Roll CRAN release 1.3.1 (#6)

* Re-generate documentation... * Change order... * Avoid building vignettes... * Bump news [skip-ci] * Missed the build args... * Fix spelling errors
tmsalab · Mar 22, 2020 · 50e6ebf · 50e6ebf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: cIRT
 Type: Package
 Title: Choice Item Response Theory
-Version: 1.3.0.900
+Version: 1.3.1
 Authors@R: c(
     person("Steven Andrew", "Culpepper", 
            email = "sculpepp@illinois.edu",
@@ -15,7 +15,7 @@ Authors@R: c(
           )
     )
 Description: Jointly model the accuracy of cognitive responses and item choices
-    within a bayesian hierarchical framework as described by Culpepper and
+    within a Bayesian hierarchical framework as described by Culpepper and
     Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package
     contains the datasets used within the analysis of the paper.
 License: GPL (>= 2)
@@ -29,8 +29,9 @@ Suggests:
     knitr,
     rmarkdown,
     covr
-VignetteBuilder: knitr
+LazyData: true
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+Language: en-US
+VignetteBuilder: knitr
+RoxygenNote: 7.1.0
 Roxygen: list(markdown = TRUE)
-LazyData: true
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# cIRT 1.3.0.900
+# cIRT 1.3.1
 
 ## Changes
 
@@ -54,7 +54,7 @@
 # cIRT 1.0.0
 
 ## Modeling Framework
-- Implementation of the hiercharical framework described in "A Hierarchical Model for Accuracy and Choice on Standardized Tests"
+- Implementation of the hierarchical framework described in "A Hierarchical Model for Accuracy and Choice on Standardized Tests"
 - Specifically, a choice inclusive Probit HLM and a Two Parameter Ogive Model.
 
 ## C++ Functions

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -130,9 +130,9 @@ TwoPLChoicemcmc <- function(unique_subject_ids, subject_ids, choices_nk, fixed_e
     .Call(`_cIRT_TwoPLChoicemcmc`, unique_subject_ids, subject_ids, choices_nk, fixed_effects, B, rv_effects_design, gamma, beta, zeta_rv, Sigma_zeta_inv, Y, theta0, a0, b0, mu_xi0, Sig_xi0)
 }
 
-#' Probit Hierarchial Level Model
+#' Probit Hierarchical Level Model
 #'
-#' Performs modeling procedure for a Probit Hierarchial Level Model.
+#' Performs modeling procedure for a Probit Hierarchical Level Model.
 #'
 #' @param unique_subject_ids   A `vector` with length N x 1 containing
 #'                             unique subject IDs.

diff --git a/README.Rmd b/README.Rmd
@@ -24,7 +24,7 @@ knitr::opts_chunk$set(
 <!-- badges: end -->
 
 Jointly model the accuracy of cognitive responses and item choices
-within a bayesian hierarchical framework as described by Culpepper and
+within a Bayesian hierarchical framework as described by Culpepper and
 Balamuta (2015) <doi:10.1007/s11336-015-9484-7>.
 
 ## Installation

diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ Downloads](http://cranlogs.r-pkg.org/badges/grand-total/cIRT?color=brightgreen)]
 <!-- badges: end -->
 
 Jointly model the accuracy of cognitive responses and item choices
-within a bayesian hierarchical framework as described by Culpepper and
+within a Bayesian hierarchical framework as described by Culpepper and
 Balamuta (2015) <doi:10.1007/s11336-015-9484-7>.
 
 ## Installation

diff --git a/cIRT.Rproj b/cIRT.Rproj
@@ -14,5 +14,7 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
+PackageInstallArgs: --no-multiarch --with-keep.source --no-build-vignettes
+PackageBuildArgs: --no-build-vignettes
+PackageCheckArgs: --no-build-vignettes
 PackageRoxygenize: rd,collate,namespace
diff --git a/man/Generate_Choice.Rd b/man/Generate_Choice.Rd
diff --git a/man/TwoPLChoicemcmc.Rd b/man/TwoPLChoicemcmc.Rd
diff --git a/man/cIRT-package.Rd b/man/cIRT-package.Rd
diff --git a/man/cIRT.Rd b/man/cIRT.Rd
diff --git a/man/choice_matrix.Rd b/man/choice_matrix.Rd
diff --git a/man/direct_sum.Rd b/man/direct_sum.Rd
diff --git a/man/payout_matrix.Rd b/man/payout_matrix.Rd
diff --git a/man/probitHLM.Rd b/man/probitHLM.Rd
diff --git a/man/survey_data.Rd b/man/survey_data.Rd
diff --git a/man/trial_matrix.Rd b/man/trial_matrix.Rd
diff --git a/src/project_source.cpp b/src/project_source.cpp
@@ -305,9 +305,9 @@ Rcpp::List TwoPLChoicemcmc(/* New Parameters */
                               Rcpp::Named("Wzeta_0", Wzeta_0));
 }
 
