aestears · aestears · May 3, 2023 · Apr 11, 2023 · Apr 11, 2023 · Apr 14, 2023
diff --git a/R/aggregateByGenet.R b/R/aggregateByGenet.R
@@ -13,7 +13,7 @@
 #'
 #' @param dat An sf data.frame. Typically this is a data.frame that has been
 #' returned from the [trackSpp()] function, although 'dat' can be any sf
-#' data.frame of plant demographic data in which each genet is given unique
+#' data.frame of organism demographic data in which each genet is given unique
 #' identifying value (what we call here a 'trackID'). If 'dat' already only has
 #' one row for each unique trackID in each unique year (i.e. there are no
 #' vegetative individuals--no ramets), then the output of [aggregateByGenet()]

diff --git a/R/assign.R b/R/assign.R
@@ -1,19 +1,25 @@
 #' Tracks genets through time
 #'
-#' @description This function tracks individual plants through time, but only
+#' @description This function tracks individual organisms through time, but only
 #' for one species in one quadrat. It is designed for use within the
 #'  \code{\link{trackSpp}} function, and is not intended for use on its own.
 #'
 #' @details see \code{\link{trackSpp}} for details of arguments and usage.
 #'
 #' @param dat An sf data.frame of the same format as
 #' \code{\link{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 (default name is "Site"), species name
-#' (default name is "Species"), quadrat identifier (default name is "Quad"),
-#' year of data collection (default name is "Year") and an s.f 'geometry' column
-#' that contains a polygon or multipolygon data type for each
-#' individual observation.
+#' 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.
@@ -872,8 +878,8 @@
               }
 
               ## check: for individuals that are dormant (and only if dorm = 1),
-              # then a really tiny plant can't become a really big plant (i.e. a
-              # plant that is really tiny probably can't go dormant)
+              # then a really tiny organism can't become a really big organism
+              # (i.e. an organism that is really tiny probably can't go dormant)
               if (dorm >= 1 & ## if the dorm argument is > 0...
                   length(unique(round(dat$basalArea_ramet, 5))) > 3 ## if the
                   # sizes are not all the same (i.e. if the species is  measured

diff --git a/R/checkDat.R b/R/checkDat.R
@@ -10,12 +10,17 @@
 #' plantTracker functions.
 #'
 #' @param dat An sf data.frame of the same format as
-#' \code{\link{grasslandData}}. It must have columns that contains a unique
-#' identification for each research site (default name is "Site"), species name
-#' (default name is "Species"), quadrat identifier (default name is "Quad"),
-#' year of data collection (default name is "Year") and an s.f 'geometry' column
-#' that contains a polygon or multipolygon data type for each
-#' individual observation.
+#' \code{\link{grasslandData}}. 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")
 #' @param inv The name of each element of the list is a
 #' quadrat name in 'dat', and the contents of that list element is a numeric
 #' vector of all of the years in which that quadrat (or other unique spatial

diff --git a/R/drawQuadMap.R b/R/drawQuadMap.R
@@ -7,12 +7,19 @@
 #' (either a genet or a ramet) in a unique site/quadrat/year combination. It is
 #' recommended that you only input data for one quadrat at a time. A data.frame
 #' returned by \code{\link{trackSpp}} can be put into this function after being
-#' subset by quadrat. 'dat' must have columns that contain a unique
-#' identification for each research site (default name is "Site"), species name
-#' (default name is "Species"), quadrat identifier (default name is "Quad"),
-#' year of data collection (default name is "Year"), a unique identifier for
-#' each genet (default name is 'trackID') and an s.f 'geometry' column that
-#' contains a polygon or multipolygon data type for each individual observation.
+#' subset by quadrat. 'dat' 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")
+#' * a unique identifier for each genet in character format with no NAs (the
+#' default column name is "trackID")
+#' * an s.f 'geometry' column that contains a polygon or multipolygon data type
+#' for each individual observation (the default column name is "geometry")
 #' @param type A character argument indicating how the plots returned by
 #' `drawQuadMap()` will be color coded. If `type = "bySpecies"`, then
 #' observations are color-coded by species. If `type = "bytrackID"`, then

