R/SummaryTables_WithAttributes.R
In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data
Defines functions
SummaryTables_WithAttributes
Documented in
SummaryTables_WithAttributes
SummaryTables_WithAttributes <- function(EcoSitePlots, Species_plots_ecosite,
SummaryVar, SummarizeBy, Attributed_Pks){
#Prep
SpeciesList <- SpeciesList %>% dplyr::select(Species, ScientificName, CommonName,
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()
# For some reason there are plots in here with no data. Filtering them out.
Species_plots_ecosite_attributed <- Species_plots_ecosite_attributed %>% filter(!is.na(Species)) %>% filter(!is.na(GrowthHabit))
#Attributing EcoSitePlots
EcoSitePlots_Attributed <- merge(EcoSitePlots, Attributed_Pks, by = "PrimaryKey", all = TRUE)
# Filtering empty plots
EcoSitePlots_Attributed <- EcoSitePlots_Attributed %>% filter(!is.na(TotalFoliarCover))
#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)
# Prep species richness for trace species
#Prep
#Detected in richness only on plot
RichnessPresent <- Species_plots_ecosite_attributed %>% filter(is.na(AH_SpeciesCover))
#Detected in LPI on plot
LPI_Present <- Species_plots_ecosite_attributed %>% filter(AH_SpeciesCover > 0.000000)
#Removes duplicates
LPI_Present_String <- unique(LPI_Present$Species)
#Removes values from richness that also occurred in LPI
RichnessSpecies_Only <- RichnessPresent[!(RichnessPresent[["Species"]] %in% LPI_Present_String),]
#Removes duplicates
TraceCover_List <- unique(RichnessSpecies_Only$Species)
#Get into dataframe (just select state species that were trace)
TraceSpeciesCover <- Species_plots_ecosite_attributed[Species_plots_ecosite_attributed[["Species"]] %in% TraceCover_List,]
TraceCover_Table_SpList <- TraceSpeciesCover %>%
dplyr::select(Species, ScientificName , Family , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group ,
SynonymOf , CommonName ,
UpdatedSpeciesCode, link, ALLOT_NAME, ALLOT_NO) %>% unique() %>% filter(!is.na(Species))
if(SummaryVar == "Species" & SummarizeBy == "Plot"){
#hyperlink species
Species_plots_ecosite_attributed$Species <- paste0("<a href='",Species_plots_ecosite_attributed$link,"'>",Species_plots_ecosite_attributed$Species,"</a>")
table <- Species_plots_ecosite_attributed %>% select(-link) %>% filter(!is.na(AH_SpeciesCover)) %>%
DT::datatable(escape = FALSE, extensions = 'Buttons', filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(extend = 'collection', buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Percent Cover by Species by Plot within " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Species" & SummarizeBy == "EcologicalSite"){
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
#hyperlink species
Species_cover_summary$Species <- paste0("<a href='",Species_cover_summary$link,"'>", Species_cover_summary$Species,"</a>")
table <- Species_cover_summary %>% select(-link) %>% DT::datatable(escape = FALSE,
extensions = 'Buttons',
filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Average Percent Cover Values Across" , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar== "GrowthHabitSub" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>%
group_by(PrimaryKey , PlotID , GrowthHabitSub , Duration) %>%
filter(!is.na(AH_SpeciesCover)) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
filter(!is.na(GrowthHabitSub)) %>%
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("Percent Cover by Structure and Functional Group by Plot within " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar == "GrowthHabitSub" & SummarizeBy == "EcologicalSite"){
#removes trace species
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(GrowthHabitSub, Duration, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
select(-Tally) %>%
filter(!is.na(GrowthHabitSub)) %>%
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("Percent Cover by Structure and Functional Group in " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar== "Noxious" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, AH_NoxCover, AH_NonNoxCover, ALLOT_NAME, ALLOT_NO) %>%
filter(!is.na(AH_NonNoxCover)) %>%
rename(NonNoxious = AH_NonNoxCover, Noxious = AH_NoxCover) %>%
dplyr::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("Percent Cover Noxious Versus Non by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar== "Noxious" & SummarizeBy == "EcologicalSite"){
prep <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, AH_NoxCover, AH_NonNoxCover) %>%
