Release version 0.1.5

FBerding · Jan 25, 2024 · 66bfbee · 66bfbee
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diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ Trial/
 Trial
 /doc/
 /Meta/
+cran-comments.md
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: iotarelr
 Title: Iota Inter Coder Reliability for Content Analysis
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: c(
     person("Berding", "Florian", , "florian.berding@uni-hamburg.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3593-1695")),
@@ -24,10 +24,10 @@ License: GPL-3
 URL: https://fberding.github.io/iotarelr/
 BugReports: https://github.com/FBerding/iotarelr/issues
 Depends: 
-    R (>= 3.5.0),
+    R (>= 3.5.0)
+Imports: 
     ggplot2,
     ggalluvial,
-Imports: 
     gridExtra,
     methods,
     Rcpp,
@@ -44,4 +44,4 @@ VignetteBuilder:
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,10 @@
-# iotarelr 0.1.4 (developer version)
+# iotarelr 0.1.5
+* Changed the package dependencies of the function plot_iota2_alluvial.
+* Updated syntax for using ggplot2 within functions.
+* Added options to plot_iota2_alluvial and plot_iota allowing to choose legend's
+position and direction.
+
+# iotarelr 0.1.4
 * Correction of a test in testthat which depends on drawing random samples.
 * Introducing the possibility to freely estimate the Assignment Error Matrix
 within the function check_new_rater. Default is FALSE.
@@ -14,16 +20,10 @@ stability of the results. This is the new default for all functions estimating
 a iota2 object.
 
