Merge pull request #16 from nimble-dev/HMM-error-fix

0.3.0

Author: dochvam

.Rbuildignore

@@ -5,6 +5,3 @@
 \.RDataTmp
 run_tests\.R
 ^\.travis\.yml$
-^doc$
-^Meta$
-\.Rmd$

.gitignore

@@ -4,3 +4,7 @@
 .Ruserdata
 .RDataTmp
 ..Rcheck
+doc
+Meta
+inst/doc
+nimbleEcology.Rproj

DESCRIPTION

@@ -1,21 +1,22 @@
 Package: nimbleEcology
 Type: Package
 Title: Distributions for Ecological Models in 'nimble'
-Version: 0.2.2
+Version: 0.3.0
 Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu>
 Authors@R: c(person("Benjamin R.", "Goldstein", role = c("aut", "cre"),
                      email = "ben.goldstein@berkeley.edu"),
               person("Daniel", "Turek", role = "aut"),
               person("Lauren", "Ponisio", role = "aut"),
               person("Perry", "de Valpine", role = "aut"))
-Date: 2020-05-12
+Date: 2020-05-27
 Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. 
   Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models.
   (Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
 License: GPL-3
 Copyright: Copyright (c) 2019, Perry de Valpine, Ben Goldstein, Daniel Turek, Lauren Ponisio
 Depends: R (>= 3.4.0), nimble
 Encoding: UTF-8
+VignetteBuilder: knitr
 LazyData: true
 URL: https://github.com/nimble-dev/nimbleEcology
 Collate:
@@ -29,4 +30,5 @@ Collate:
 RoxygenNote: 7.1.0
 Suggests: 
     rmarkdown,
+    knitr,
     testthat (>= 2.1.0)

NAMESPACE

@@ -1,4 +1,3 @@
-# Generated by roxygen2: do not edit by hand
 
 export(dCJS_ss)
 export(dCJS_sv)

R/dCJS.R

@@ -8,7 +8,7 @@
 #'
 #' @name dCJS
 #'
-#' @param x capture-history vector of 0s (not captured) and 1s (captured).
+#' @param x capture history vector of 0s (not captured) and 1s (captured).
 #' Include the initial capture, so \code{x[1]} should equal 1.
 #' @param probSurvive survival probability, either a time-independent scalar
 #' (for dCJS_s*) or a time-dependent vector (for dCJS_v*) with length
@@ -50,9 +50,8 @@
 #' \code{nimble} model code (via \code{nimbleCode}), \code{len} must be provided
 #' (even though it may seem redundant).
 #'
-#' For more explanation, see
-#' \href{../doc/Introduction_to_nimbleEcology.html}{package vignette} (or
-#' \code{vignette("Introduction_to_nimbleEcology")}).
+#' For more explanation, see package vignette
+#' (\code{vignette("Introduction_to_nimbleEcology")}).
 #'
 #' Compared to writing \code{nimble} models with a discrete latent state for
 #' true alive/dead status at each time and a separate scalar datum for each
@@ -108,7 +107,6 @@
 #' @importFrom stats rbinom runif dbinom
 #'
 #' @examples
-#' \donttest{
 #' # Set up constants and initial values for defining the model
 #' dat <- c(1,1,0,0,0) # A vector of observations
 #' probSurvive <- c(0.6, 0.3, 0.3, 0.1)
@@ -130,7 +128,6 @@
 #' # Calculate log probability of data from the model
 #' CJS_model$calculate()
 #' # Use the model for a variety of other purposes...
-#' }
 
 
 NULL

R/dDHMM.R

@@ -46,8 +46,8 @@
 #'
 #' The probability (or likelihood) of observation \code{x[t, o]} depends on
 #' the occupancy status of the site at time t-1, the transitition
-#' probability of persistence (\code{probPersist} or \code{probPersist[t]}),
-#' colonization (\code{probColonize} or \code{probColonize[t]}), and a
+#' probability of persistence (\code{probPersist} or \code{probPersist[t-1]}),
+#' colonization (\code{probColonize} or \code{probColonize[t-1]}), and a
 #' detection probability (\code{p}, \code{p[t]}, or \code{p[t, o]}).
 #'
 #' The first two letters following the 'dDynOcc_' indicate whether the
@@ -57,7 +57,7 @@
 #' probabilities \code{probColonize[1:(T-1)]}.
 #'
 #' When vectors, \code{probColonize} and \code{probPersist} may be of any
-#' length greater than \code{length(x) - 1}. Only the first \code{length(x) - 1}
+#' length greater than or equal to \code{length(x) - 1}. Only the first \code{length(x) - 1}
 #' indices are used, each corresponding to the transition from time t to t+1
 #' (e.g. \code{probColonize[2]} describes the transition probability from
 #' t = 2 to t = 3). All extra values are ignored. This is to make it easier to
@@ -76,9 +76,8 @@
 #' \code{end = c(4,4,3)}. In this case, the value of \code{x[4,4]} would
 #' be ignored.
 #'
-#' For more explanation, see
-#' \href{../doc/Introduction_to_nimbleEcology.html}{package vignette} (or
-#' \code{vignette("Introduction_to_nimbleEcology")}).
+#' For more explanation, see package vignette
+#' (\code{vignette("Introduction_to_nimbleEcology")}).
 #'
 #' Compared to writing \code{nimble} models with a discrete latent state for
 #' true occupancy status and a separate scalar datum for each observation, use
@@ -115,13 +114,13 @@
 #'
 #' If an algorithm using a \code{nimble} model with this declaration
 #' needs to generate a random draw for \code{detections[1:T, 1:O]}, it
-#' will make a similar invocation of \code{rDynOcc_svm}, with \code{n = 1}.
+#' will make a similar invocation of \code{rDynOcc_ssm}, with \code{n = 1}.
 #'
 #' If the colonization probabilities are time-dependent, one would use:
 #'
 #' \code{detections[1:T] ~ dDynOcc_svm(nrep, init = init_prob,
 #' probPersist = persistence_prob,
-#' probColonize = colonization_prob[1:(T-1)], p = p[1:S, 1:T])}
+#' probColonize = colonization_prob[1:(T-1)], p = p[1:T, 1:O])}
 #'
 #' @return
 #' For \code{dDynOcc_***}: the probability (or likelihood) or log probability
@@ -131,7 +130,6 @@
 #' @seealso For basic occupancy models, see documentation for
 #'   \code{\link{dOcc}}.
 #' @examples
-#' \donttest{
 #' # Set up constants and initial values for defining the model
 #'   x <- matrix(c(0,0,0,0,
 #'                 1,1,1,0,
@@ -176,7 +174,6 @@
 #' # Calculate log probability of data from the model
 #' DynOcc_model$calculate("x")
 #' # Use the model for a variety of other purposes...
-#' }
 
 NULL
 #' @rdname dDynOcc