filter(!is.na(AH_NonNoxCover)) %>%
dplyr::rename(NonNoxious = AH_NonNoxCover, Noxious = AH_NoxCover) %>%
gather(key = "Noxious", value = Percent,
NonNoxious:Noxious) %>%
dplyr::mutate(Tally = 1)
prep$Noxious <- gsub("NonNoxious" , "No", prep$Noxious)
prep$Noxious <- gsub("Noxious", "Yes", prep$Noxious)
table <- prep %>% group_by(Noxious) %>%
summarize(AveragePercentCover = mean(Percent) ,
StandardDeviation = sd(Percent),
MinCover = min(Percent) ,
MaxCover = max(Percent) , n = sum(Tally)) %>%
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("Percent Cover Noxious Versus Non in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Woody" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
group_by(GrowthHabit , PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover Woody vs. Non by Plot within: " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Woody" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(GrowthHabit , Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
subset(AveragePercentCover > 0.0000) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(-Tally) %>%
filter(!is.na(GrowthHabit)) %>%
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("Percent Cover Woody vs. Non in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SageGrouseGroup" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(SG_Group)) %>%
filter(!is.na(AH_SpeciesCover)) %>%
group_by(SG_Group, PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover by Sage-Grouse Group by Plot within: " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar == "SageGrouseGroup" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(SG_Group)) %>%
filter(!is.na(AH_SpeciesCover)) %>% mutate(Tally = 1) %>%
group_by(SG_Group, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(-Tally) %>%
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("Percent Cover by Sage-Grouse Group in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "PreferredForb" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>%
mutate(PreferredForb = (SG_Group == "PreferredForb")) %>%
subset(PreferredForb == TRUE) %>%
subset(AH_SpeciesCover > 0.0000) %>%
filter(!is.na(AH_SpeciesCover)) %>%
group_by(Species, PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover by Preferred Forb By Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "PreferredForb" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>%
mutate(PreferredForb = (SG_Group == "PreferredForb")) %>%
subset(PreferredForb == TRUE) %>%
subset(AH_SpeciesCover > 0.0000) %>%
filter(!is.na(AH_SpeciesCover)) %>%
filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>% dplyr::select(-Tally) %>%
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("Percent Cover by Preferred Forb in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "Plot"){
RichnessPresent <- RichnessPresent %>%
dplyr::select(Species, ScientificName , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group,
PrimaryKey, PlotID, link, ALLOT_NAME, ALLOT_NO) %>% filter(!is.na(Species))
RichnessPresent$Species <- paste0("<a href='",RichnessPresent$link,"'>", RichnessPresent$Species,"</a>")
table <- RichnessPresent %>% select(-link) %>%
DT::datatable(escape = FALSE, extensions = 'Buttons',
filter = "top" , options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace Species by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "EcologicalSite"){
TraceCover_Table_SpList$Species <- paste0("<a href='",TraceCover_Table_SpList$link,"'>", TraceCover_Table_SpList$Species,"</a>")
table <- TraceCover_Table_SpList %>% arrange(Species) %>%
select(-link) %>%
DT::datatable(escape = FALSE,
extensions = 'Buttons',
filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace species in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "GroundCover" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>%
filter(!is.na(Percent)) %>% mutate(Tally = 1) %>%
group_by(PlotID, PrimaryKey, Indicator) %>%
mutate_if(is.numeric, round , digits = 2) %>% select(-Tally) %>%
rename(PercentCover = Percent) %>%
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("Percent cover by plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "GroundCover" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>%
filter(!is.na(Percent)) %>% mutate(Tally = 1) %>%
group_by(Indicator) %>%
summarize(AveragePercentCover = mean(Percent) ,
Standard_Deviation = sd(Percent) ,
Low = min(Percent) ,
High = max(Percent), n = sum(Tally)) %>%
