minor documentation edits

Minor formatting
kacurtis · Sep 15, 2022 · b08aa20 · b08aa20
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: ObsCovgTools
 Type: Package
 Title: Evaluate Fishery Observer Coverage for Bycatch Estimation
 Version: 3.3.0
-Date: 2022-09-14
+Date: 2022-09-15
 URL: https://kacurtis.github.io/ObsCovgTools, https://github.com/kacurtis/ObsCovgTools
 Depends: R (>= 3.4.0)
 Imports: 

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,6 @@
 # ObsCovgTools 3.3.0
 
-* Implemented an analytical solution for CV corresponding to observer coverage, combining sim_cv_obscov.r and plot_cv_obscov.r into one function analogous to those for the other two management objectives. Elimination of Monte Carlo simulations provides major efficiency gains and increases precision of result. 
+* Implemented an analytical solution for CV corresponding to observer coverage, replacing sim_cv_obscov.r and plot_cv_obscov.r with a single function analogous to those for the other two management objectives. Elimination of Monte Carlo simulations provides major efficiency gains and increases precision of results. 
 
 
 # ObsCovgTools 3.2.1-2

diff --git a/R/plot_cv.r b/R/plot_cv.r
@@ -24,10 +24,10 @@
 #' weight) per unit effort, and (3) the specified dispersion index reflects 
 #' the highest level of any hierarchical variance (e.g., using dispersion index 
 #' at trip level if greater than that at set level). Violating these assumptions 
-#' will likely result in negatively biased projections of bycatch estimation CV 
-#' for a given level of observer coverage. More conservative projections can be 
-#' obtained by using a higher dispersion index \code{d}. Users may want to 
-#' explore uncertainty in dispersion index and in bycatch per unit effort by 
+#' will likely result in negatively biased projections of the observer coverage 
+#' needed to meet a specified objective. More conservative (higher) projections 
+#' can be obtained by using a higher dispersion index \code{d}. Users may want 
+#' to explore uncertainty in dispersion index and in bycatch per unit effort by 
 #' varying those inputs.
 #'   
 #' @return If \code{targetcv} is non-zero, a list with one component:

diff --git a/R/plot_probposobs.r b/R/plot_probposobs.r
@@ -39,11 +39,11 @@
 #' weight) per unit effort, and (3) the specified dispersion index reflects 
 #' the highest level of any hierarchical variance (e.g., using dispersion index 
 #' at trip level if greater than that at set level). Violating these assumptions 
-#' will likely result in positively biased projections of the probability of 
-#' observing bycatch at a given level of observer coverage. More conservative 
-#' projections can be obtained by using a higher dispersion index \code{d}. Users 
-#' may want to explore uncertainty in dispersion index and in bycatch per unit 
-#' effort by varying those inputs.
+#' will likely result in negatively biased projections of the observer coverage 
+#' needed to meet a specified objective. More conservative (higher) projections 
+#' can be obtained by using a higher dispersion index \code{d}. Users may want 
+#' to explore uncertainty in dispersion index and in bycatch per unit effort by 
+#' varying those inputs.
 #' 
 #' @return A list with two components:
 #'   \item{targetoc}{minimum observer coverage in terms of percentage.} 

diff --git a/R/plot_uclnegobs.r b/R/plot_uclnegobs.r
@@ -38,11 +38,11 @@
 #' effort,and (3) the specified dispersion index reflects the highest level of 
 #' any hierarchical variance (e.g., using dispersion index at trip level if 
 #' greater than that at set level). Violating these assumptions will likely 
-#' result in negatively biased projections of the upper confidence limit of total 
-#' bycatch given zero observed. More conservative projections can be obtained by 
-#' using a higher dispersion index \code{d}. Users may want to explore 
-#' uncertainty in dispersion index and in bycatch per unit effort by varying 
-#' those inputs.
+#' result in negatively biased projections of the observer coverage needed to 
+#' meet a specified objective. More conservative (higher) projections can be 
+#' obtained by using a higher dispersion index \code{d}. Users may want to 
+#' explore uncertainty in dispersion index and in bycatch per unit effort by 
+#' varying those inputs.
 #' 
 #' @return A list with components:
 #'   \item{ucldat}{a tibble with the following fields for each coverage level included: 

diff --git a/README.Rmd b/README.Rmd
@@ -15,27 +15,23 @@ output:
 
