makeSppList: makeSppList: creates a species list for each plot

In KateMMiller/forestNETNarch: Package for importing, joining and querying MS Access based NETN forest database tables.

Description

This function creates a plot-level species list from live trees, microplots, quadrats, and additional species lists.

Usage

makeSppList(
  speciesType = c("all", "native", "exotic", "invasive"),
  park = "all",
  from = 2007,
  to = 2018,
  QAQC = FALSE,
  locType = "VS",
  panels = 1:4,
  eventType = "complete",
  output,
  ...
)

Arguments

speciesType

Allows you to filter on native, exotic or include all species. "all" Default. Returns all species. "native" Returns native species only "exotic" Returns exotic species only "invasive" Returns species on the Indicator Invasive List

Value

Returns a dataframe with species list for each plot.

Examples

importData()

# Compile number of invasive species found per plot in most recent survey for all parks
inv_spp <- makeSppList(speciesType = 'invasive', from = 2015, to = 2018)
inv_spp$present<-ifelse(is.na(inv_spp$Latin_Name),0,1)
num_inv_per_plot <- inv_spp %>% group_by(Plot_Name) %>% summarise(numspp=sum(present, na.rm=T))

# Compile species list for a given panel of a park
SARA_spp <- makeSppList(park = 'SARA', panels = 1, from = 2018)

#--- arrange and drop unnecessary fields.
SARA_spp_final <- SARA_spp %>% arrange(Plot_Name, Latin_Name) %>%
  select(Plot_Name, Latin_Name, Common, tree.stems, stocking.index, avg.quad.cover, shrub.cover,
  addspp.present)

#--- make species list for a given plot from 2018
SARA_001_2018_spp <- SARA_spp %>% filter(Plot_Name == 'SARA-001') %>%
  select(Plot_Name, Year, Latin_Name, Common) %>% droplevels()

KateMMiller/forestNETNarch documentation built on Dec. 18, 2021, 2:41 a.m.