Combine_AIM_LMF: Combine_AIM_LMF

In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data

Description

Puts TerrADat (Assessment, Inventory, and Monitoring dataset) and LMF (Landscape Monitoring Framework dataset) in the same format, adds R or F prefix to EcologicalSiteId for LMF based on the official ecological site list from EDIT, and merges the two datasets into one. Returns dataframe.

Usage

Combine_AIM_LMF(TerrADat_Path, EDIT_List_Path, Internal)

Arguments

TerrADat_Path	file path to the TerrADat geodatabase. Set to NULL if you are internal (within Bureau of Land Management network/vpn)
EDIT_List_Path	file path to the .csv with list of formal ecological site ids (on the sharepoint with Site Summary Tool template)
Internal	logical. TRUE if within BLM network/on vpn. FALSE if accessing TerrADat via external geodatabase.

Author(s)

Rachel Burke, ecologist/analyst @ Jornada

Examples

# If external:
TDat_LMF <- Combine_AIM_LMF(TerrADat_Path = "~/gdbs/TerrADat.gdb",
                   EDIT_List_Path = "~/Projects/ESSTool/Defaults",
                   Internal = FALSE)
# If internal:
TDat_LMF <- Combine_AIM_LMF(TerrADat_Path = NULL,
                   EDIT_List_Path = "~/Projects/ESSTool/Defaults",
                   Internal = TRUE)

## The function is currently defined as
function (TerrADat_Path, EDIT_List_Path, Internal)
{
    if (!Internal) {
        TerrADat <- sf::st_read(dsn = TerrADat_Path, layer = "TerrADat")
        LMF <- sf::st_read(dsn = TerrADat_Path, layer = "LMF")
        TerrADat <- as.data.frame(TerrADat)
        TerrADat <- dplyr::select(TerrADat, -Shape)
        LMF <- as.data.frame(LMF)
        LMF <- dplyr::select(LMF, -Shape)
    }
    if (Internal) {
        TerrADat <- TerrADat
        LMF <- LMF
    }
    EDIT <- read.csv(file = paste0(EDIT_List_Path, "/", "EDIT_public_ecological_site_list.csv"))
    EDIT[["EcoSiteId_Stripped"]] <- gsub(EDIT[["new_es_symbol"]],
        pattern = "^[RF]", replacement = "")
    ecosite_lut <- unique(EDIT[, c("new_es_symbol", "EcoSiteId_Stripped")])
    any(table(ecosite_lut[["EcoSiteId_Stripped"]]) > 1)
    trouble_ids <- names(table(ecosite_lut[["EcoSiteId_Stripped"]]))[table(ecosite_lut[["EcoSiteId_Stripped"]]) >
        1]
    ecosite_lut_drop_bad <- dplyr::filter(ecosite_lut, !EcoSiteId_Stripped ==
        trouble_ids)
    EcoSites_Update <- dplyr::mutate(ecosite_lut_drop_bad, EcologicalSiteId = EcoSiteId_Stripped)
    LMF_EcoSite <- merge(LMF, EcoSites_Update, by = "EcologicalSiteId")
    LMF_EcoSite <- dplyr::select(LMF_EcoSite, -EcologicalSiteId)
    LMF_EcoSite <- dplyr::rename(LMF_EcoSite, EcologicalSiteId = new_es_symbol)
    LMF_EcoSite <- dplyr::select(LMF_EcoSite, -EcoSiteId_Stripped)
    TerrADat[setdiff(names(LMF_EcoSite), names(TerrADat))] <- NA
    LMF_EcoSite[setdiff(names(TerrADat), names(LMF_EcoSite))] <- NA
    TerrADat[setdiff(names(LMF_EcoSite), names(TerrADat))] <- NA
    LMF_EcoSite[setdiff(names(TerrADat), names(LMF_EcoSite))] <- NA
    TDat_LMF <- rbind(TerrADat, LMF_EcoSite)
    TDat_LMF$DateVisited <- sub("^(\d{4}).*$", "\1", TDat_LMF$DateVisited)
    TDat_LMF <- TDat_LMF %>% dplyr::rename(Year = DateVisited)
    EDIT_rename <- EDIT %>% rename(EcologicalSiteId = new_es_symbol)
    output <- merge(TDat_LMF, EDIT_rename, by = "EcologicalSiteId",
        all = TRUE)
    output <- output %>% dplyr::select(-EcoSiteId_Stripped)
    return(output)
  }

R-Burke/SiteSummaryTool documentation built on Oct. 15, 2020, 8:21 p.m.