examples{ +NA +} +\seealso{ +NA +} +\section{Super classes}{ +\code{\link[hydrotools:dHVariablePluginDefault]{hydrotools::dHVariablePluginDefault}} -> \code{\link[hydrotools:dHOMDataMatrix]{hydrotools::dHOMDataMatrix}} -> \code{\link[hydrotools:dHOMHydroImpoundment]{hydrotools::dHOMHydroImpoundment}} -> \code{dHOMHydroImpoundmentSmall} +} +\section{Public fields}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{name}}{what is it called} + +\item{\code{object_class}}{model object type} +} +\if{html}{\out{
    }} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-dHOMHydroImpoundmentSmall-exportOpenMIBase}{\code{dHOMHydroImpoundmentSmall$exportOpenMIBase()}} +\item \href{#method-dHOMHydroImpoundmentSmall-exportOpenMIpost}{\code{dHOMHydroImpoundmentSmall$exportOpenMIpost()}} +\item \href{#method-dHOMHydroImpoundmentSmall-clone}{\code{dHOMHydroImpoundmentSmall$clone()}} +} +} +\if{html}{\out{ +
    Inherited methods + +
    +}} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMHydroImpoundmentSmall-exportOpenMIBase}{}}} +\subsection{Method \code{exportOpenMIBase()}}{ +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{dHOMHydroImpoundmentSmall$exportOpenMIBase(entity)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{entity}}{the local object to work on} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +an updated config if necessary or FALSE if it fails +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMHydroImpoundmentSmall-exportOpenMIpost}{}}} +\subsection{Method \code{exportOpenMIpost()}}{ +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{dHOMHydroImpoundmentSmall$exportOpenMIpost(entity, export = list())}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{entity}}{the local object to work on} + +\item{\code{export}}{current export object} +} +\if{html}{\out{
    }} +} +\subsection{Returns}{ +Returns a modified list of property and children +} +} +\if{html}{\out{
    }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMHydroImpoundmentSmall-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
    }}\preformatted{dHOMHydroImpoundmentSmall$clone(deep = FALSE)}\if{html}{\out{
    }} +} + +\subsection{Arguments}{ +\if{html}{\out{
    }} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
    }} +} +} +} diff --git a/man/dHOMObjectClass.Rd b/man/dHOMObjectClass.Rd index 22ca24c0..2d9344fa 100644 --- a/man/dHOMObjectClass.Rd +++ b/man/dHOMObjectClass.Rd @@ -34,6 +34,7 @@ NA
    Inherited methods
    • hydrotools::dHVariablePluginDefault$exportOpenMI()
      • +
    • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
    • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
    • hydrotools::dHVariablePluginDefault$param_info()
    • hydrotools::dHOMAlphanumericConstant$initialize()
      • diff --git a/man/dHOMPublicVars.Rd b/man/dHOMPublicVars.Rd index a6451e63..6e463cb9 100644 --- a/man/dHOMPublicVars.Rd +++ b/man/dHOMPublicVars.Rd @@ -28,9 +28,10 @@ NA } } \if{html}{\out{ -
      Inherited methods +
      Inherited methods
      • hydrotools::dHVariablePluginDefault$exportOpenMI()
        • +
      • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
      • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
      • hydrotools::dHVariablePluginDefault$param_info()
      • hydrotools::dHOMAlphanumericConstant$exportOpenMIBase()
