#' Load the veg data from Oracle database
#'
#'
#' @description This function is to load the sample header data from VGIS Oracle database. And
#' associated them with cluster.
#'
#' @param userName character, Specifies a valid user name in VGIS Oracle database.
#' @param password character, Specifies the password to the user name.
#' @param saveThem logical, Specifies whether the loaded data should be saved or returned.
#' The default value is FALSE, which means the function will not save files
#' for you.
#' @param savePath character, Specifies the path to save your outputs, you do not need to
#' specify if \code{saveThem} is turned off. If missing, the current working
#' directory will be choosed.
#'
#' @return Depends on \code{saveThem}, if it hs turned off (i.e., \code{FALSE}). The
#' function returns three datasets:
#' \itemize{
#' \item{\code{} contains the crews for conducting QA;}
#' \item{\code{}}
#' }
#'
#' @importFrom data.table ':=' data.table
#' @importFrom dplyr '%>%'
#' @importFrom ROracle dbConnect dbGetQuery dbDisconnect
#' @importFrom DBI dbDriver
#'
#' @rdname loadVGISVeg
#' @author Yong Luo
loadVGISVeg <- function(userName, password, saveThem = FALSE,
savePath = file.path(".")){
drv <- dbDriver("Oracle")
connect.string <-"(DESCRIPTION=(ADDRESS=(PROTOCOL=TCP)
(HOST=nrk1-scan.bcgov)(PORT=1521))
(CONNECT_DATA=(SERVER=DEDICATED)(SERVICE_NAME=ENVPROD1.NRS.BCGOV)))"
con <- dbConnect(drv, username = userName, password = password,
dbname = connect.string)
c14veg <- dbGetQuery(con, "SELECT
vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY AS CL_KEY,
vgis.vgis_projects.PROJECT_SKEY AS PROJ_KEY,
vgis.vgis_projects.PROJECT_BUSINESS_ID AS PROJ_ID,
vgis.PLOT_CLUSTERS.SAMPLE_EXP_PLOT_NUM AS SAMP_NO,
vgis.DESIGN_SPECIFICATIONS.BUSINESS_IDENTIFIER_VALUE AS TYPE_,
vgis.MEASMT_VISITATIONS.SAMPLE_INTENT AS INTENT,
vgis.MEASMT_VISITATIONS.MEASMT_VISITN_NUM AS VISIT,
vgis.VEGETATION_LYR_COVER_ASSMTS.FIELD_SEQ_NUM AS ITEM_NUM,
vgis.TAXONOMIC_NAMES.LONG_CD AS SPECIES,
vgis.VEGETATION_LYR_COVER_ASSMTS.COVER_PCT AS CVR_PCT,
vgis.SPECIES_GROUP_DEFINITIONS.GROUP_CD AS LIFE_GRP,
vgis.VEGETATION_LYR_COVER_ASSMTS.STRATA_AVERAGE_HT AS AVG_HT,
vgis.VEGETATION_LYR_COVER_ASSMTS.VLC_VEGETATION_LAYER_CD AS LYR_CD
FROM vgis.MEASMT_VISITATIONS,
vgis.PLOT_CLUSTERS,
vgis.POINT_LOCATION_VISITATIONS,
vgis.vgis_projects,
vgis.PROJECT_ASSOCIATIONS,
vgis.CLUSTER_ELEMENTS,
vgis.TAXONOMIC_NAMES,
vgis.GROUP_TAXON_MEMBERSHIPS,
vgis.SPECIES_GROUP_DEFINITIONS,
vgis.VEGETATION_LYR_COVER_ASSMTS,
vgis.DESIGN_SPECIFICATIONS
WHERE vgis.MEASMT_VISITATIONS.PSTAT_PROCESS_STATE_CD='DDL'
AND ((vgis.MEASMT_VISITATIONS.PCLTR_PLOT_CLUSTER_SKEY
=vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY)
AND (vgis.POINT_LOCATION_VISITATIONS.MEAVT_MEASMT_VISIT_SKEY
