Tracks genets through time

This function tracks individual organisms through time, but only for one species in one quadrat. It is designed for use within the trackSpp function, and is not intended for use on its own.

Usage

assign(
  dat,
  inv,
  dorm,
  buff,
  buffGenet,
  clonal,
  flagSuspects = FALSE,
  shrink = 0.1,
  dormSize = 0.05,
  inheritsFromTrackSpp = FALSE,
  nearEdgeBox = NULL,
  ...
)

Arguments

dat

An sf data.frame of the same format as grasslandData. 'dat' must contain data for only one species in one quadrat. It must have columns that contain...

a unique identification for each research site in character format with no NAs (the default column name is "Site")
species name in character format with no NAs (the default column name is "Species")
unique quadrat identifier in character format with no NAs (the default column name is "Quad")
year of data collection in integer format with no NAs (the default column name is "Year")
an s.f 'geometry' column that contains a= polygon or multipolygon data type for each individual observation (the default column name is "geometry")

This function will add columns called "basalArea_ramet", "trackID", "age", "size_tplus1", "recruit" and "survives_tplus1", so 'dat' should not contain columns with these names.

inv

An integer vector that contains all of years in which this quadrat (or other unique spatial area) was sampled. Years must be ordered sequentially.

dorm

A numeric vector of length 1, indicating the number of years this species is allowed to go dormant, i.e. be absent from the map but be considered the same individual when it reappears. This must be an integer greater than or equal to 0.

buff

A numeric vector of length 1 that is greater than or equal to zero, indicating how far (in the same units as spatial values in 'dat') a polygon can move from year t to year t+1 and still be considered the same individual.

buffGenet

A numeric vector of length 1 that is greater than or equal to zero, indicating how close (in the same units as spatial values in 'dat') polygons must be to one another in the same year to be grouped as a genet (if 'clonal' argument = TRUE). This argument is passed to the groupByGenet function, which is used inside the assign function.

clonal

A logical argument of length 1, indicating whether this species is allowed to be clonal or not (i.e. if multiple polygons (ramets) can be grouped into one individual (genet)). If clonal = TRUE, the species is allowed to be clonal, and if clonal = FALSE, the species is not allowed to be clonal.

flagSuspects

A logical argument of length 1, indicating whether observations that are 'suspect' will be flagged. The default is flagSuspects = FALSE. If flagSuspects = TRUE, then a column called 'Suspect' is added to the output data.frame. Any suspect observations get a 'TRUE' in the 'Suspect' column, while non-suspect observations receive a 'FALSE'. There are two ways that an observation can be classified as 'suspect'. First, if two consecutive observations have the same trackID, but the basal area of the observation in year t+1 is less that a certain percentage (defined by the shrink arg.) of the basal area of the observation in year t, it is possible that the observation in year t+1 is a new recruit and not the same individual. The second way an observation can be classified as 'suspect' is if it is very small before going dormant. It is unlikely that a very small individual will survive dormancy, so it is possible that the function has mistakenly given a survival value of '1' to this individual. A 'very small individual' is any observation with an area below a certain percentile (specified by 'dormSize') of the size distribution for this species, which is generated using all of the size data for this species in 'dat'.

shrink

A single numeric value. This value is only used when flagSuspects = TRUE. When two consecutive observations have the same trackID, and the ratio of size_t+1 to size_t is smaller than the value of shrink, the observation in year t gets a 'TRUE' in the 'Suspect' column. For example, shrink = 0.2, and an individual that the tracking function has identified as 'BOUGRA_1992_5' has an area of 9 cm^2 in year t and an area of 1.35 cm^2 in year t+1. The ratio of size t+1 to size t is 1.35/9 = 0.15, which is smaller than the cutoff specified by shrink, so the observation of BOUGRA_1992_5' in year t gets a 'TRUE' in the 'Suspect' column. The default value is shrink = 0.10.

dormSize

A single numeric value. This value is only used when flagSuspects = TRUE and dorm is greater than or equal to 1. An individual is flagged as 'suspect' if it 'goes dormant' and has a size that is less than or equal to the percentile of the size distribution for this species that is designated by dormSize. For example, dormSize = 0.05, and the focal individual has a basal area of 0.5 cm^2. The 5th percentile of the distribution of size for this species, which is made using the mean and standard deviation of all observations in 'dat' for the species in question, is 0.6 cm^2. This individual does not have any overlaps in the next year (year t+1), but does have an overlap in year t+2. However, because the basal area of this observation is smaller than the 5th percentile of size for this species, the observation in year t will get a 'TRUE' in the 'Suspect' column. It is possible that the tracking function has mistakenly assigned a '1' for survival in year t, because it is unlikely that this individual is large enough to survive dormancy. The default value is dormSize = .05.

inheritsFromTrackSpp

A logical argument that is only applicable when 'assign()' is used internally in 'trackSpp()'.

nearEdgeBox

An sf data frame indicating the bounding box of the quadrat. This argument is only used if 'assign()' is used internally in 'trackSpp()'.

...

Other arguments passed on to methods. Not currently used.

Details

see trackSpp for details of arguments and usage.

Usage

Arguments

Details

See also