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("Average percent cover in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Gap" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
filter(!is.na(Percent)) %>%
mutate_if(is.numeric , round, digits = 2) %>%
group_by(PlotID , PrimaryKey) %>%
mutate_if(is.numeric, round , digits = 2) %>%
rename(Percent_Cover = Percent) %>%
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("Percent cover by canopy gap class by plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Gap" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
filter(!is.na(Percent)) %>%
mutate_if(is.numeric , round, digits = 2) %>%
group_by(Gap_Class_cm) %>%
summarize(AveragePercentCover = mean(Percent) ,
StandardDeviation = sd(Percent),
MinPercentCover = min(Percent) ,
MaxPercentCover = max(Percent)) %>%
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("Percent cover by canopy gap class in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SoilStability" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
filter(!is.na(Rating)) %>%
mutate_if(is.numeric, round, digits = 2) %>%
group_by(PrimaryKey , PlotID) %>%
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("Soil stability ratings by plot in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SoilStability" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
filter(!is.na(Rating)) %>%
mutate_if(is.numeric, round, digits = 2) %>%
group_by(Veg) %>%
summarize(AverageSoilStability = mean(Rating , na.rm = TRUE) ,
StandardDeviation = sd(Rating , na.rm = TRUE) ,
MinSoilStability = min(Rating , na.rm = TRUE) ,
MaxSoilStability = max(Rating, na.rm = TRUE)) %>%
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("Average soil stability ratings in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
return(table)
}
R-Burke/SiteSummaryTool documentation built on Oct. 15, 2020, 8:21 p.m.
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Defines functions SummaryTables_WithAttributes
Documented in SummaryTables_WithAttributes
SummaryTables_WithAttributes <- function(EcoSitePlots, Species_plots_ecosite,
SummaryVar, SummarizeBy, Attributed_Pks){
#Prep
SpeciesList <- SpeciesList %>% dplyr::select(Species, ScientificName, CommonName,
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()
# For some reason there are plots in here with no data. Filtering them out.
Species_plots_ecosite_attributed <- Species_plots_ecosite_attributed %>% filter(!is.na(Species)) %>% filter(!is.na(GrowthHabit))
#Attributing EcoSitePlots
EcoSitePlots_Attributed <- merge(EcoSitePlots, Attributed_Pks, by = "PrimaryKey", all = TRUE)
# Filtering empty plots
EcoSitePlots_Attributed <- EcoSitePlots_Attributed %>% filter(!is.na(TotalFoliarCover))
#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)
# Prep species richness for trace species
#Prep
#Detected in richness only on plot
RichnessPresent <- Species_plots_ecosite_attributed %>% filter(is.na(AH_SpeciesCover))
#Detected in LPI on plot
LPI_Present <- Species_plots_ecosite_attributed %>% filter(AH_SpeciesCover > 0.000000)
#Removes duplicates
LPI_Present_String <- unique(LPI_Present$Species)
#Removes values from richness that also occurred in LPI
RichnessSpecies_Only <- RichnessPresent[!(RichnessPresent[["Species"]] %in% LPI_Present_String),]
#Removes duplicates
TraceCover_List <- unique(RichnessSpecies_Only$Species)
#Get into dataframe (just select state species that were trace)
TraceSpeciesCover <- Species_plots_ecosite_attributed[Species_plots_ecosite_attributed[["Species"]] %in% TraceCover_List,]
TraceCover_Table_SpList <- TraceSpeciesCover %>%
dplyr::select(Species, ScientificName , Family , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group ,
SynonymOf , CommonName ,
UpdatedSpeciesCode, link, ALLOT_NAME, ALLOT_NO) %>% unique() %>% filter(!is.na(Species))
if(SummaryVar == "Species" & SummarizeBy == "Plot"){
#hyperlink species
Species_plots_ecosite_attributed$Species <- paste0("<a href='",Species_plots_ecosite_attributed$link,"'>",Species_plots_ecosite_attributed$Species,"</a>")
table <- Species_plots_ecosite_attributed %>% select(-link) %>% filter(!is.na(AH_SpeciesCover)) %>%
DT::datatable(escape = FALSE, extensions = 'Buttons', filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(extend = 'collection', buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Percent Cover by Species by Plot within " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Species" & SummarizeBy == "EcologicalSite"){
