SummaryTables_WithAttributes: SummaryTables_WithAttributes
In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data
Description
Usage
Arguments
Details
Author(s)
Examples
View source: R/SummaryTables_WithAttributes.R
Description
Produces a DT::datatable of cover summaries for species, growth habit, noxious status, woody vs. non-woody, sage-grouse group, preferred forbs for sage-grouse, ground cover indicators, canopy gap, as well as soil stability ratings, and presence of trace species. Tables can be summarized across the entire ecological site(s), or within each individual plot. Outputs are html objects that can be directly downloaded to Excel.
Usage
1
SummaryTables(EcoSitePlots, Species_plots_ecosite, SummaryVar, SummarizeBy, Attributed_Pks)
Arguments
EcoSitePlots
Combined TerrADat and LMF dataframe, subset to your ecological site. Returned object from consecutive Combine_AIM_LMF and SubsetEcologicalSite functions.
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
c("Species", "GrowthHabitSub", "Noxious", "Woody", "SageGrouseGroup", "PreferredForb", "TraceSpecies", "GroundCover", "Gap", "SoilStability")
SummarizeBy
c("Plot", "EcologicalSite")
Attributed_Pks
simplified dataframe with PrimaryKeys associated with each shapefile attribute
Details
To get Attributed_Pks-
attribute_title <- c("ALLOT_NAME", "ALLOT_NO", "PAST_NAME")
TDat_LMF_Attributed <- AttributePlots(TDat_LMF = TDat_LMF, shapefile_name = shapefile_name,
shapefile_path = shapefile_path, attribute_title = attribute_title)
Attributed_Pks <- dplyr::select(TDat_LMF_Attributed, PrimaryKey, all_of(attribute_title))
Author(s)
Rachel Burke, ecologist/analyst @ Jornada
Examples
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#To summarize ground cover variables across each individual plot:
SummaryTables_WithAttributes(EcoSitePlots, Species_plots_ecosite,
SummaryVar = "GroundCover",
SummarizeBy = "Plot",
Attributed_Pks = Attributed_Pks)
#To summarize ground cover variables across an ecological site(s):
SummaryTables_WithAttributes(EcoSitePlots, Species_plots_ecosite,
SummaryVar = "GroundCover",
SummarizeBy = "EcologicalSite",
Attributed_Pks = Attributed_Pks)
## The function is currently defined as
function(EcoSitePlots, Species_plots_ecosite,
SummaryVar, SummarizeBy, 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)
# Prep species richness for trace species
#Prep
#Detected in richness only on plot
RichnessPresent <- Species_plots_ecosite_attributed
#Detected in LPI on plot
LPI_Present <- Species_plots_ecosite_attributed
#Removes duplicates
LPI_Present_String <- unique(LPI_Present$Species)
#Removes values from richness that also occurred in LPI
RichnessSpecies_Only <- RichnessPresent[!(RichnessPresent[["Species"]]
#Removes duplicates
TraceCover_List <- unique(RichnessSpecies_Only$Species)
#Get into dataframe (just select state species that were trace)
TraceSpeciesCover <- Species_plots_ecosite_attributed[Species_plots_ecosite_attributed[["Species"]]
TraceCover_Table_SpList <- TraceSpeciesCover
dplyr::select(Species, ScientificName , Family , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group ,
SynonymOf , CommonName ,
UpdatedSpeciesCode, link, ALLOT_NAME, ALLOT_NO, PAST_NAME)
if(SummaryVar == "Species" & SummarizeBy == "Plot"){
#hyperlink species
Species_plots_ecosite_attributed$Species <- paste0("<a href='",Species_plots_ecosite_attributed$link,"'>",Species_plots_ecosite_attributed$Species,"</a>")
table <- Species_plots_ecosite_attributed
DT::datatable(escape = FALSE, extensions = 'Buttons', filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(extend = 'collection', buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Percent Cover by Species by Plot within " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Species" & SummarizeBy == "EcologicalSite"){
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed
mutate(Tally = 1)
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link)
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally))
mutate_if(is.numeric, round , digits = 2)
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
#hyperlink species
Species_cover_summary$Species <- paste0("<a href='",Species_cover_summary$link,"'>", Species_cover_summary$Species,"</a>")
table <- Species_cover_summary
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)
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
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
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
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
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
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
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(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(AH_SpeciesCover))
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)
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, PAST_NAME)
RichnessPresent$Species <- paste0("<a href='",RichnessPresent$link,"'>", RichnessPresent$Species,"</a>")
table <- RichnessPresent
DT::datatable(escape = FALSE, extensions = 'Buttons',
filter = "top" , options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace Species by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "EcologicalSite"){
TraceCover_Table_SpList$Species <- paste0("<a href='",TraceCover_Table_SpList$link,"'>", TraceCover_Table_SpList$Species,"</a>")
table <- TraceCover_Table_SpList
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
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
group_by(PlotID, PrimaryKey, Indicator)
mutate_if(is.numeric, round , digits = 2)
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
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
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
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus)
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
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)
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
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
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
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
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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Description Usage Arguments Details Author(s) Examples
View source: R/SummaryTables_WithAttributes.R
Description
Produces a DT::datatable of cover summaries for species, growth habit, noxious status, woody vs. non-woody, sage-grouse group, preferred forbs for sage-grouse, ground cover indicators, canopy gap, as well as soil stability ratings, and presence of trace species. Tables can be summarized across the entire ecological site(s), or within each individual plot. Outputs are html objects that can be directly downloaded to Excel.