 # iotarelr 0.1.2
-
-November 2022
-
 * Releasing iotarelr 0.1.2
 * Providing Iota Concept of generation two.
 
 # iotarelr 0.1.1
-
-March 2022
-
 * Releasing iotarelr 0.1.1
 * Providing Iota Concept of generation one.
 

diff --git a/R/additional_functions.R b/R/additional_functions.R
@@ -35,65 +35,49 @@
 #' The first component \code{estimates_categorical_level} comprises all
 #' elements that describe the ratings on a categorical level. The elements are
 #' sub-divided into raw estimates and chance-corrected estimates.
+#'
+#' \code{raw_estimates}
 #' \describe{
-#' \item{\code{raw_estimates}}{
-#' \itemize{
-#' \item{\code{alpha_reliability: }}{A vector containing the Alpha
+#' \item{\code{alpha_reliability:}}{A vector containing the Alpha
 #' Reliabilities for each category. These values represent probabilities.}
-#' \item{\code{beta_reliability: }}{A vector containing the Beta Reliabilities for each
+#' \item{\code{beta_reliability:}}{A vector containing the Beta Reliabilities for each
 #' category. These values represent probabilities.}
-#' \item{\code{assignment_error_matrix: }}{An Assignment Error Matrix containing the conditional
+#' \item{\code{assignment_error_matrix:}}{An Assignment Error Matrix containing the conditional
 #' probabilities for assigning a unit of category i to categories 1 to n.}
-#' #' \item{\code{iota: }}
-#' {A vector containing the Iota values for each category.}
-#' }}
-#' \item{\code{elements_chance_corrected}}{
-#' \itemize{
-#' \item{\code{alpha_reliability: }}
-#' {A vector containing the chance-corrected Alpha Reliabilities for each category.}
-#' \item{\code{beta_reliability: }}
-#' {A vector containing the chance-corrected Beta Reliabilities for each category.}
-#' }}
+#' \item{\code{iota:}}{A vector containing the Iota values for each category.}
+#' }
+#' \code{elements_chance_corrected}
+#' \describe{
+#' \item{\code{alpha_reliability:}}{A vector containing the chance-corrected Alpha Reliabilities for each category.}
+#' \item{\code{beta_reliability:}}{A vector containing the chance-corrected Beta Reliabilities for each category.}
 #' }
+#'
 #' The second component \code{estimates_scale_level} contains elements to
 #' describe the quality of the ratings on a scale level. It contains the
 #' following elements:
-#' \itemize{
-#' \item{\code{iota_index: }}
-#' {The Iota Index representing the reliability on a scale level.}
-#' \item{\code{iota_index_d4: }}
-#' {The Static Iota Index, which is a transformation of the original Iota Index,
+#' \describe{
+#' \item{\code{iota_index:}}{The Iota Index representing the reliability on a scale level.}
+#' \item{\code{iota_index_d4:}}{The Static Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
-#' \item{\code{iota_index_dyn2: }}
-#' {The Dynamic Iota Index, which is a transformation of the original Iota Index,
+#' \item{\code{iota_index_dyn2:}}{The Dynamic Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
 #' }
 #' The third component \code{information} contains important information
 #' regarding the parameter estimation. It comprises the following elements:
-#'\itemize{
-#' \item{\code{log_likelihood: }}
-#' {Log-likelihood of the best solution.}
-#' \item{\code{convergence: }}
-#' {If estimation converged 0, otherwise 1.}
-#' \item{\code{est_true_cat_sizes: }}
-#' {Estimated categorical sizes. This is the estimated amount of the categories.}
-#' \item{\code{conformity: }}
-#' {\code{0} if the solution is in line with assumptions of weak superiority.
+#'\describe{
+#' \item{\code{log_likelihood:}}{Log-likelihood of the best solution.}
+#' \item{\code{convergence:}}{If estimation converged 0, otherwise 1.}
+#' \item{\code{est_true_cat_sizes:}}{Estimated categorical sizes. This is the estimated amount of the categories.}
+#' \item{\code{conformity:}}{\code{0} if the solution is in line with assumptions of weak superiority.
 #'  A number greater 0 indicates the number of violations of the assumption
 #'  of weak superiority.}
-#'  \item{\code{random_starts: }}
-#' {Numer of random starts for the EM algorithm.}
-#' \item{\code{boundaries: }}
-#' {\code{False} if the best solution does not contain boundary values.
+#'  \item{\code{random_starts:}}{Numer of random starts for the EM algorithm.}
+#' \item{\code{boundaries:}}{\code{False} if the best solution does not contain boundary values.
 #' \code{True} if the best solution does contain boundary values}
-#' \item{\code{p_boundaries: }}
-#' {Percentage of solutions with boundary values during estimation.}
-#' \item{\code{call: }}
-#' {Name of the function that created the object.}
-#' \item{\code{n_rater: }}
-#' {Number of raters.}
-#' \item{\code{n_cunits: }}
-#' {Number of coding units.}
+#' \item{\code{p_boundaries:}}{Percentage of solutions with boundary values during estimation.}
+#' \item{\code{call:}}{Name of the function that created the object.}
+#' \item{\code{n_rater:}}{Number of raters.}
+#' \item{\code{n_cunits:}}{Number of coding units.}
 #' }
 #'@note The returned object contains further slots since the returned object is
 #'of class \code{iotarelr_iota2}. These slots are empty because they are not part of the
@@ -103,7 +87,7 @@
 #'the coding process with random guessing.
 #'@references  Florian Berding and Julia Pargmann (2022). Iota Reliability Concept
 #'of the Second Generation. Measures for Content Analysis Done by
-#'Humans or Artificial Intelligences. Berlin: Logos.
+#'Humans or Artificial Intelligences. Berlin:Logos.
 #'https://doi.org/10.30819/5581
 #'@export
 check_new_rater<-function(true_values,
@@ -272,7 +256,7 @@ check_new_rater<-function(true_values,
 #'that documentation.
 #'@references  Florian Berding and Julia Pargmann (2022).Iota Reliability Concept
 #'of the Second Generation. Measures for Content Analysis Done by
-#'Humans or Artificial Intelligences. Berlin: Logos.
+#'Humans or Artificial Intelligences. Berlin:Logos.
 #'https://doi.org/10.30819/5581
 #'@export
 
@@ -333,7 +317,7 @@ check_dgf<-function(data,
 #' probability of each true category, and the expected category for every coding unit.
 #'@references  Florian Berding and Julia Pargmann (2022).Iota Reliability Concept
 #'of the Second Generation. Measures for Content Analysis Done by
-#'Humans or Artificial Intelligences. Berlin: Logos.
+#'Humans or Artificial Intelligences. Berlin:Logos.
 #'https://doi.org/10.30819/5581
 #' @export
 