        • diff --git a/man/dHOMWaterSystemTieredFlowBy.Rd b/man/dHOMWaterSystemTieredFlowBy.Rd new file mode 100644 index 00000000..0ac4c4c4 --- /dev/null +++ b/man/dHOMWaterSystemTieredFlowBy.Rd @@ -0,0 +1,116 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/dHVariablePluginDefault.R +\name{dHOMWaterSystemTieredFlowBy} +\alias{dHOMWaterSystemTieredFlowBy} +\title{dHOMWaterSystemTieredFlowBy} +\value{ +reference class of type openmi.om.base. +} +\description{ +Simple class to hold tabular flow by values +} +\details{ +Tiered flowby meta-model object + +Has standard methods for managing data and meta data +} +\examples{ +NA +} +\seealso{ +NA +} +\section{Super classes}{ +\code{\link[hydrotools:dHVariablePluginDefault]{hydrotools::dHVariablePluginDefault}} -> \code{\link[hydrotools:dHOMDataMatrix]{hydrotools::dHOMDataMatrix}} -> \code{dHOMWaterSystemTieredFlowBy} +} +\section{Public fields}{ +\if{html}{\out{
        }} +\describe{ +\item{\code{name}}{what is it called} + +\item{\code{object_class}}{model object type} +} +\if{html}{\out{
        }} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-dHOMWaterSystemTieredFlowBy-exportOpenMIBase}{\code{dHOMWaterSystemTieredFlowBy$exportOpenMIBase()}} +\item \href{#method-dHOMWaterSystemTieredFlowBy-list2matrix}{\code{dHOMWaterSystemTieredFlowBy$list2matrix()}} +\item \href{#method-dHOMWaterSystemTieredFlowBy-translateOMtoDH}{\code{dHOMWaterSystemTieredFlowBy$translateOMtoDH()}} +\item \href{#method-dHOMWaterSystemTieredFlowBy-clone}{\code{dHOMWaterSystemTieredFlowBy$clone()}} +} +} +\if{html}{\out{ +
        Inherited methods + +
        +}} +\if{html}{\out{
        }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMWaterSystemTieredFlowBy-exportOpenMIBase}{}}} +\subsection{Method \code{exportOpenMIBase()}}{ +\subsection{Usage}{ +\if{html}{\out{
        }}\preformatted{dHOMWaterSystemTieredFlowBy$exportOpenMIBase(entity)}\if{html}{\out{
        }} +} + +\subsection{Arguments}{ +\if{html}{\out{
        }} +\describe{ +\item{\code{entity}}{the local object to work on} +} +\if{html}{\out{
        }} +} +\subsection{Returns}{ +an updated config if necessary or FALSE if it fails +} +} +\if{html}{\out{
        }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMWaterSystemTieredFlowBy-list2matrix}{}}} +\subsection{Method \code{list2matrix()}}{ +\subsection{Usage}{ +\if{html}{\out{
        }}\preformatted{dHOMWaterSystemTieredFlowBy$list2matrix(l)}\if{html}{\out{
        }} +} + +} +\if{html}{\out{
        }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMWaterSystemTieredFlowBy-translateOMtoDH}{}}} +\subsection{Method \code{translateOMtoDH()}}{ +\subsection{Usage}{ +\if{html}{\out{
        }}\preformatted{dHOMWaterSystemTieredFlowBy$translateOMtoDH(entity, om_json)}\if{html}{\out{
        }} +} + +\subsection{Arguments}{ +\if{html}{\out{
        }} +\describe{ +\item{\code{entity}}{list or object with entity info} +} +\if{html}{\out{
        }} +} +} +\if{html}{\out{
        }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHOMWaterSystemTieredFlowBy-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
        }}\preformatted{dHOMWaterSystemTieredFlowBy$clone(deep = FALSE)}\if{html}{\out{
        }} +} + +\subsection{Arguments}{ +\if{html}{\out{
        }} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
        }} +} +} +} diff --git a/man/dHOMbroadCastObject.Rd b/man/dHOMbroadCastObject.Rd index 6374a4dd..4914feec 100644 --- a/man/dHOMbroadCastObject.Rd +++ b/man/dHOMbroadCastObject.Rd @@ -43,6 +43,7 @@ NA
        Inherited methods
        • hydrotools::dHVariablePluginDefault$exportOpenMI()
          • +
        • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
        • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
        • hydrotools::dHVariablePluginDefault$initialize()
        • hydrotools::dHVariablePluginDefault$param_info()
          • diff --git a/man/dHOMtextField.Rd b/man/dHOMtextField.Rd index 00491717..db08175d 100644 --- a/man/dHOMtextField.Rd +++ b/man/dHOMtextField.Rd @@ -43,6 +43,7 @@ NA
          Inherited methods
          • hydrotools::dHVariablePluginDefault$exportOpenMI()
            • +
          • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
          • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
          • hydrotools::dHVariablePluginDefault$initialize()
          • hydrotools::dHVariablePluginDefault$param_info()
            • diff --git a/man/dHVarAnnotation.Rd b/man/dHVarAnnotation.Rd index 34647403..a09aea02 100644 --- a/man/dHVarAnnotation.Rd +++ b/man/dHVarAnnotation.Rd @@ -43,6 +43,7 @@ NA
            Inherited methods
            • hydrotools::dHVariablePluginDefault$exportOpenMI()
              • +
            • hydrotools::dHVariablePluginDefault$exportOpenMIpost()
            • hydrotools::dHVariablePluginDefault$fromOpenMIBase()
            • hydrotools::dHVariablePluginDefault$initialize()
            • hydrotools::dHVariablePluginDefault$param_info()
              • diff --git a/man/dHVarImage.Rd b/man/dHVarImage.Rd index 717295c4..11e8f417 100644 --- a/man/dHVarImage.Rd +++ b/man/dHVarImage.Rd @@ -44,6 +44,7 @@ NA
              Inherited methods diff --git a/man/dHVariablePluginDefault.Rd b/man/dHVariablePluginDefault.Rd index 5fb8b83b..3c6c94ff 100644 --- a/man/dHVariablePluginDefault.Rd +++ b/man/dHVariablePluginDefault.Rd @@ -37,6 +37,7 @@ NA \item \href{#method-dHVariablePluginDefault-new}{\code{dHVariablePluginDefault$new()}} \item \href{#method-dHVariablePluginDefault-exportOpenMI}{\code{dHVariablePluginDefault$exportOpenMI()}} \item \href{#method-dHVariablePluginDefault-exportOpenMIBase}{\code{dHVariablePluginDefault$exportOpenMIBase()}} +\item \href{#method-dHVariablePluginDefault-exportOpenMIpost}{\code{dHVariablePluginDefault$exportOpenMIpost()}} \item \href{#method-dHVariablePluginDefault-fromOpenMIBase}{\code{dHVariablePluginDefault$fromOpenMIBase()}} \item \href{#method-dHVariablePluginDefault-param_info}{\code{dHVariablePluginDefault$param_info()}} \item \href{#method-dHVariablePluginDefault-clone}{\code{dHVariablePluginDefault$clone()}} @@ -73,8 +74,6 @@ object instance \if{html}{\out{
              }} \describe{ \item{\code{entity}}{the local object to work on} - -\item{\code{load_remote}}{automatically query REST data source for matches?} } \if{html}{\out{
              }} } @@ -102,6 +101,24 @@ an updated config if necessary or FALSE if it fails } } \if{html}{\out{
              }} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-dHVariablePluginDefault-exportOpenMIpost}{}}} +\subsection{Method \code{exportOpenMIpost()}}{ +\subsection{Usage}{ +\if{html}{\out{
              }}\preformatted{dHVariablePluginDefault$exportOpenMIpost(entity, export)}\if{html}{\out{
              }} +} + +\subsection{Arguments}{ +\if{html}{\out{
              }} +\describe{ +\item{\code{entity}}{the local object to work on} + +\item{\code{export}}{list of properties and subproperties to export} +} +\if{html}{\out{
              }} +} +} +\if{html}{\out{
              }} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-dHVariablePluginDefault-fromOpenMIBase}{}}} \subsection{Method \code{fromOpenMIBase()}}{ diff --git a/man/fn_get_runfile.Rd b/man/fn_get_runfile.Rd index 05d1beff..84d15f03 100644 --- a/man/fn_get_runfile.Rd +++ b/man/fn_get_runfile.Rd @@ -11,7 +11,8 @@ fn_get_runfile( site = "http://deq2.bse.vt.edu", cached = TRUE, outaszoo = TRUE, - use_tz = FALSE + use_tz = FALSE, + cleanup = FALSE ) } \arguments{ @@ -28,6 +29,11 @@ fn_get_runfile( \item{outaszoo}{boolean return as a zoo timeseries if TRUE, or as data frame} \item{use_tz}{character pass in a custom timezone for zoo} + +\item{cleanup}{Logical - Should the log file be deleted (TRUE) or written to +working directory (FALSE)? Note that the cached argument requires these log +files so setting cleanup to FALSE will prevent caching regardless of cached +argument} } \value{ reference class of type