DESCRIPTION

 Package: tvgeom
 Title: The Time-Varying (Right-Truncated) Geometric Distribution
-Version: 1.0.0
+Version: 1.0.1
 [email protected]: c(
     person(given = "Vincent", family = "Landau", role = c("aut", "cre"),
            email = "[email protected]"),
@@ -9,23 +9,31 @@ [email protected]: c(
     person(given = "Conservation Science Partners, Inc.", role = c("cph"),
            email = "[email protected]")
            )
-Description: R package for the time-varying geometric distribution and related
-    functions.
+Description: Probability mass (d), distribution (p), quantile (q), and random 
+    number generating (r and rt) functions for the time-varying right-truncated 
+    geometric (tvgeom) distribution. Also provided are functions to calculate the first 
+    and second central moments of the distribution. The tvgeom distribution
+    is similar to the geometric distribution, but the probability 
+    of success is allowed to vary at each time step, and there are a limited 
+    number of trials. This distribution is essentially a Markov chain, and it
+    is useful for modeling Markov chain systems with a set 
+    number of time steps.
 License: MIT + file LICENSE
 Copyright: 2019 Conservation Science Partners, Inc.
 Encoding: UTF-8
 LazyData: true
+Depends:
+    R (>= 3.5.0)
 Suggests:
     ggthemes,
     ggplot2,
     dplyr,
     tidyr,
     purrr,
-    magrittr,
-    gridExtra
-Imports:
-    utils,
     knitr,
+    rmarkdown,
+    magrittr,
+    gridExtra,
     testthat
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 6.1.1

NEWS.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [1.0.1]
+- Added depends entry for R and cleaned up imports and suggests
+
 ## 1.0.0
-- The initial release of the time-varying geometric distribution R package.
+- The initial release of the tvgeom R package.
 
+[1.0.1]: https://gitlab.com/actionable-phenology/tvgeom/compare/v1.0.0...v1.0.1

R/tvgeom-moments.R

@@ -4,7 +4,8 @@
 #' moment \code{tvgeom_var()} for the time-varying geometric distribution.
 #'
 #' @param prob vector of the probability of success for each trial/time step.
-#'
+#' @return \code{tvgeom_mean} returns the moment (the mean), and
+#' \code{tvgeom_var} returns the second central moment (the variance).
 #' @name tvgeom-moments
 #' @examples
 #' tvgeom_mean(prob = rep(0.1, 5))

R/tvgeom.R

@@ -9,8 +9,10 @@
 #' The time-varying geometric distribution describes the number of independent
 #' Bernoulli trials needed to obtain one success. The probability of success,
 #' \code{prob}, may vary for each trial. It has mass \deqn{p(x) = prob[x] *
-#' prod(1 - prob[1:(x-1)])} with support \eqn{x = 1, 2, ..., n}. For \eqn{i} in
-#' \eqn{prob, 0 \le i \le 1}.
+#' prod(1 - prob[1:(x-1)])} with support \eqn{x = 1, 2, ..., n + 1}, 
+#' where \code{n} equals then length of \code{prob}. For \eqn{i} in
+#' \eqn{prob, 0 \le i \le 1}. The \code{n+1} case represents the case that the event did not
+#' happen in the first n trials.
 #'
 #' @param x,q vector of quantiles representing the trial at which the first
 #' success occurred.
@@ -26,6 +28,10 @@
 #' @param log,log.p logical; if \code{TRUE}, probabilities, p, are given as
 #' \code{log(p)}. Defaults to \code{FALSE}.
 #' @param lower.tail logical; if \code{FALSE}, \code{ptvgeom} returns
+#' @return dtvgeom gives the probability mass, qtvgeom gives the 
+#' quantile functions, ptvgeom gives the distribution function, rtvgeom
+#' generates random numbers, and rttvgeom gives random numbers from the 
+#' distribution truncated at bounds provided by the user.
 #' \eqn{P(X > x)} instead of \eqn{P(X \le x)}. Defaults to \code{TRUE}.
 #' @name tvgeom
 #' @examples