=vgis.MEASMT_VISITATIONS.MEASMT_VISIT_SKEY)
AND (vgis.PROJECT_ASSOCIATIONS.PCLTR_PLOT_CLUSTER_SKEY
= vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY)
AND (vgis.PROJECT_ASSOCIATIONS.PRJ_PROJECT_SKEY
= vgis.vgis_projects.PROJECT_SKEY)
AND (vgis.POINT_LOCATION_VISITATIONS.CELMT_CLUSTER_ELEMENT_SKEY
=vgis.CLUSTER_ELEMENTS.CLUSTER_ELEMENT_SKEY)
AND (vgis.PLOT_CLUSTERS.DES_DESIGN_SKEY
=vgis.DESIGN_SPECIFICATIONS.DESIGN_SKEY)
AND (vgis.GROUP_TAXON_MEMBERSHIPS.TAXC_TAXONOMIC_CD_SKEY
=vgis.TAXONOMIC_NAMES.TAXONOMIC_CD_SKEY)
AND (vgis.GROUP_TAXON_MEMBERSHIPS.SGDEF_SPP_GROUP_SKEY
=vgis.SPECIES_GROUP_DEFINITIONS.SPP_GROUP_SKEY)
AND (VEGETATION_LYR_COVER_ASSMTS.GTO_GROUP_TAXON_SKEY
=vgis.GROUP_TAXON_MEMBERSHIPS.GROUP_TAXON_SKEY)
AND (vgis.VEGETATION_LYR_COVER_ASSMTS.CEV_CE_VISIT_SKEY
=vgis.POINT_LOCATION_VISITATIONS.CE_VISIT_SKEY))
AND (vgis.SPECIES_GROUP_DEFINITIONS.SPP_GROUP_SKEY IN (
SELECT SGDEF_SPP_GROUP_SKEY
FROM SPECIES_GROUP_ASSOCIATIONS
CONNECT BY PRIOR SGDEF_SPP_GROUP_SKEY = SGDEF_SPP_GROUP_SKEY_PARENT
START WITH SGDEF_SPP_GROUP_SKEY_PARENT =
( SELECT SPP_GROUP_SKEY FROM SPECIES_GROUP_DEFINITIONS
WHERE GROUP_CD = 'LIFEFORM' )))") %>%
data.table
set(c14veg, , c("CL_KEY", "PROJ_KEY"), NULL)
c14veg[,':='(CLSTR_ID = getClusterID(PROJ_ID, SAMP_NO, TYPE_,
INTENT, VISIT),
PLOT = "I")]
set(c14veg, , c("PROJ_ID", "SAMP_NO", "TYPE_", "INTENT", "VISIT"), NULL)
c14veg[, ITEM_NUM := gsub(" ", "", ITEM_NUM)]
c14veg[nchar(ITEM_NUM) == 1, ITEM_NUM := paste("0", ITEM_NUM, sep = "")]
c14veg[nchar(ITEM_NUM) %in% c(0, NA), ITEM_NUM := "00"]
setnames(c14veg, "ITEM_NUM", "ITEM_NO")
c14veg2 <- c14veg[LYR_CD %in% c("B1", "B2", "A"),]
c15veg2 <- c14veg[LYR_CD %in% c("C"),]
c14veg2 <- rbind(c14veg2,
c14veg[(!(LYR_CD %in% c("B1", "B2", "A", "C")) | is.na(LYR_CD))
& LIFE_GRP == "TREE",])
c15veg2 <- rbind(c15veg2,
c14veg[(!(LYR_CD %in% c("B1", "B2", "A", "C")) | is.na(LYR_CD))
& (LIFE_GRP != "TREE" | is.na(LIFE_GRP)),])
c14hdr <- dbGetQuery(con, "SELECT
vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY AS CL_KEY,
vgis.vgis_projects.PROJECT_SKEY AS PROJ_KEY,
vgis.vgis_projects.PROJECT_BUSINESS_ID AS PROJ_ID,
vgis.PLOT_CLUSTERS.SAMPLE_EXP_PLOT_NUM AS SAMP_NO,
vgis.DESIGN_SPECIFICATIONS.BUSINESS_IDENTIFIER_VALUE AS TYPE_,
vgis.MEASMT_VISITATIONS.SAMPLE_INTENT AS INTENT,
vgis.MEASMT_VISITATIONS.MEASMT_VISITN_NUM AS VISIT,
vgis.SPATIAL_DELIMITERS.RADIUS AS RADIUS,
vgis.VEGETATION_LAYER_OVERALL_COVER.VLC_VEGETATION_LAYER_CD AS LYR_CD,
vgis.VEGETATION_LAYER_OVERALL_COVER.COVER_PCT AS CVR_PCT
FROM vgis.MEASMT_VISITATIONS,
vgis.PLOT_CLUSTERS,
vgis.POINT_LOCATION_VISITATIONS,
vgis.vgis_projects,
vgis.PROJECT_ASSOCIATIONS,
vgis.CLUSTER_ELEMENTS,
vgis.VEGETATION_LAYER_OVERALL_COVER,
vgis.BIOMETRIC_DESIGN_SPECIFICATION,
vgis.SPATIAL_DELIMITERS,
vgis.DESIGN_SPECIFICATIONS