openmi.om.equation diff --git a/man/group1.Rd b/man/group1.Rd index a7ed0125..13d116ea 100644 --- a/man/group1.Rd +++ b/man/group1.Rd @@ -29,6 +29,16 @@ month+water year or calendar month+calendar year depending on user input See IHA documentation: \url{http://www.nature.org/initiatives/freshwater/conservationtools/art17004.html} } +\examples{ +# #Get data for NF Shenandoah Mount Jackson +# flows <- dataRetrieval::readNWISdv("01633000",parameterCd = "00060") +# flows <- dataRetrieval::renameNWISColumns(flows) +# #Convert flows to zoo +# flows_zoo <- zoo::as.zoo(x = flows$Flow) +# zoo::index(flows_zoo) <- flows$Date +# #Use group 1 to get the minimum monthly flows: +# hydrotools::group1(flows_zoo,"water",FUN = min) +} \references{ \url{http://www.nature.org/initiatives/freshwater/conservationtools/art17004.html} } diff --git a/man/group2.Rd b/man/group2.Rd index ba98ede6..3dfdd5d5 100644 --- a/man/group2.Rd +++ b/man/group2.Rd @@ -33,6 +33,16 @@ and finds the 1, 3, 7, 30, and 90 day rolling averages of the zoo. Then, it finds the range, base index, and days of zero flow of each year, with base index defined as the minimum 7-day flow divided by the average flow } +\examples{ +# #Get data for NF Shenandoah Mount Jackson +# flows <- dataRetrieval::readNWISdv("01633000",parameterCd = "00060") +# flows <- dataRetrieval::renameNWISColumns(flows) +# #Convert flows to zoo +# flows_zoo <- zoo::as.zoo(x = flows$Flow) +# zoo::index(flows_zoo) <- flows$Date +# #Use group 2 to get critical period flows and stats: +# hydrotools::group2(flows_zoo,"water",mimic.tnc = TRUE) +} \references{ \url{http://www.conservationgateway.org/Files/Pages/indicators-hydrologic-altaspx47.aspx} } diff --git a/man/om_get_rundata.Rd b/man/om_get_rundata.Rd index ba94d0b9..229c0d83 100644 --- a/man/om_get_rundata.Rd +++ b/man/om_get_rundata.Rd @@ -2,36 +2,48 @@ % Please edit documentation in R/om_get_rundata.R \name{om_get_rundata} \alias{om_get_rundata} -\title{The base class for executable equation based meta-model components.} +\title{Get OM Model Data} \usage{ om_get_rundata( elid, runid, site = "http://deq2.bse.vt.edu", cached = FALSE, - hydrowarmup = TRUE + hydrowarmup = TRUE, + cleanup = FALSE ) } \arguments{ -\item{elid}{integer OM model element id} +\item{elid}{integer OM element connection ID e.g. the original OM model ID} -\item{runid}{integer run id} +\item{runid}{integer run id representing the scenario. Ask the modeling team +for scenario IDs if you are unsure otherwise see the WSPA Shiny Dashboard +for more information} -\item{site}{URL of om server} +\item{site}{URL of OM server, typically established in WSPA config files} \item{cached}{boolean - if TRUE will use recently stored local copy} -\item{hydrowarmup}{boolean - if TRUE will trim beginning of model time frame} +\item{hydrowarmup}{boolean - if TRUE will trim beginning of model time frame +to account for potential model warm up as water routes downstream from the +headwaters and operational rules engage} + +\item{cleanup}{Logical. Should the function delete the log file create for +the cached argument? If this is TRUE, the .log files will be deleted after +download from OM server} } \value{ -reference class of type openmi.om.equation +data.frame of model results } \description{ -The base class for executable equation based meta-model components. +Retrieve model results (run data) from the VA Hydro server for a + particular model and run ID (scenario ID). } -\examples{ -NA +\details{ +A wrapper of \code{hydrotools::fn_get_runfile()}. This function + returns the results in a zoo (see zoo::zoo()) that has the timestamp as the + index. See \code{hydrotools::fn_get_runfile()} for more details. } -\seealso{ -NA +\examples{ +#om_get_rundata(72446, 600, site=omsite) }