README.md

@@ -2,7 +2,7 @@
 
 ### Description
 
-This R package contains pmf, cdf, quantile, and random number generation functions for the time-varying geometric distribution. The time-varying geometric distribution is derived from the geometric distribution and has a vector of success probabilities as its parameter. Whereas the geometric distribution has a constant probability of success over time and has no upper bound of support, the time-varying geometric distribution has a probability of success that changes over time. Additionally, to accommodate situations in which the event can only occur in $n$ days, after which success can not occur, the time-varying geometric distribution is right-truncated (it has a maximum possible value of the length, *n*, of the probability vector plus 1). When a time-varying geometric distributed variable has value *n+1*, this means the event did not occur in the first *n* time steps. For more detailed information on this package and the time-varying geometric distribution, please see the package vignette.
+This R package contains PMF, CDF, quantile, and random number generation functions for the time-varying right-truncated geometric (tvgeom) distribution. The tvgeom distribution is derived from the geometric distribution and has a vector of success probabilities as its parameter. Whereas the geometric distribution has a constant probability of success over time and has no upper bound of support, the tvgeom distribution has a probability of success that changes over time. Additionally, to accommodate situations in which the event can only occur in $n$ days, after which success can not occur, the tvgeom distribution is right-truncated (it has a maximum possible value of the length, *n*, of the probability vector plus 1). When a tvgeom distributed variable has value *n+1*, this means the event did not occur in the first *n* time steps. For more detailed information on this package and the tvgeom distribution, please see the package vignette.
 
 ### Example
 The following example demonstrates the relationship between the geometric distribution and the time-varying geometric distribution.
@@ -68,4 +68,4 @@ install.packages("tvgeom")
 or to get the latest development version
 ```
 devtools::install_gitlab("actionable-phenology/tvgeom")
-```
\ No newline at end of file
+```

inst/CITATION

@@ -5,12 +5,12 @@ citEntry(entry = "Manual",
   author       = personList(as.person("Vincent A. Landau"),
                    as.person("Luke J. Zachmann")),
   year         = "2019",
-  note         = "R package version X.Y.Z",
+  note         = "R package version 1.0.1",
   url          = "https://gitlab.com/actionable-phenology/tvgeom/",
 
   textVersion  =
   paste("Landau, V. A. and L. J. Zachmann (2019).",
         "tvgeom: an R package for the time-varying geometric distribution.",
-        "R package version X.Y.Z.",
+        "R package version 1.0.1.",
         "URL https://gitlab.com/actionable-phenology/tvgeom/.")
 )

man/tvgeom-moments.Rd

@@ -13,6 +13,10 @@ tvgeom_var(prob)
 \arguments{
 \item{prob}{vector of the probability of success for each trial/time step.}
 }
+\value{
+\code{tvgeom_mean} returns the moment (the mean), and
+\code{tvgeom_var} returns the second central moment (the variance).
+}
 \description{
 Functions to calculate first moment \code{tvgeom_mean()} and second central
 moment \code{tvgeom_var()} for the time-varying geometric distribution.

man/tvgeom.Rd

@@ -30,8 +30,7 @@ success occurred.}
 \item{log, log.p}{logical; if \code{TRUE}, probabilities, p, are given as
 \code{log(p)}. Defaults to \code{FALSE}.}
 
-\item{lower.tail}{logical; if \code{FALSE}, \code{ptvgeom} returns
-\eqn{P(X > x)} instead of \eqn{P(X \le x)}. Defaults to \code{TRUE}.}
+\item{lower.tail}{logical; if \code{FALSE}, \code{ptvgeom} returns}
 
 \item{p}{vector of probabilities at which to evaluate the quantile function.}
 
@@ -45,6 +44,13 @@ distribution is not left-truncated.}
 for random number generation. Defaults to \code{length(prob)}, in which case
 the distribution is not right-truncated.}
 }
+\value{
+dtvgeom gives the probability mass, qtvgeom gives the
+quantile functions, ptvgeom gives the distribution function, rtvgeom
+generates random numbers, and rttvgeom gives random numbers from the
+distribution truncated at bounds provided by the user.
+\eqn{P(X > x)} instead of \eqn{P(X \le x)}. Defaults to \code{TRUE}.
+}
 \description{
 The tvgeom package provides two categories of important functions:
 probability distribution functions (d, p, q, r) and moments (tvgeom_mean and
@@ -60,8 +66,10 @@ distribution with parameter \code{prob}.
 The time-varying geometric distribution describes the number of independent
 Bernoulli trials needed to obtain one success. The probability of success,
 \code{prob}, may vary for each trial. It has mass \deqn{p(x) = prob[x] *
-prod(1 - prob[1:(x-1)])} with support \eqn{x = 1, 2, ..., n}. For \eqn{i} in
-\eqn{prob, 0 \le i \le 1}.
+prod(1 - prob[1:(x-1)])} with support \eqn{x = 1, 2, ..., n + 1},
+where \code{n} equals then length of \code{prob}. For \eqn{i} in
+\eqn{prob, 0 \le i \le 1}. The \code{n+1} case represents the case that the event did not
+happen in the first n trials.
 }
 \section{Package functions}{