SummaryTables_Height_WithAttributes: SummaryTables_Height_WithAttributes

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

Description

Produces a DT::datatable of height summaries grouped by individual species, growth habit, or sagebrush species. Summarized across each individual plot or across the entire ecological site(s). Fields for spatial attribute are included (currently hard coded for BLM grazing allotment naming convention. Outputs are html objects that can be directly downloaded to Excel.

Usage

SummaryTables_Height(Species_plots_ecosite, SummaryVar, SummarizeBy, GroupBy, Attributed_Pks)

Arguments

Species_plots_ecosite	Combined AIM and LMF species indicator, subset to your ecological site(s). Returned output from Combine_AIM_LMF_Species and SubsetEcologicalSite_Species.
SummaryVar	"Height"
SummarizeBy	c("Plot", "EcologicalSite")
GroupBy	c("Species", "GrowthHabit", "Sagebrush")
Attributed_Pks	simplified dataframe with PrimaryKeys associated with each shapefile attribute

Author(s)

Rachel Burke, ecologist/analyst @ Jornada

Examples

# To summarize heights by growth habit for each individual plot:

SummaryTables_Height(Species_plots_ecosite, SummaryVar = "Height",
                     SummarizeBy = "Plot", GroupBy = "GrowthHabit", 
                     Attributed_Pks = Attributed_Pks)

# To summarize heights by growth habit across the ecological site(s):

SummaryTables_Height(Species_plots_ecosite, SummaryVar = "Height",
                     SummarizeBy = "EcologicalSite", GroupBy = "GrowthHabit", 
                     Attributed_Pks = Attributed_Pks)


## The function is currently defined as
function(Species_plots_ecosite, 
                          SummaryVar, SummarizeBy, GroupBy, Attributed_Pks){

#Prep
SpeciesList <- SpeciesList 
                                             Family, SpeciesState, 
                                             SynonymOf, UpdatedSpeciesCode, SpeciesState) 
  dplyr::mutate(link = paste("https://plants.sc.egov.usda.gov/core/profile?symbol=", Species, sep = ""))

#Merge with species list so we can hover for scientific name

Species_plots_ecosite <- merge(Species_plots_ecosite , SpeciesList , by = c("Species" , "SpeciesState")) 
      dplyr::select(Species, ScientificName, CommonName, Family, PrimaryKey, 
                PlotID,  AH_SpeciesCover, 
                AH_SpeciesCover_n, Hgt_Species_Avg, 
                Hgt_Species_Avg_n, GrowthHabit, GrowthHabitSub, Duration, 
                Noxious, SG_Group, link, SpeciesState, SynonymOf,
                UpdatedSpeciesCode) 
                dplyr::mutate_if(is.numeric, round , digits = 2) 

#Merge with Attributed_Pks
Species_plots_ecosite_attributed <- merge(Species_plots_ecosite, Attributed_Pks, by = "PrimaryKey", all = TRUE) 
                                    unique() 

EcoSitePlots_Attributed <- merge(EcoSitePlots, Attributed_Pks, by = "PrimaryKey", all = TRUE)

    
#Get Noxious versus Non in Standard Format
    
Species_plots_ecosite_attributed$Noxious <- gsub("YES" , "Yes", Species_plots_ecosite_attributed$Noxious)
Species_plots_ecosite_attributed$Noxious <- gsub("NO", "No", Species_plots_ecosite_attributed$Noxious)  

HgtPrep <- Species_plots_ecosite_attributed 
           filter(!is.na(GrowthHabitSub))  

if(SummaryVar == "Height" & SummarizeBy == "Plot" & GroupBy == "GrowthHabit"){
  
 table  <- HgtPrep 
              summarize(AverageHeight_cm = mean(Hgt_Species_Avg) ,
              Standard_Deviation_cm = sd(Hgt_Species_Avg),
              MinHeight_cm = min(Hgt_Species_Avg) ,
              MaxHeight_cm = max(Hgt_Species_Avg), 
              n= sum(Hgt_Species_Avg_n),
              Allotment = ALLOT_NAME,
              Pasture = PAST_NAME)
              mutate_if(is.numeric, round , digits = 2) 
              DT::datatable(extensions = 'Buttons', filter = "top" , 
                            options = list(scrollX = TRUE ,
                            dom = 'Bfrtip',
                            buttons =
                            list(list(
                            extend = 'collection',
                            buttons = c('csv', 'excel'),
                            text = 'Download Table'))) , 
                 caption = paste("Heights by functional group in: " , 
                                 toString(EcologicalSiteId)) , 
                 rownames = FALSE)
  