WHERE vgis.MEASMT_VISITATIONS.PSTAT_PROCESS_STATE_CD='DDL'
AND ((vgis.MEASMT_VISITATIONS.PCLTR_PLOT_CLUSTER_SKEY
=vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY)
AND (vgis.POINT_LOCATION_VISITATIONS.MEAVT_MEASMT_VISIT_SKEY
=vgis.MEASMT_VISITATIONS.MEASMT_VISIT_SKEY)
AND (vgis.PROJECT_ASSOCIATIONS.PCLTR_PLOT_CLUSTER_SKEY
= vgis.PLOT_CLUSTERS.PLOT_CLUSTER_SKEY)
AND (vgis.PROJECT_ASSOCIATIONS.PRJ_PROJECT_SKEY
= vgis.vgis_projects.PROJECT_SKEY)
AND (vgis.PLOT_CLUSTERS.DES_DESIGN_SKEY
=vgis.DESIGN_SPECIFICATIONS.DESIGN_SKEY)
AND (vgis.POINT_LOCATION_VISITATIONS.CELMT_CLUSTER_ELEMENT_SKEY
=vgis.CLUSTER_ELEMENTS.CLUSTER_ELEMENT_SKEY)
AND (vgis.VEGETATION_LAYER_OVERALL_COVER.CEV_CE_VISIT_SKEY
=vgis.POINT_LOCATION_VISITATIONS.CE_VISIT_SKEY)
AND (vgis.CLUSTER_ELEMENTS.BDSPEC_BD_SPEC_SKEY
=vgis.BIOMETRIC_DESIGN_SPECIFICATION.BD_SPEC_SKEY)
AND (vgis.BIOMETRIC_DESIGN_SPECIFICATION.SPTLD_SPATIAL_DELIM_SKEY
=vgis.SPATIAL_DELIMITERS.SPATIAL_DELIM_SKEY))") %>%
data.table
set(c14hdr, , c("CL_KEY", "PROJ_KEY"), NULL)
c14hdr[,':='(CLSTR_ID = getClusterID(PROJ_ID, SAMP_NO, TYPE_,
INTENT, VISIT),
PLOT = "I")]
set(c14hdr, , c("PROJ_ID", "SAMP_NO", "TYPE_", "INTENT", "VISIT"), NULL)
c14hdr2 <- c14hdr[LYR_CD %in% c("B1", "B2", "A"),]
c15hdr2 <- c14hdr[!(LYR_CD %in% c("B1", "B2", "A")) | is.na(LYR_CD),]
cd_ehh <- reshape(data = c15hdr2,
v.names = "CVR_PCT",
timevar = "LYR_CD",
idvar = "CLSTR_ID",
direction = "wide")
setnames(cd_ehh, paste("CVR_PCT.", c("C", "DH", "DR", "DW"), sep = ""),
toupper(c("iherb", "imoss_dh", "imoss_dr", "imoss_dw")))
c14hdr2_1 <- c14hdr2[,.(CLSTR_ID, PLOT, RADIUS, LYR_CD, LYR = CVR_PCT)]
cd_eth <- reshape(data = c14hdr2_1,
v.names = "LYR",
idvar = "CLSTR_ID",
timevar = "LYR_CD",
direction = "wide",
sep = "_")
c15veg2_1 <- c15veg2[,.(CLSTR_ID, PLOT, ITEM_NO, SPECIES, CVR_PCT, LYR_CD)]
## quick check for multiple records for each idvar
# c15veg2_1[, obslen := length(PLOT), by = c("CLSTR_ID", "ITEM_NO", "SPECIES", "LYR_CD")]
# c15veg2_1[obslen>1]
cd_ehi <- reshape(data = c15veg2_1,
v.names = "CVR_PCT",
timevar = "LYR_CD",
idvar = c("CLSTR_ID", "ITEM_NO", "SPECIES"),
direction = "wide")
cd_eti <- reshape(data = c14veg2,
v.names = c("CVR_PCT", "AVG_HT"),
timevar = "LYR_CD",
idvar = c("CLSTR_ID", "ITEM_NO"),
direction = "wide")
cd_eti <- cd_eti[,.(CLSTR_ID, PLOT, ITEM_NO, SPECIES,
CVR_A = CVR_PCT.A, CVR_B1 = CVR_PCT.B1,
CVR_B2 = CVR_PCT.B2, MOSS_DW = CVR_PCT.DW,
MOSS_DR = CVR_PCT.DR, MOSS_DH = CVR_PCT.DH,
HT_B1 = AVG_HT.B1, HT_B2 = AVG_HT.B2)]
alldata <- list(cd_ehh = cd_ehh,
cd_eth = cd_eth,
cd_ehi = cd_ehi,
cd_eti = cd_eti)
dbDisconnect(con)
if(saveThem){
saveRDS(alldata, file.path(savePath, "veg_card_vgis.rds"))
} else if (!saveThem){
return(alldata)
} else{
stop("saveThem must be logical.")
}
}
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