@@ -508,7 +492,7 @@ summary.iotarelr_iota2<-get_summary
 #' Sciences (2nd Ed.). Taylor & Francis.
 #' @references  Berding, Florian, and Pargmann, Julia (2022).Iota Reliability Concept
 #'of the Second Generation.Measures for Content Analysis Done by
-#'Humans or Artificial Intelligences. Berlin: Logos.
+#'Humans or Artificial Intelligences. Berlin:Logos.
 #'https://doi.org/10.30819/5581
 #' @export
 get_consequences<-function(measure_typ="dynamic_iota_index",

diff --git a/R/iota_version_2.R b/R/iota_version_2.R
@@ -97,69 +97,51 @@ get_patterns<-function(data,categorical_levels){
 #' sub-divided into raw estimates and chance-corrected estimates.
 #' \describe{
 #' \item{\code{raw_estimates}}{
-#' \itemize{
-#' \item{\code{alpha_reliability: }}{A vector containing the Alpha
+#' \describe{
+#' \item{\code{alpha_reliability:}}{A vector containing the Alpha
 #' Reliabilities for each category. These values represent probabilities.}
-#' \item{\code{beta_reliability: }}{A vector containing the Beta Reliabilities for each
+#' \item{\code{beta_reliability:}}{A vector containing the Beta Reliabilities for each
 #' category. These values represent probabilities.}
-#' \item{\code{assignment_error_matrix: }}{Assignment Error Matrix containing the conditional
+#' \item{\code{assignment_error_matrix:}}{Assignment Error Matrix containing the conditional
 #' probabilities for assigning a unit of category i to categories 1 to n.}
-#'  \item{\code{iota: }}
-#' {A vector containing the Iota values for each category.}
-#'  \item{\code{iota_error_1: }}
-#' {A vector containing the Iota Error Type I values for each category.}
-#'  \item{\code{iota_error_2: }}
-#' {A vector containing the Iota Error Type II values for each category.}
+#'  \item{\code{iota:}}{A vector containing the Iota values for each category.}
+#'  \item{\code{iota_error_1:}}{A vector containing the Iota Error Type I values for each category.}
+#'  \item{\code{iota_error_2:}}{A vector containing the Iota Error Type II values for each category.}
 #' }}
 #'
 #' \item{\code{elements_chance_corrected}}{
-#' \itemize{
-#' \item{\code{alpha_reliability: }}
-#' {A vector containing the chance-corrected Alpha Reliabilities for each category.}
-#' \item{\code{beta_reliability: }}
-#' {A vector containing the chance-corrected Beta Reliabilities for each category.}
+#' \describe{
+#' \item{\code{alpha_reliability:}}{A vector containing the chance-corrected Alpha Reliabilities for each category.}
+#' \item{\code{beta_reliability:}}{A vector containing the chance-corrected Beta Reliabilities for each category.}
 #' }}
 #'
 #' The second component \code{estimates_scale_level} contains elements for
 #' describing the quality of the ratings on a scale level. It comprises the
 #' following elements:
-#' \itemize{
-#' \item{\code{iota_index: }}
-#' {The Iota Index, representing the reliability on a scale level.}
-#' \item{\code{iota_index_d4: }}
-#' {The Static Iota Index, which is a transformation of the original Iota Index,
+#' \describe{
+#' \item{\code{iota_index:}}{The Iota Index, representing the reliability on a scale level.}
+#' \item{\code{iota_index_d4:}}{The Static Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
-#' \item{\code{iota_index_dyn2: }}
-#' {The Dynamic Iota Index, which is a transformation of the original Iota Index,
+#' \item{\code{iota_index_dyn2:}}{The Dynamic Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
 #' }
 #'
 #' The third component \code{information} contains important information
 #' regarding the parameter estimation. It comprises the following elements:
-#'\itemize{
-#' \item{\code{log_likelihood: }}
-#' {Log-likelihood of the best solution.}
-#' \item{\code{convergence: }}
-#' {If estimation converged 0, otherwise 1.}
-#' \item{\code{est_true_cat_sizes: }}
-#' {Estimated categorical sizes. This is the estimated amount of the categories.}
-#' \item{\code{conformity: }}
-#' {\code{0} if the solution is in line with assumptions of weak superiority.
+#'\describe{
+#' \item{\code{log_likelihood:}}{Log-likelihood of the best solution.}
+#' \item{\code{convergence:}}{If estimation converged 0, otherwise 1.}
+#' \item{\code{est_true_cat_sizes:}}{Estimated categorical sizes. This is the estimated amount of the categories.}
+#' \item{\code{conformity:}}{\code{0} if the solution is in line with assumptions of weak superiority.