 ### Description
 
-ObsCovgTools provides tools for evaluating fishery observer coverage, 
-particularly with respect to documenting and estimating rare bycatch. Current 
-functionality includes evaluating observer coverage in terms of (1) probabilities 
-of observing a bycatch event and of any bycatch occurring in total effort, given 
-mean bycatch rate, dispersion index (variance to mean ratio in the bycatch rate), 
-and total fishery effort; (2) upper confidence limit of bycatch when none was 
-observed, given total fishery effort and dispersion index; and (3) bycatch 
-estimation CV (coefficient of variation), given bycatch rate, dispersion 
-index, and total fishery effort. Estimates in all cases are based directly on the 
-corresponding Poisson or negative binomial probability distribution.
+ObsCovgTools provides tools for evaluating fishery observer coverage, particularly with respect to documenting and estimating rare bycatch. Current functionality includes evaluating observer coverage in terms of 
+
+(1) probabilities of observing a bycatch event and of any bycatch occurring in total effort, given mean bycatch rate, dispersion index (variance to mean ratio in the bycatch rate), and total fishery effort; 
+(2) upper confidence limit of bycatch when none was observed, given total fishery effort and dispersion index; and
+(3) bycatch estimation CV (coefficient of variation), given bycatch rate, dispersion index, and total fishery effort. 
+
+Estimates in all cases are based directly on the corresponding Poisson or negative binomial probability distribution.
 
 ### Caveat
 
-The current implementation of ObsCovgTools assumes that (1) observer coverage is 
-representative, (2) bycatch is in terms of individuals (not weight) per unit 
-effort, and (3) the specified dispersion index reflects the highest level of any 
-hierarchical variance (e.g., using dispersion index at trip level if greater than 
-that at set level). Violating these assumptions may result in negatively biased 
-projections of observer coverage required to meet specific objectives. Users may 
-want to explore uncertainty in dispersion index and in bycatch per unit effort by 
-varying those inputs.
+The ObsCovgTools package assumes that 
+
+* observer coverage is representative, 
+* bycatch is in terms of individuals (not weight) per unit effort, and 
+* the specified dispersion index reflects the highest level of any hierarchical variance (e.g., using dispersion index at trip level if greater than that at set level). 
+
+Violating these assumptions may result in negatively biased projections of observer coverage required to meet specific objectives. Users may want to explore uncertainty in dispersion index and in bycatch per unit effort by varying those inputs.
 
 ### Shiny app
 

diff --git a/README.md b/README.md
@@ -14,27 +14,33 @@ date)](https://img.shields.io/github/v/release/kacurtis/ObsCovgTools)](https://g
 ObsCovgTools provides tools for evaluating fishery observer coverage,
 particularly with respect to documenting and estimating rare bycatch.
 Current functionality includes evaluating observer coverage in terms of
-(1) probabilities of observing a bycatch event and of any bycatch
-occurring in total effort, given mean bycatch rate, dispersion index
-(variance to mean ratio in the bycatch rate), and total fishery effort;
-(2) upper confidence limit of bycatch when none was observed, given
-total fishery effort and dispersion index; and (3) bycatch estimation CV
-(coefficient of variation), given bycatch rate, dispersion index, and
-total fishery effort. Estimates in all cases are based directly on or
-simulated from the corresponding Poisson or negative binomial
-probability distribution.
+
+1.  probabilities of observing a bycatch event and of any bycatch
+    occurring in total effort, given mean bycatch rate, dispersion index
+    (variance to mean ratio in the bycatch rate), and total fishery
+    effort;
+2.  upper confidence limit of bycatch when none was observed, given
+    total fishery effort and dispersion index; and
+3.  bycatch estimation CV (coefficient of variation), given bycatch
+    rate, dispersion index, and total fishery effort.
+
+Estimates in all cases are based directly on the corresponding Poisson
+or negative binomial probability distribution.
 