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
#hyperlink species
Species_cover_summary$Species <- paste0("<a href='",Species_cover_summary$link,"'>", Species_cover_summary$Species,"</a>")
table <- Species_cover_summary %>% select(-link) %>% DT::datatable(escape = FALSE,
extensions = 'Buttons',
filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Average Percent Cover Values Across" , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar== "GrowthHabitSub" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>%
group_by(PrimaryKey , PlotID , GrowthHabitSub , Duration) %>%
filter(!is.na(AH_SpeciesCover)) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
filter(!is.na(GrowthHabitSub)) %>%
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("Percent Cover by Structure and Functional Group by Plot within " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar == "GrowthHabitSub" & SummarizeBy == "EcologicalSite"){
#removes trace species
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(GrowthHabitSub, Duration, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
select(-Tally) %>%
filter(!is.na(GrowthHabitSub)) %>%
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("Percent Cover by Structure and Functional Group in " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar== "Noxious" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, AH_NoxCover, AH_NonNoxCover, ALLOT_NAME, ALLOT_NO) %>%
filter(!is.na(AH_NonNoxCover)) %>%
rename(NonNoxious = AH_NonNoxCover, Noxious = AH_NoxCover) %>%
dplyr::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("Percent Cover Noxious Versus Non by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar== "Noxious" & SummarizeBy == "EcologicalSite"){
prep <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, AH_NoxCover, AH_NonNoxCover) %>%
filter(!is.na(AH_NonNoxCover)) %>%
dplyr::rename(NonNoxious = AH_NonNoxCover, Noxious = AH_NoxCover) %>%
gather(key = "Noxious", value = Percent,
NonNoxious:Noxious) %>%
dplyr::mutate(Tally = 1)
prep$Noxious <- gsub("NonNoxious" , "No", prep$Noxious)
prep$Noxious <- gsub("Noxious", "Yes", prep$Noxious)
table <- prep %>% group_by(Noxious) %>%
summarize(AveragePercentCover = mean(Percent) ,
StandardDeviation = sd(Percent),
MinCover = min(Percent) ,
MaxCover = max(Percent) , n = sum(Tally)) %>%
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("Percent Cover Noxious Versus Non in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Woody" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
group_by(GrowthHabit , PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover Woody vs. Non by Plot within: " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Woody" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(GrowthHabit , Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
subset(AveragePercentCover > 0.0000) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(-Tally) %>%
filter(!is.na(GrowthHabit)) %>%
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("Percent Cover Woody vs. Non in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SageGrouseGroup" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(SG_Group)) %>%
filter(!is.na(AH_SpeciesCover)) %>%
group_by(SG_Group, PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover by Sage-Grouse Group by Plot within: " ,
toString(EcologicalSiteId))),
rownames = FALSE)
}
if(SummaryVar == "SageGrouseGroup" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>% filter(!is.na(SG_Group)) %>%
filter(!is.na(AH_SpeciesCover)) %>% mutate(Tally = 1) %>%
group_by(SG_Group, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>%
dplyr::select(-Tally) %>%
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("Percent Cover by Sage-Grouse Group in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "PreferredForb" & SummarizeBy == "Plot"){
table <- Species_plots_ecosite_attributed %>%
mutate(PreferredForb = (SG_Group == "PreferredForb")) %>%
subset(PreferredForb == TRUE) %>%
subset(AH_SpeciesCover > 0.0000) %>%
filter(!is.na(AH_SpeciesCover)) %>%
group_by(Species, PrimaryKey , PlotID) %>%
summarize(PercentCover = sum(AH_SpeciesCover)) %>%
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("Percent Cover by Preferred Forb By Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "PreferredForb" & SummarizeBy == "EcologicalSite"){
table <- Species_plots_ecosite_attributed %>%
mutate(PreferredForb = (SG_Group == "PreferredForb")) %>%