Usage
1 | SummaryTables(EcoSitePlots, Species_plots_ecosite, SummaryVar, SummarizeBy, Attributed_Pks)
|
Arguments
EcoSitePlots |
Combined TerrADat and LMF dataframe, subset to your ecological site. Returned object from consecutive Combine_AIM_LMF and SubsetEcologicalSite functions. |
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 |
c("Species", "GrowthHabitSub", "Noxious", "Woody", "SageGrouseGroup", "PreferredForb", "TraceSpecies", "GroundCover", "Gap", "SoilStability") |
SummarizeBy |
c("Plot", "EcologicalSite") |
Attributed_Pks |
simplified dataframe with PrimaryKeys associated with each shapefile attribute |
Details
To get Attributed_Pks- attribute_title <- c("ALLOT_NAME", "ALLOT_NO", "PAST_NAME") TDat_LMF_Attributed <- AttributePlots(TDat_LMF = TDat_LMF, shapefile_name = shapefile_name, shapefile_path = shapefile_path, attribute_title = attribute_title) Attributed_Pks <- dplyr::select(TDat_LMF_Attributed, PrimaryKey, all_of(attribute_title))
Author(s)
Rachel Burke, ecologist/analyst @ Jornada
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | #To summarize ground cover variables across each individual plot:
SummaryTables_WithAttributes(EcoSitePlots, Species_plots_ecosite,
SummaryVar = "GroundCover",
SummarizeBy = "Plot",
Attributed_Pks = Attributed_Pks)
#To summarize ground cover variables across an ecological site(s):
SummaryTables_WithAttributes(EcoSitePlots, Species_plots_ecosite,
SummaryVar = "GroundCover",
SummarizeBy = "EcologicalSite",
Attributed_Pks = Attributed_Pks)
## The function is currently defined as
function(EcoSitePlots, Species_plots_ecosite,
SummaryVar, SummarizeBy, 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)
# Prep species richness for trace species
#Prep
#Detected in richness only on plot
RichnessPresent <- Species_plots_ecosite_attributed
#Detected in LPI on plot
LPI_Present <- Species_plots_ecosite_attributed
#Removes duplicates
LPI_Present_String <- unique(LPI_Present$Species)
#Removes values from richness that also occurred in LPI
RichnessSpecies_Only <- RichnessPresent[!(RichnessPresent[["Species"]]
#Removes duplicates
TraceCover_List <- unique(RichnessSpecies_Only$Species)
#Get into dataframe (just select state species that were trace)
TraceSpeciesCover <- Species_plots_ecosite_attributed[Species_plots_ecosite_attributed[["Species"]]
TraceCover_Table_SpList <- TraceSpeciesCover
dplyr::select(Species, ScientificName , Family , GrowthHabit ,
GrowthHabitSub , Duration, Noxious , SG_Group ,
SynonymOf , CommonName ,
UpdatedSpeciesCode, link, ALLOT_NAME, ALLOT_NO, PAST_NAME)
if(SummaryVar == "Species" & SummarizeBy == "Plot"){
#hyperlink species
Species_plots_ecosite_attributed$Species <- paste0("<a href='",Species_plots_ecosite_attributed$link,"'>",Species_plots_ecosite_attributed$Species,"</a>")
table <- Species_plots_ecosite_attributed
DT::datatable(escape = FALSE, extensions = 'Buttons', filter = "top" ,
options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(extend = 'collection', buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Percent Cover by Species by Plot within " , toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "Species" & SummarizeBy == "EcologicalSite"){
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite_attributed
mutate(Tally = 1)
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link)
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally))
mutate_if(is.numeric, round , digits = 2)
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
#hyperlink species
Species_cover_summary$Species <- paste0("<a href='",Species_cover_summary$link,"'>", Species_cover_summary$Species,"</a>")
table <- Species_cover_summary
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)
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
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
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
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
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
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
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(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(AH_SpeciesCover))
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)
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, PAST_NAME)
RichnessPresent$Species <- paste0("<a href='",RichnessPresent$link,"'>", RichnessPresent$Species,"</a>")
table <- RichnessPresent
DT::datatable(escape = FALSE, extensions = 'Buttons',
filter = "top" , options = list(scrollX = TRUE ,
dom = 'Bfrtip',
buttons =
list(list(
extend = 'collection',
buttons = c('csv', 'excel'),
text = 'Download Table'))) ,
caption = (paste("Trace Species by Plot within " ,
toString(EcologicalSiteId))) ,
rownames = FALSE)
}
if(SummaryVar == "TraceSpecies" & SummarizeBy == "EcologicalSite"){
TraceCover_Table_SpList$Species <- paste0("<a href='",TraceCover_Table_SpList$link,"'>", TraceCover_Table_SpList$Species,"</a>")
table <- TraceCover_Table_SpList
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
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
group_by(PlotID, PrimaryKey, Indicator)
mutate_if(is.numeric, round , digits = 2)
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
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
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
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus)
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
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)
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
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected, ALLOT_NAME, ALLOT_NO, PAST_NAME)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
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
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
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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