 ### Caveat
 
-The current implementation of ObsCovgTools assumes that (1) observer
-coverage is representative, (2) bycatch is in terms of individuals (not
-weight) per unit effort, and (3) the specified dispersion index reflects
-the highest level of any hierarchical variance (e.g., using dispersion
-index at trip level if greater than that at set level). Violating these
-assumptions may result in negatively biased projections of observer
-coverage required to meet specific objectives. Users may want to explore
-uncertainty in dispersion index and in bycatch per unit effort by
-varying those inputs.
+The ObsCovgTools package assumes that
+
+-   observer coverage is representative,
+-   bycatch is in terms of individuals (not weight) per unit effort, and
+-   the specified dispersion index reflects the highest level of any
+    hierarchical variance (e.g., using dispersion index at trip level if
+    greater than that at set level).
+
+Violating these assumptions may result in negatively biased projections
+of observer coverage required to meet specific objectives. Users may
+want to explore uncertainty in dispersion index and in bycatch per unit
+effort by varying those inputs.
 
 ### Shiny app
 

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.11.4
 pkgdown: 1.5.1
 pkgdown_sha: ~
 articles: []
-last_built: 2022-09-15T08:22Z
+last_built: 2022-09-15T19:14Z
 
diff --git a/docs/reference/plot_cv.html b/docs/reference/plot_cv.html
diff --git a/docs/reference/plot_probposobs.html b/docs/reference/plot_probposobs.html
diff --git a/docs/reference/plot_uclnegobs.html b/docs/reference/plot_uclnegobs.html
diff --git a/inst/shinyapp/obscov/html/about.html b/inst/shinyapp/obscov/html/about.html
@@ -9,22 +9,20 @@
 and total fishery effort; (2) upper confidence limit of bycatch when none was 
 observed, given total fishery effort and dispersion index; and (3) bycatch 
 estimation CV (coefficient of variation), given bycatch rate, dispersion 
-index, and total fishery effort. Estimates in all cases are based directly on or
-simulated from the corresponding Poisson or negative binomial probability 
-distribution.
+index, and total fishery effort. Estimates in all cases are based directly on the corresponding Poisson or negative binomial probability distribution.
 </p>
 <h4>
 Caveat
 </h4>
 <p>
-The current implementation of ObsCovgTools assumes that (1) observer coverage is 
-representative, (2) bycatch is in terms of individuals (not weight) per unit 
-effort, and (3) the specified dispersion index reflects the highest level of any 
-hierarchical variance (e.g., using dispersion index at trip level if greater than 
-that at set level). Violating these assumptions may result in negatively biased 
-projections of observer coverage required to meet specific objectives. Users may 
-want to explore uncertainty in dispersion index and in bycatch per unit effort by 
-varying those inputs.
+The current implementation of ObsCovgTools assumes that 
+<ul>
+  <li>observer coverage is representative,</li>
+  <li>bycatch is in terms of individuals (not weight) per unit effort, and</li>
+  <li>the specified dispersion index reflects the highest level of any 
+hierarchical variance (e.g., using dispersion index at trip level if greater than that at set level).</li>
+</ul>
+Violating these assumptions may result in negatively biased projections of observer coverage required to meet specific objectives. More conservative (higher) projections can be obtained by using a higher dispersion index. Users may want to explore uncertainty in dispersion index and in bycatch per unit effort by varying those inputs.
 </p>
 </div>
 <br/>