add spell check and fix typos that it found

.github/workflows/call-spell-check.yml

@@ -0,0 +1,15 @@
+# run devtools::spell_check()
+name: call-spell-check
+# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+# this workflow runs on pushing to main, pull requests to main, and manually.
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+jobs:
+  call-workflow:
+    uses: nmfs-fish-tools/ghactions4r/.github/workflows/spell-check.yml@main

DESCRIPTION

@@ -34,6 +34,7 @@ Imports:
     stats,
     TMB (>= 1.8.0)
 Suggests:
+    spelling,
     knitr    
 LinkingTo:
     RcppEigen,
@@ -49,3 +50,4 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 SystemRequirements: GNU make, C++17
+Language: en-US

NEWS.md

@@ -16,7 +16,7 @@
 # nwfscAgeingError 1.3.3
 
 * Added a `NEWS.md` file to track changes to the package.
-* Included TMB agemat2.cpp souce code from A. E. Punt
+* Included TMB agemat2.cpp source code from A. E. Punt
 
 # nwfscAgeingError 1.3.2
 

R/estgrowth.vb.R

@@ -9,7 +9,7 @@
 #' @param Ages A vector of ages in years. Values of \code{NA} are accepted.
 #' @param Lengths A vector of Lengths in cm. Lengths can be \code{NULL} if
 #' \code{ReturnType == "Pred"} because you are only predicting using ages, where
-#' the lengths are just needed for estimation purpopses. If not \code{NULL},
+#' the lengths are just needed for estimation purposes. If not \code{NULL},
 #' ensure that there is one length measurement for every age measurement.
 #' Values of \code{NA} are accepted.
 #' @param ReturnType A single character value with \code{"NLL"} being the default,

inst/WORDLIST

@@ -0,0 +1,92 @@
+ADMB
+AFMA
+AICc
+Acknowledgements
+Ageing
+André
+Anoplopoma
+Aquat
+Australias
+BG
+Bertanlaffy
+Bessell
+CSIRO
+Centroberyx
+CreateData
+Curin
+Curvilinear
+Forsythe
+GABRAG
+GLMMs
+Hollings
+KrusicGolub
+Linf
+Macruronus
+MaxAge
+Menten
+Michaelis
+Moler
+NOAA
+NWFSC
+Nreaders
+ORCID
+Osorio
+Pia
+Pinheiro
+Prespecify
+Redfish
+ReturnType
+Rtools
+SERAG
+SESSF
+Sablefish
+Scalefish
+SigmaOpt
+Sillago
+Sporcic
+Springer
+TMB
+TrueAge
+ag
+ageing
+agemat
+al
+cmd
+cpp
+csv
+curvilinear
+dat
+doi
+et
+fimbria
+flindersi
+frac
+gerrardi
+github
+hte
+hyperdistribution
+lda
+maxage
+modelling
+novaezelandiae
+nwfscAgeingError
+otolith
+otoliths
+pers
+png
+pre
+prespecify
+purpopses
+rpt
+sablefish
+scalefish
+selex
+shoudl
+spc
+summarised
+th
+theSERAG
+tpl
+von
+xvec
+yvec

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

vignettes/getting_started.Rmd

@@ -38,7 +38,7 @@ The NOAA Northwest Fisheries Science Center (NWFSC) GitHub site hosts the
 version in the main branch of the repository in May 2024. The ADMB version is 
 still available via the git history.
 
-You can install the TMB branch directly from Github using the code below. Note
+You can install the TMB branch directly from GitHub using the code below. Note
 both TMB and Rtools need to be installed to do this.
 
 ```{r, echo=TRUE, eval=FALSE}
@@ -235,7 +235,7 @@ $$
   \end{cases}
  $$ 
 
-*	`2` The parameters relate to the standard deviation (Michaelis-Menton equation). This option has three parameters that need to be specified for each pair of independent readers in the specification (.spc) file. The standard deviation of random age-reading error, $\sigma_a$, is given by:
+*	`2` The parameters relate to the standard deviation (Michaelis-Menten equation). This option has three parameters that need to be specified for each pair of independent readers in the specification (.spc) file. The standard deviation of random age-reading error, $\sigma_a$, is given by:
 
 $$ 
   \sigma_a = 
@@ -246,7 +246,7 @@ $$
 $$ 
 
 
-* `3` The parameters relate to the coefficient of variation (Michaelis-Menton equation). This option has three parameters that need to be specified for each pair of independent readers in the specification (.spc) file. The coefficient of variation of random age-reading error, $CV_a$, is given by: 
+* `3` The parameters relate to the coefficient of variation (Michaelis-Menten equation). This option has three parameters that need to be specified for each pair of independent readers in the specification (.spc) file. The coefficient of variation of random age-reading error, $CV_a$, is given by: 
 
 $$ 
   CV_a = 
@@ -260,7 +260,7 @@ $$
 
 *	`5` The standard deviation of random age-reading error, $\sigma_a$, is a spline function of age (a Forsythe, Malcolm, and Moler type spline as implemented by `tmbutils::splinefun()`). The number and location (ages) of the knots must be specified, with the number of parameters equal to the number of knots. Bounds and initial parameters need to be specified in log space.
 
-*	`6` The standard deviation of random age-reading error, $\sigma_a$, is a piecewise linear function of age.  The number and location (ages) of the knots must be specified, with the number of parameters equal to the number of knots. Boounds and initial parameters need to be specified in log space.
+*	`6` The standard deviation of random age-reading error, $\sigma_a$, is a piecewise linear function of age.  The number and location (ages) of the knots must be specified, with the number of parameters equal to the number of knots. Bounds and initial parameters need to be specified in log space.
 
 * `7` A linear change in the standard deviation of random age-reading error, $\sigma_a$, with age. This option has two parameters that need to be specified for each pair of independent readers in the specifications (.spc) file.