active.nest: A Function to Infer Nesting Chronology from Nest Observations...
In frousseu/rNest: Estimating Nesting Chronology and Breeding Phenology in Birds

Description Usage Arguments Details Value Note Author(s) See Also Examples

Infers nest chronology from nest observations

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active.nest(d, useprecalc = FALSE, error = FALSE, nparam = NULL, sp = FALSE, year = FALSE, layer = FALSE, region = FALSE, id = FALSE,
int.choice = FALSE, locations = FALSE, progress = TRUE, lsc = NULL, spgroup = NULL, lang = "english", fromtk = FALSE ...)

`d`	A `data.frame` containing observations for one or several nests. An object of class `data.frame` with column names?: nest_id, species_code, date, eggs, young and optionally status_code, lon and lat.
`useprecalc`	When used with the `nestwatch` database, precalculated data can be used to speed up the process whent set to `TRUE`.
`error`	When set to `TRUE`, nest ids generating an error (either due to erroneous data or a bug in Rnest) will be displayed.
`nparam`	A `data.frame` containing nesting parameters for the species. An object of class `data.frame` with column names?: species_code, cmin, cmax, clutch, laying, start, incub and rearing.
`sp`	A set of species for which the nesting chronology has to be inferred. All species are included when the argument is set to `FALSE`. Otherwise, a `vector` with the species code has to be given.
`year`	Used to subset nests to be included based on their date of initiation. All nests are included when the argument is set to `FALSE`. Otherwise, either a `vector` containing dates (in character format) or years (in numeric/integer format) to be included. Years and dates given can precede or exceed values observed in the database. When the nesting chronology of a nest encompasses two years and years are given as an argument, it will be included if its date of initiation corresponds to a year given in the subset. If the argument is a set of dates, nests for which either the initiation or the fledging date correspond to one of the dates given will be included.
`layer`	Name of a layer (ESRI shapefile) used to restrict the subset of nests studied to polygons contained in the layer. All nests are used when layer is set to `FALSE`, unless the argument `int.choice` is set to `TRUE`. Otherwise, a character string giving the name of a layer (without the extension) containing the region of interest has to be given. The file has to be located in the R working directory along with other necessary files to interpret the layer. The shapefile has to be in geographic coordinates with the NAD83 system. Used in conjonction with `region` and `int.choice`.
`region`	Regions to which the nests should be restricted. The two possible values are `FALSE` or a `vector` of the names of regions of interest. When `int.choice` is `TRUE`, the name of the first region will be given to the selected polygon and a warning will be given if more than one region is specified. When `int.choice` is `FALSE`, a layer containing the names of the regions in its data slot has to be given, otherwise, an error message will be returned.
`id`	Names of the columns in the attribute table of the shapefile to be used to create the regions of interest. A character `vector` with the names of columns in the attribute table. When set to `FALSE`, the first column is used to describe the regions.
`int.choice`	Let's the user draw a polygon containing the region of interest. When set to `TRUE`, the user is asked to draw a polygon in the graphic device. If a layer is specified, the polygon is drawn in a plot showing the layer. If layer is set to `FALSE`, a world map is plotted and the user is asked for a polygon. The first 4 clicks on the graphic device will be used to rescale the map to get a greater accuracy in the drawing of the polygon.
`locations`	Used to map the locations of the nests within the region studied. When set to `TRUE`, nest locations contained in the regions of interest are plotted.
`progress`	Displays the progression of the function (number of nests for which the chronology has been estimated). The progression is displayed when progress is set to `TRUE`. This argument uses the function `progress` from the svMisc package.
`lsc`	A named `list` with stages as names and each element of the `list` has to be status codes to be interpreted as such.
`spgroup`	A named `list` with group names as names. Each element of the `list` has to be a `vector` of characters with the species 4-letters AOU codes.
`lang`	Used within the tcltk interface to choose the language used. Default value `"english"`, otherwise `"fran?ais"` is used.
`fromtk`	Used when the function is called within the tcltk interface to generate error and warning messages with `tkmessageBox`. Default value `FALSE`.
`...`	Further arguments to be passed to the `chronology` function.

Details of the algorithm are described in the Rnest manual.

A data.frame with the following columns:

`sp`	species 4-letters AOU code
`id`	nest id
`region`	region where the nest is found
`initiation`	estimated initiation date (character)
`fledging`	estimated fledging date or of departure from the nest date (character)
`warning`	warning encountered when backcalculating