ebirdst (version 0.3.3)

ebirdst_ppms_ts: Time series of eBird Status and Trends PPMs summarized temporally

Description

Calculate a time series of predictive performance metrics (PPMs) for the eBird Status and Trends model. For each week or month of the year, PPMs will be summarized independently to produce a time series. For further details on eBird Status and Trends PPMs consult the help for ebirdst_ppms.

Usage

ebirdst_ppms_ts(path, ext, summarize_by = c("weeks", "months"), ...)
# S3 method for ebirdst_ppms_ts
plot(x, type = c("binary", "occurrence", "abundance"), metric = "kappa", ...)

Arguments

path

character; directory that the Status and Trends data for a given species was downloaded to. This path is returned by ebirdst_download() or get_species_path().

ext

ebirdst_extent object (optional); the spatial extent over which to calculate the PPMs. Note that ebirdst_extent objects typically specify both a spatial and temporal extent, however, within this function only the spatial component of the extent is used.

summarize_by

character; periods over which to summarize PPMs. PPMs can either be calculated for eBird Status and Trends weeks (as defined in ebirdst_weeks) or for the months of the year.

...

ignored.

x

ebirdst_ppms_ts object; PPMs summarized by weeks or months as calculated by ebirdst_ppms_ts().

type

character; the PPM type to plot, either a binary, occurrence, or abundance PPM can be plotted.

metric

character; the specific metric to plot, the list list of possible metrics varies by PPM type:

• Binary or occurrence: auc, ppc, kappa, bernoulli_dev, sensitivity, specificity

• Abundance: poisson_dev_abd, poisson_dev_occ, spearman_abd, spearman_occ

Value

An ebirdst_pppms_ts object containing a list of three data frames: binary_ppms, occ_ppms, and abd_ppms. Each row of these data frames corresponds to the PPMs from one Monte Carlo iteration for a given time period. Columns correspond to the different PPMS. binary_ppms contains binary or range-based PPMS, occ_ppms contains within-range occurrence probability PPMs, and abd_ppms contains within-range abundance PPMs. In some cases, PPMs may be missing, either because there isn't a large enough test set within the spatiotemporal extent or because average occurrence or abundance is too low. In these cases, try increasing the size of the ebirdst_extent object. plot() can be called on the returned ebirdst_pppms_ts object to plot a time series of a single PPM.

Examples

# NOT RUN {
# download example data
path <- ebirdst_download("example_data", tifs_only = FALSE)
# or get the path if you already have the data downloaded
path <- get_species_path("example_data")

# define a spatial extent to calculate ppms over
e <- ebirdst_extent(c(xmin = -86, xmax = -83, ymin = 42.5, ymax = 44.5))

# compute predictive performance metrics, summarized by months
ppms <- ebirdst_ppms_ts(path = path, ext = e, summarize_by = "months")

# plot time series
# binary, kappa
plot(ppms, type = "binary", metric = "kappa")
# occurrence, sensitivity
plot(ppms, type = "occurrence", metric = "sensitivity")
#' # abundance, poisson deviance
plot(ppms, type = "abundance", metric = "poisson_dev_abd")
# }