Made every instance of fossilsToDraw fossilsFormat. Also changed mino…

…r things to pass CRAN checks (using is() instead of class()).
brpetrucci · Oct 17, 2023 · 2165b43 · 2165b43
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,8 +24,10 @@ Suggests:
  fitdistrplus,
  knitr,
  rmarkdown
+Imports:
+ methods
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
 VignetteBuilder: knitr
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
@@ -30,5 +30,6 @@ importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,segments)
 importFrom(graphics,text)
+importFrom(methods,is)
 importFrom(utils,head)
 importFrom(utils,tail)
diff --git a/NEWS.md b/NEWS.md
@@ -45,7 +45,7 @@ BiSSE, MuSSE, and QuaSSE. See documentation for full reference.
  time. Customization options include which colors to use for each
  state, whether to plot fossils as true occurrence times or ranges
  (already present in 1.0, but now with a dedicated argument for such,
- `fossilsToDraw`), and where to place trait value legend. See
+ `fossilsFormat`), and where to place trait value legend. See
  `?draw.sim`, `?bd.sim.traits`, `?sample.clade.traits`, and the
  `overview` vignette for examples.
 

diff --git a/R/bd.sim.R b/R/bd.sim.R
@@ -49,7 +49,10 @@
 #' simulation will be set for one of the times where \code{N} species are
 #' alive, chosen from all the times there were \code{N} species alive weighted
 #' by how long the simulation was in that situation. Exactly one of \code{tMax}
-#' and \code{N} must be non-\code{Inf}.
+#' and \code{N} must be non-\code{Inf}. Note that if \code{N} is the chosen
+#' condition, \code{mu} cannot be \code{0}, since paelobuddy's current
+#' algorithm would mean only species 1 would have children. Future features
+#' will hopefully remove this limitation.
 #'
 #' @param lShape Shape parameter defining the degree of age-dependency in 
 #' speciation rate. This will be equal to the shape parameter in a Weibull 

diff --git a/R/draw.sim.R b/R/draw.sim.R
@@ -401,11 +401,12 @@ draw.sim <- function (sim, traits = NULL, fossils = NULL, lineageColors = NULL,
  }
 
  # check sortBy
- if (!class(sortBy) %in% c("character", "integer")) {
+ if (!(is(sortBy, "numeric") || 
+ (is(sortBy, "character") && length(sortBy) == 1))) {
  stop("sortBy should be a character or a vector of integers.")
  }
 
- else if ((class(sortBy) == "integer") & !(all(1:length(sim$TE) %in% 
+ else if ((is(sortBy, "numeric")) & !(all(1:length(sim$TE) %in% 
  unique(sortBy)))) {
  stop("sortBy must skip no lineage, and all lineages
  should have unique indices.")

diff --git a/R/phylo.to.sim.R b/R/phylo.to.sim.R
@@ -152,6 +152,8 @@
 #' # testing if simulation and converted object are the same
 #' all.equal(sim, res)
 #' 
+#' @importFrom methods is
+#' 
 #' @name phylo.to.sim
 #' @rdname phylo.to.sim
 #' @export
@@ -382,7 +384,7 @@ phylo.to.sim <- function(phy, mothers, extant, dateFromPresent = TRUE,
  }
 
  # one simple transformation if all lineages are extant:
- if (class(res$TE) == "logical") {
+ if (is(res$TE, "logical")) {
  res$TE <- as.numeric(res$TE)
  }
 

diff --git a/R/sample.clade.R b/R/sample.clade.R
@@ -139,7 +139,7 @@
 #' bins = bins, returnTrue = FALSE)
 #' 
 #' # draw simulation with fossil occurrences as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # sampling can be any function of time 
@@ -170,7 +170,7 @@
 #' bins = bins, returnTrue = FALSE)
 #' 
 #' # draw simulation with fossil occurrences as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # now we can try a step function rate
@@ -206,7 +206,7 @@
 #' bins = bins, returnTrue = FALSE)
 #' 
 #' # draw simulation with fossil occurrences as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # finally, sample.clade also accepts an environmental variable
@@ -317,7 +317,7 @@
 #' # the warning is to let you know the ranges won't be used
 #' 
 #' # and also as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # we can have more parameters on adFun
@@ -397,7 +397,7 @@
 #' # of age (a given percentile of the age, for instance) - see below
 #' 
 #' # draw simulation with fossil occurrences as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # we can also have a hat-shaped increase through the duration of a species
@@ -543,7 +543,7 @@
 #' returnTrue = FALSE)
 #' 
 #' # draw simulation with fossil occurrences as time ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' ###
 #' # we can also have a mix of age-independent and age-dependent
@@ -634,7 +634,7 @@
 #' bins = bins, returnTrue = FALSE)
 #' 
 #' # draw simulation with fossil occurrences as ranges
-#' draw.sim(sim, fossils = fossils, fossilsToDraw = "ranges")
+#' draw.sim(sim, fossils = fossils, fossilsFormat = "ranges")
 #' 
 #' # note how occurrences cluster close to the speciation time of
 #' # species 1, but not its extinction time, since around 5mya

diff --git a/R/sample.clade.traits.R b/R/sample.clade.traits.R
@@ -177,7 +177,7 @@
 #' 
 #' # draw simulation with fossil occurrences as time points AND ranges
 #' draw.sim(sim$SIM, traits = sim$TRAITS, fossils = fossils$FOSSILS,
-#' fossilsToDraw = "all", traitLegendPlacement = "bottomleft")
+#' fossilsFormat = "all", traitLegendPlacement = "bottomleft")
 #' # note that there are a lot of fossils, so the ranges are difficult to see
 #' 
 #' # see ?sample.clade for further examples using different return types

diff --git a/man/bd.sim.Rd b/man/bd.sim.Rd
diff --git a/man/bd.sim.traits.Rd b/man/bd.sim.traits.Rd
diff --git a/man/sample.clade.Rd b/man/sample.clade.Rd
diff --git a/man/sample.clade.traits.Rd b/man/sample.clade.traits.Rd
diff --git a/vignettes/overview.Rmd b/vignettes/overview.Rmd
@@ -192,11 +192,11 @@ simHead <- head(sim, 10)
 suppressMessages(draw.sim(simHead, fossils = fossils))
 ```
 
-We can also visualize the fossil ranges if we take away the `SampT` column, and set the `fossilsToDraw` parameter to `ranges`.
+We can also visualize the fossil ranges if we take away the `SampT` column, and set the `fossilsFormat` parameter to `ranges`.
 
 ```{r}
 # draw longevities with fossil time ranges
-suppressMessages(draw.sim(simHead, fossils = fossils[, -3], fossilsToDraw = "ranges"))
+suppressMessages(draw.sim(simHead, fossils = fossils[, -3], fossilsFormat = "ranges"))
 ```
 
 This fossil record's data frame organization allows for easy evaluation of its components, and is close to ready for use in PyRate, one of the most widely used birth-death rates estimators in the field currently. To make it ready we must manipulate the `Extant` column, left like this for clarity. In PyRate, that column must be `status`, with extant species marked `extant` and extinct species marked `extinct`.