-//' Probit Hierarchial Level Model
+//' Probit Hierarchical Level Model
 //'
-//' Performs modeling procedure for a Probit Hierarchial Level Model.
+//' Performs modeling procedure for a Probit Hierarchical Level Model.
 //'
 //' @param unique_subject_ids   A `vector` with length N x 1 containing
 //'                             unique subject IDs.

diff --git a/vignettes/Estimating-the-Model-in-the-Paper.Rmd b/vignettes/Estimating-the-Model-in-the-Paper.Rmd
@@ -17,7 +17,7 @@ each section in the example displayed in `cIRT()` function.
 # Data
 
 Within this vignette, we used two different data sets to generate a Choice
-Item Response Theory Model with the rountine located in `cIRT`.
+Item Response Theory Model with the routine located in `cIRT`.
 
 ```{r load_pkg}
 library(cIRT)

diff --git a/vignettes/Package-Overview.Rmd b/vignettes/Package-Overview.Rmd
@@ -10,11 +10,11 @@ vignette: >
 
 # Intro
 
-The package is a companion to the paper A hierarchical model for accuracy and choice on standardized tests in [Psychometrika](http://link.springer.com/article/10.1007/s11336-015-9484-7) written by Culpepper, S. A. & Balamuta, J. J. Within this package, we make available the code used for the analysis within the paper as well as the data. 
+The package is a companion to the paper "A hierarchical model for accuracy and choice on standardized tests" in [Psychometrika](http://link.springer.com/article/10.1007/s11336-015-9484-7) written by Culpepper, S. A. & Balamuta, J. J. Within this package, we make available the code used for the analysis within the paper as well as the data. 
 
 # Functions
 
-The package provides C++ implementations of the hierarchial bayesian modeling framework for choice. The primary functions that are novel contributions to psychometric literature are the `probitHLM()` and `TwoPLChoicemcmc()` that respectively provide a choice inclusive Probit HLM and a Two Parameter Ogive Model and are called by an overall wrapper function `cIRT()`. These functions do have an overall dependency on other components that have also been coded within C++ and may benefit a practitioner seeking to do use the same functionality elsewhere.
+The package provides C++ implementations of the hierarchical bayesian modeling framework for choice. The primary functions that are novel contributions to psychometric literature are the `probitHLM()` and `TwoPLChoicemcmc()` that respectively provide a choice inclusive Probit HLM and a Two Parameter Ogive Model and are called by an overall wrapper function `cIRT()`. These functions do have an overall dependency on other components that have also been coded within C++ and may benefit a practitioner seeking to do use the same functionality elsewhere.
 
 * Random Number Generation for the following distributions: Wishart `rwishart()`, Inverse Wishart `riwishart()`, and Multivariate Normal `rmvnorm()`.
 * Matrix Centering `center_matrix()`

diff --git a/vignettes/Simulation-Study-with-cIRT.Rmd b/vignettes/Simulation-Study-with-cIRT.Rmd
@@ -14,7 +14,7 @@ The document addresses the simulation study that was performed to understand whe
 
 # Simulation
 
-The simulation study below is configured to generate results one might obtain from a pool of 1,000 subjects taking a 20 item test. We obtain summarize the results obtained from running the model 100 times over slightly differring $\theta$ and $\eta$. 
+The simulation study below is configured to generate results one might obtain from a pool of 1,000 subjects taking a 20 item test. We obtain summarize the results obtained from running the model 100 times over slightly differing $\theta$ and $\eta$. 
 
 ```{r sim_setup, eval = F}
 ### Variables