 #'  A number greater 0 indicates the number of violations of the assumption
 #'  of weak superiority.}
-#'  \item{\code{random_starts: }}
-#' {Numer of random starts for the EM algorithm.}
-#' \item{\code{boundaries: }}
-#' {\code{False} if the best solution does not contain boundary values.
+#'  \item{\code{random_starts:}}{Numer of random starts for the EM algorithm.}
+#' \item{\code{boundaries:}}{\code{False} if the best solution does not contain boundary values.
 #' \code{True} if the best solution does contain boundary values}
-#' \item{\code{p_boundaries: }}
-#' {Percentage of solutions with boundary values during the estimation.}
-#' \item{\code{call: }}
-#' {Name of the function that created the object.}
-#' \item{\code{n_rater: }}
-#' {Number of raters.}
-#' \item{\code{n_cunits: }}
-#' {Number of coding units.}
+#' \item{\code{p_boundaries:}}{Percentage of solutions with boundary values during the estimation.}
+#' \item{\code{call:}}{Name of the function that created the object.}
+#' \item{\code{n_rater:}}{Number of raters.}
+#' \item{\code{n_cunits:}}{Number of coding units.}
 #' }}
 #'@references  Florian Berding and Julia Pargmann (2022).Iota Reliability Concept
 #'of the Second Generation. Measures for Content Analysis Done by
@@ -318,39 +300,31 @@ compute_iota2<-function(data,
 #' sub-divided into raw estimates and chance-corrected estimates.
 #' \describe{
 #' \item{\code{raw_estimates}}{
-#' \itemize{
-#' \item{\code{iota: }}
-#' {A vector containing the Iota values for each category.}
-#'  \item{\code{iota_error_1: }}
-#' {A vector containing the Iota Error Type I values for each category.}
-#'  \item{\code{iota_error_2: }}
-#' {A vector containing the Iota Error Type II values for each category.}
-#' \item{\code{alpha_reliability: }}{A vector containing the Alpha
+#' \describe{
+#' \item{\code{iota:}}{A vector containing the Iota values for each category.}
+#'  \item{\code{iota_error_1:}}{A vector containing the Iota Error Type I values for each category.}
+#'  \item{\code{iota_error_2:}}{A vector containing the Iota Error Type II values for each category.}
+#' \item{\code{alpha_reliability:}}{A vector containing the Alpha
 #' Reliabilities for each category. These values represent probabilities.}
-#' \item{\code{beta_reliability: }}{A vector containing the Beta Reliabilities for each
+#' \item{\code{beta_reliability:}}{A vector containing the Beta Reliabilities for each
 #' category. These values represent probabilities.}
-#' \item{\code{assignment_error_matrix: }}{Assignment Error Matrix containing the conditional
+#' \item{\code{assignment_error_matrix:}}{Assignment Error Matrix containing the conditional
 #' probabilities for assigning a unit of category i to categories 1 to n.}
 #' }}
 #' \item{\code{elements_chance_corrected}}{
-#' \itemize{
-#' \item{\code{alpha_reliability: }}
-#' {A vector containing the chance-corrected Alpha Reliabilities for each category.}
-#' \item{\code{beta_reliability: }}
-#' {A vector containing the chance-corrected Beta Reliabilities for each category.}
+#' \describe{
+#' \item{\code{alpha_reliability:}}{A vector containing the chance-corrected Alpha Reliabilities for each category.}
+#' \item{\code{beta_reliability:}}{A vector containing the chance-corrected Beta Reliabilities for each category.}
 #' }}
 #' }
 #' The second component \code{estimates_scale_level} contains elements for
 #' describing the quality of the ratings on a scale level. It comprises the
 #' following elements:
-#' \itemize{
-#' \item{\code{iota_index: }}
-#' {The Iota Index, representing the reliability on a scale level.}
-#' \item{\code{iota_index_d4: }}
-#' {The Static Iota Index, which is a transformation of the original Iota Index,
+#' \describe{
+#' \item{\code{iota_index:}}{The Iota Index, representing the reliability on a scale level.}
+#' \item{\code{iota_index_d4:}}{The Static Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
-#' \item{\code{iota_index_dyn2: }}
-#' {The Dynamic Iota Index, which is a transformation of the original Iota Index,
+#' \item{\code{iota_index_dyn2:}}{The Dynamic Iota Index, which is a transformation of the original Iota Index,
 #' in order to consider the uncertainty of estimation.}
 #' }
  #'@references  Florian Berding and Julia Pargmann (2022).Iota Reliability Concept