}

if(SummaryVar == "Height" & SummarizeBy == "EcologicalSite" & GroupBy == "GrowthHabit"){
  
  table <- HgtPrep 
                     summarize(AverageHeight_cm = mean(Hgt_Species_Avg) ,
                     Standard_Deviation_cm = sd(Hgt_Species_Avg),
                     MinHeight_cm = min(Hgt_Species_Avg) ,
                     MaxHeight_cm = max(Hgt_Species_Avg), 
                     n= sum(Hgt_Species_Avg_n)) 
                     mutate_if(is.numeric, round , digits = 2) 
                     DT::datatable(extensions = 'Buttons', filter = "top" , 
                       options = list(scrollX = TRUE ,
                                 dom = 'Bfrtip',
                                 buttons =
                                 list(list(
                                 extend = 'collection',
                                 buttons = c('csv', 'excel'),
                                 text = 'Download Table'))) , 
                  caption = paste("Heights by functional group in: " , 
                                  toString(EcologicalSiteId)) , 
                  rownames = FALSE)
}


if(SummaryVar == "Height" & SummarizeBy == "Plot" & GroupBy == "Species"){
  # Figure out why this isn't working
  #HgtPrep$Species <- paste0("<a href='",HgtPrep$link,"'>", HgtPrep$Species,"</a>")
              
  table <- HgtPrep 
                                           ScientificName , CommonName , 
                                           GrowthHabitSub, Duration) 
                                   dplyr::select(GrowthHabitSub , Duration , PlotID , 
                                   PrimaryKey , Hgt_Species_Avg , 
                                   Hgt_Species_Avg_n, ALLOT_NAME, ALLOT_NO, PAST_NAME) 
                                   dplyr::rename(Allotment = ALLOT_NAME, 
                                                 AllotmentNumber = ALLOT_NO, 
                                                 Pasture = PAST_NAME) 
                                   DT::datatable(extensions = 'Buttons', 
                                                 filter = "top" , 
                                                 options = list(scrollX = TRUE ,
                                                 dom = 'Bfrtip',
                                                 buttons =
                                                 list(list(
                                                 extend = 'collection',
                                                 buttons = c('csv', 'excel'),
                                                 text = 'Download Table'))) , 
                                   caption = (paste("Species heights in: " , 
                                                    toString(EcologicalSiteId))) , 
                                   rownames = FALSE)

}

if(SummaryVar == "Height" & SummarizeBy == "EcologicalSite" & GroupBy == "Species"){
  
  table <- HgtPrep 
                                CommonName , GrowthHabitSub, Duration) 
                                summarize(AverageHeight_cm = mean(Hgt_Species_Avg) ,
                                Standard_Deviation_cm = sd(Hgt_Species_Avg),
                                MinHeight_cm = min(Hgt_Species_Avg) ,
                                MaxHeight_cm = max(Hgt_Species_Avg),
                                n = sum(Hgt_Species_Avg_n)) 
                                mutate_if(is.numeric, round , digits = 2) 
                                DT::datatable(extensions = 'Buttons', filter = "top" , options = list(scrollX = TRUE ,
                                              dom = 'Bfrtip',
                                              buttons =
                                              list(list(
                                              extend = 'collection',
                                              buttons = c('csv', 'excel'),
                                              text = 'Download Table'))) , 
                               caption = (paste("Heights by species in " , 
                                                toString(EcologicalSiteId))) ,
                                          rownames = FALSE)
  
}

if(SummaryVar == "Height" & SummarizeBy == "Plot" & GroupBy == "Sagebrush"){
    
        table <- HgtPrep 
                 subset(SG_Group == "Sagebrush") 
                  group_by(PlotID, PrimaryKey, Species, ScientificName , 
                           CommonName , SG_Group) 
                  dplyr::select(Species, PlotID , 
                  PrimaryKey , Hgt_Species_Avg , 
                  Hgt_Species_Avg_n, ALLOT_NAME, ALLOT_NO, PAST_NAME) 
                  dplyr::rename(Allotment = ALLOT_NAME, 
                  AllotmentNumber = ALLOT_NO, 
                  Pasture = PAST_NAME) 
                  mutate_if(is.numeric, round , digits = 2) 
                  DT::datatable(extensions = 'Buttons', 
                                filter = "top" , 
                                options = list(scrollX = TRUE ,
                                dom = 'Bfrtip',
                                buttons =
                                list(list(
                                extend = 'collection',
                                buttons = c('csv', 'excel'),
                                text = 'Download Table'))) ,
                caption = (paste("Heights by sagebrush species by plots within " , 
                                 toString(EcologicalSiteId))) ,
                           rownames = FALSE)
  
  
}

if(SummaryVar == "Height" & SummarizeBy == "EcologicalSite" & GroupBy == "Sagebrush"){

                 table <- HgtPrep 
                          subset(SG_Group == "Sagebrush") 
                          group_by(Species, ScientificName , 
                          CommonName , SG_Group) 
                          summarize(AverageHeight_cm = mean(Hgt_Species_Avg) ,
                          Standard_Deviation_cm = sd(Hgt_Species_Avg),
                          MinHeight_cm = min(Hgt_Species_Avg) ,
                          MaxHeight_cm = max(Hgt_Species_Avg),
                          n = sum(Hgt_Species_Avg_n)) 
                          mutate_if(is.numeric, round , digits = 2) 
                          DT::datatable(extensions = 'Buttons', 
                          filter = "top" , 
                          options = list(scrollX = TRUE ,
                                     dom = 'Bfrtip',
                                     buttons =
                                     list(list(
                                     extend = 'collection',
                                     buttons = c('csv', 'excel'),
                                     text = 'Download Table'))) ,
                  caption = (paste("Heights by sagebrush species in " , 
                                   toString(EcologicalSiteId))) ,
                  rownames = FALSE)
  
}

return(table)

}

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