diff --git a/R/getBasalAreas.R b/R/getBasalAreas.R
@@ -18,11 +18,19 @@
 #' data.frame returned by \code{\link{trackSpp}} can be put directly into this
 #' function. However, it is not necessary for 'dat' to have demographic data or
 #' unique identifiers (i.e. 'trackIDs') assigned. 'dat' must have columns that
-#' contain a unique identification for each research site (default name is
-#' "Site"), species name (default name is "Species"), quadrat identifier
-#' (default name is "Quad"), year of data collection (default name is "Year"),
-#' and an s.f 'geometry' column that contains a polygon or multipolygon data
-#' type for each individual observation. This function should only be used if
+#' 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 should only be used if
 #' the individuals in 'dat' were mapped as polygons that are representative of
 #' their actual basal area, i.e. were not mapped as points.
 #' @param inv The name of each element of the list is a
@@ -61,12 +69,12 @@
 #' four of these columns. The column "absolute_basalArea" has the area of the
 #' quadrat that is occupied by a species in a given unique site/quadrat/year
 #' combination. This is in the same units as the area in 'dat'.
-#' "quad_basalArea" gives the combined basal area of all plants in a given
+#' "quad_basalArea" gives the combined basal area of all organisms in a given
 #' site/quadrat/year. "percent_basalArea" gives the percentage of occupied basal
 #' area within a quadrat that is occupied by each species in a given
 #' site/quadrat/year. For example, species A has a basal area of 22 cm^2 in
 #' quadrat 1 in 2005 ("absolute_basalArea = 22). In 2005, there are 50 cm^2 of
-#' quadrat 1 that are occupied by plants ("quad_basalArea" = 55). 44% of the
+#' quadrat 1 that are occupied by organisms ("quad_basalArea" = 55). 44% of the
 #' occupied basal area in quadrat 1 in 2005 is occupied by species A
 #' ("percent_basalArea" = 44). There may be an 'NA' in the "percent_basalArea"
 #' column if the "quad_basalArea" for that species and year is 0.
@@ -171,13 +179,14 @@ getBasalAreas <- function(dat,
                 by.y = c("Site","Quad","Species", "yearInv"),
                 all = TRUE)
   ## put 0s where they are appropriate (i.e. in years when quad was sampled but
-  # no plants of that species were present)
+  # no organisms of that species were present)
   tempArea[is.na(tempArea$absolute_basalArea),"absolute_basalArea"] <- 0
   datArea <- tempArea
 
   ## calculate the percent of total basal area in that year
-  # (the basal area of species A / basal area of quadrat occupied by any plants)
-  ## get the total plant area by site/quad/year
+  # (the basal area of species A / basal area of quadrat occupied by
+  # any organisms)
+  ## get the total organism area by site/quad/year
   quadBasalArea <- aggregate(x = datArea$absolute_basalArea,
                              by = list(
                                Year = datArea$Year,

diff --git a/R/getLambda.R b/R/getLambda.R
@@ -8,8 +8,8 @@
 #' greater than 1 indicates a population is growing, while a value less than 1
 #' indicates population decline. Lambda is 'infinity' when the basal area or
 #' number of individuals in year t is 0, and is NA when basal area or number of
-#' individuals in year t is zero (i.e. when there are no plants present in year
-#' t). Note that a lambda value is calculated between of the years when a
+#' individuals in year t is zero (i.e. when there are no organims present in
+#' year =t). Note that a lambda value is calculated between of the years when a
 #' quadrat was sampled, even if there is a gap in sampling. For example, a
 #' quadrat is sampled in 1998, 1999, 2001, and 2002 (but skipped in 2000). A
 #' lambda value will be calculated for 1998-1999 and 2001-2002, which is a
@@ -22,13 +22,21 @@
 #' @param dat An sf data.frame in which each row represents a unique polygon
 #' (either a genet or a ramet) in a unique site/quadrat/year combination. A
 #' data.frame returned by \code{\link{trackSpp}} can be put directly into this
-#' function. However, it is not necessary for 'dat' to have demographic data or
-#' unique identifiers (i.e. 'trackIDs') assigned. 'dat' must have columns that
-#' contain a unique identification for each research site (default name is
-#' "Site"), species name (default name is "Species"), quadrat identifier
-#' (default name is "Quad"), year of data collection (default name is "Year"),
-#' and an s.f 'geometry' column that contains a polygon or multipolygon data
-#' type for each individual observation.
+#' function. However, it is not strictly necessary for 'dat' to have demographic
+#' data or unique identifiers (i.e. 'trackIDs') assigned. If there are not
+#' trackIDs assigned for each individual, then the function assumes that each
+#' row of data repesents one genetic individual.'dat' *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")
 #' @param inv The name of each element of the list is a
 #' quadrat name in 'dat', and the contents of that list element is a numeric
 #' vector of all of the years in which that quadrat (or other unique spatial
@@ -284,7 +292,7 @@ getLambda <- function(dat,
           ## get the 'Year_tplus1' value (the next sequential year of sampling,
           # NOT necessarily the next sequential year)
           datSpp$Year_tplus1 <- c(datSpp$Year_t[2:length(datSpp$Year_t)], NA)
-          ## get the 'Yabsolute_basalArea_tplus1' value (the next sequential
+          ## get the 'absolute_basalArea_tplus1' value (the next sequential
           # year of sampling, NOT necessarily the next sequential year)
           datSpp$absolute_basalArea_tplus1 <-
             c(datSpp$absolute_basalArea_t[2:length(
@@ -311,10 +319,6 @@ getLambda <- function(dat,
   # (have an NA for year_tplus1)
   datLambda <- datLambda[is.na(datLambda$Year_tplus1) == FALSE,]
 