subset(PreferredForb == TRUE) %>%
subset(AH_SpeciesCover > 0.0000) %>%
filter(!is.na(AH_SpeciesCover)) %>%
filter(!is.na(AH_SpeciesCover)) %>%
mutate(Tally = 1) %>%
group_by(Species, Tally) %>%
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally)) %>%
mutate_if(is.numeric, round , digits = 2) %>% dplyr::select(-Tally) %>%
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("Percent Cover by Preferred Forb in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "Plot"){
RichnessPresent <- RichnessPresent %>%
dplyr::select(Species, ScientificName , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group,
PrimaryKey, PlotID, link, ALLOT_NAME, ALLOT_NO) %>% filter(!is.na(Species))
RichnessPresent$Species <- paste0("<a href='",RichnessPresent$link,"'>", RichnessPresent$Species,"</a>")
table <- RichnessPresent %>% select(-link) %>%
DT::datatable(escape = FALSE, extensions = 'Buttons',
filter = "top" , options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace Species by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "EcologicalSite"){
TraceCover_Table_SpList$Species <- paste0("<a href='",TraceCover_Table_SpList$link,"'>", TraceCover_Table_SpList$Species,"</a>")
table <- TraceCover_Table_SpList %>% arrange(Species) %>%
select(-link) %>%
DT::datatable(escape = FALSE,
extensions = 'Buttons',
filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace species in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "GroundCover" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>%
filter(!is.na(Percent)) %>% mutate(Tally = 1) %>%
group_by(PlotID, PrimaryKey, Indicator) %>%
mutate_if(is.numeric, round , digits = 2) %>% select(-Tally) %>%
rename(PercentCover = Percent) %>%
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("Percent cover by plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "GroundCover" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover) %>%
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover) %>%
filter(!is.na(Percent)) %>% mutate(Tally = 1) %>%
group_by(Indicator) %>%
summarize(AveragePercentCover = mean(Percent) ,
Standard_Deviation = sd(Percent) ,
Low = min(Percent) ,
High = max(Percent), n = sum(Tally)) %>%
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("Average percent cover in " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Gap" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
filter(!is.na(Percent)) %>%
mutate_if(is.numeric , round, digits = 2) %>%
group_by(PlotID , PrimaryKey) %>%
mutate_if(is.numeric, round , digits = 2) %>%
rename(Percent_Cover = Percent) %>%
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("Percent cover by canopy gap class by plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Gap" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus) %>%
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus) %>%
filter(!is.na(Percent)) %>%
mutate_if(is.numeric , round, digits = 2) %>%
group_by(Gap_Class_cm) %>%
summarize(AveragePercentCover = mean(Percent) ,
StandardDeviation = sd(Percent),
MinPercentCover = min(Percent) ,
MaxPercentCover = max(Percent)) %>%
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("Percent cover by canopy gap class in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SoilStability" & SummarizeBy == "Plot"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected, ALLOT_NAME, ALLOT_NO) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
filter(!is.na(Rating)) %>%
mutate_if(is.numeric, round, digits = 2) %>%
group_by(PrimaryKey , PlotID) %>%
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("Soil stability ratings by plot in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "SoilStability" & SummarizeBy == "EcologicalSite"){
table <- EcoSitePlots_Attributed %>% dplyr::select(PlotID , PrimaryKey ,
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected) %>%
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected) %>%
filter(!is.na(Rating)) %>%
mutate_if(is.numeric, round, digits = 2) %>%
group_by(Veg) %>%
summarize(AverageSoilStability = mean(Rating , na.rm = TRUE) ,
StandardDeviation = sd(Rating , na.rm = TRUE) ,
MinSoilStability = min(Rating , na.rm = TRUE) ,
MaxSoilStability = max(Rating, na.rm = TRUE)) %>%
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("Average soil stability ratings in: " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
return(table)
}
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