getClusterInfo: Cluster Info

In leppott/CASTfxn: Functions for Causal Assessment Screening Tool (CAST)

Description

Get cluster information.

Usage

getClusterInfo(TargetSiteID, site.COMID, site.Clusters, refSiteCOMIDs,
  data.cluster, dir_results = file.path(getwd(), "Results"),
  dir_sub = "ClusterInfo")

Arguments

TargetSiteID	SiteID
site.COMID	SiteID
site.Clusters	site clusters.
refSiteCOMIDs	reference site COMIDs
data.cluster	The StreamCat data for each reach with cluster assignments.
dir_results	Directory to save plots. Default = working directory and Results.
dir_sub	Subdirectory for outputs from this function. Default = "ClusterInfo"

Details

Summary cluster information

Required objects:

* TargetSiteID

* data.cluster; COMID, H6_noland, H6_land, ElevWs, WsAreaSqKm, PrecipWs, TmeanWs, W___AGRIC, W___URBAN, W___FOREST

Value

A jpeg in the "Results" "ClusterInfo" subdirectory of the working directory.

Examples

TargetSiteID <- "SRCKN001.61"
dir_results <- file.path(getwd(), "Results")

# Data getSiteInfo
# data, example included with package
data.Stations.Info <- data_Sites       # need for getSiteInfo and getChemDataSubsets
data.SampSummary   <- data_SampSummary
data.303d.ComID    <- data_303d
data.bmi.metrics   <- data_BMIMetrics
data.algae.metrics <- data_AlgMetrics
data.mod           <- data_ReachMod

# Cluster based on elevation category  # need for getSiteInfo and getChemDataSubsets
elev_cat <- toupper(data.Stations.Info[data.Stations.Info[,"StationID_Master"]==TargetSiteID
                   , "ElevCategory"])
if(elev_cat=="HI"){
   data.cluster <- data_Cluster_Hi
} else if(elev_cat=="LO") {
   data.cluster <- data_Cluster_Lo
}

# Map data
# San Diego
#flowline <- rgdal::readOGR(dsn = "data_gis/NHDv2_Flowline_Ecoreg85", layer = "NHDv2_eco85_Project")
#outline <- rgdal::readOGR(dsn = "data_gis/Eco85", layer = "Ecoregion85")
# AZ
map_flowline  <- data_GIS_Flow_HI
map_flowline2 <- data_GIS_Flow_LO
if(elev_cat=="HI"){
   map_flowline <- data_GIS_Flow_HI
} else if(elev_cat=="LO") {
   map_flowline <- data_GIS_Flow_LO
}
map_outline   <- data_GIS_AZ_Outline
# Project site data to USGS Albers Equal Area
usgs.aea <- "+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23
              +lon_0=-96 +x_0=0 +y_0=0 +datum=NAD83
              +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
# projection for outline
my.aea <- "+proj=aea +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-96 +x_0=0 +y_0=0 
           +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
map_proj <- my.aea
# 
dir_sub <- "SiteInfo"

# Run getSiteInfo
list.SiteSummary <- getSiteInfo(TargetSiteID, dir_results, data.Stations.Info
                                , data.SampSummary, data.303d.ComID
                                , data.bmi.metrics, data.algae.metrics
                                , data.cluster, data.mod
                                , map_proj, map_outline, map_flowline
                                , dir_sub=dir_sub)
 
# Data getChemDataSubsets
# data, example included with package
data.chem.raw <- data_Chem
data.chem.info <- data_ChemInfo
site.COMID <- list.SiteSummary$COMID
site.Clusters <- list.SiteSummary$ClustIDs

#
# Run getChemDataSubsets
list.data <- getChemDataSubsets(TargetSiteID, comid=site.COMID, cluster=site.Clusters
                                , data.cluster=data.cluster, data.Stations.Info=data.Stations.Info
                                , data.chem.raw=data.chem.raw, data.chem.info=data.chem.info)

# Data getClusterInfo
ref.reaches <- list.data$ref.reaches
refSiteCOMIDs <- list.data$ref.reaches
dir_sub <- "ClusterInfo"

# Run getClusterInfo
getClusterInfo(TargetSiteID, site.COMID, site.Clusters, ref.reaches, 
               data.cluster, dir_results, dir_sub)

leppott/CASTfxn documentation built on Sept. 6, 2019, 11:04 p.m.