-  ## change the values for lambda when area_t and area_tplus1 are both zero
-  # from NaN to NA
-  datLambda[is.nan(datLambda$lambda) == TRUE,"lambda"] <- NA
-
   ## rename the columns to the user-defined columns
   ## from above, user-provided names are stored in 'usrNames'
   defaultNames <- c("Species", "Site", "Quad")

diff --git a/R/getNeighbors.R b/R/getNeighbors.R
@@ -18,12 +18,19 @@
 #'
 #' @param dat An sf data.frame. Each row must represent a unique individual
 #' organism in a unique year. This argument can be a data.frame that is returned
-#' by the \code{\link{trackSpp}} function. It must have columns that contain a
-#' unique identification for each research site (default name is "Site"),
-#' species name (default name is "Species"), quadrat identifier (default name is
-#' "Quad"), year of data collection (default name is "Year"), genet identity
-#' (default name is "trackID"), and an s.f 'geometry' column that contains a
-#' polygon or multipolygon data type for each individual observation.
+#' by the \code{\link{trackSpp}} function. 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")
+#' * a unique identifier for each genet in character format with no NAs (the
+#' default column name is "trackID")
+#' * an s.f 'geometry' column that contains a polygon or multipolygon data type
+#' for each individual observation (the default column name is "geometry")
 #' @param buff A numeric value that is greater than or equal to zero. This
 #' indicates the distance (in the same units as the spatial data in 'dat')
 #' around each focal individual within which you want to look for competitors.

diff --git a/R/getRecruits.R b/R/getRecruits.R
@@ -1,6 +1,6 @@
 #' Calculates the number of recruits of each species per year in each quadrat
 #'
-#' @description This function calculates the number of new plant recruits of
+#' @description This function calculates the number of new recruits of
 #' each species in each quadrat in each year. The input data must already
 #' contain a column indicating whether each observation is classified as a
 #' recruit or not. This recruit status can be generated from the
@@ -12,12 +12,19 @@
 #' @param dat An sf data.frame in which each row represents a unique polygon
 #' (either a genet or a ramet) in a unique site/quadrat/year combination. A
 #' data.frame returned by \code{\link{trackSpp}} can be put directly into this
-#' function. 'dat' must have columns that contain a unique identification for
-#' each research site (default name is "Site"), species name (default name is
-#' "Species"), quadrat identifier (default name is "Quad"), year of data
-#' collection (default name is "Year"), a unique identifier for each genet
-#' (default name is 'trackID'), and an s.f 'geometry' column that contains a
-#' polygon or multipolygon data type for each individual observation.
+#' function. 'dat' 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")
+#' * a unique identifier for each genet in character format with no NAs (the
+#' default column name is "trackID")
+#' * an s.f 'geometry' column that contains a polygon or multipolygon data type
+#' for each individual observation (the default column name is "geometry")
 #' @param byGenet A logical argument. `TRUE` indicates that a new genet will be
 #' considered as only one recruit, even if it consists of multiple ramets.
 #' `FALSE` indicates that each new ramet will be considered as a new recruit,

diff --git a/R/trackSpp.R b/R/trackSpp.R
@@ -1,6 +1,6 @@
 #' Tracks genets through time for multiple species and sites
 #'
-#' @description This function tracks individual plants in mapped quadrats
+#' @description This function tracks individual organisms in mapped quadrats
 #' through time to generate a demographic dataset that includes survival
 #' and growth for each individual.
 #'
@@ -32,12 +32,20 @@
 #' package = "plantTracker")}
 #'
 #' @param dat An sf data.frame of the same format as
-#' \code{\link{grasslandData}}. It must have columns that contain a unique
-#' identification for each research site (default name is "Site"), species name
-#' (default name is "Species"), quadrat identifier (default name is "Quad"),
-#' year of data collection (default name is "Year") and an s.f 'geometry' column
-#' that contains a polygon or multipolygon data type for each
-#' individual observation. This function will add columns called
+#' \code{\link{grasslandData}}. 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")
+#' and an s.f 'geometry' column
+#'
+#' This function will add columns called
 #' "basalArea_ramet", "trackID", "age", "size_tplus1", "recruit," "nearEdge,"
 #' and "survives_tplus1", so 'dat' should not contain columns with these names.
 #' @param inv A named list of the same format as

diff --git a/man/aggregateByGenet.Rd b/man/aggregateByGenet.Rd