Merge pull request #3 from Kimitsuna-Goblin/develop

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Kimitsuna-Goblin · Jan 8, 2024 · 24b5146 · 24b5146
2 parents d593e49 + 2395ba7
commit 24b5146
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,3 +6,4 @@
 ^\.github$
 ^README(\.|\.[a-z]+\.)md$
 ^LICENSE\.md$
+^cran.comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ggd
 Type: Package
 Title: Gradational Gaussian Distribution Reference Class
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person( given   = "Kimitsuna",
             family  = "Ura",

diff --git a/R/ggd.1.R b/R/ggd.1.R
@@ -60,8 +60,8 @@ f.t3.p <- list( function( x, m, s )
 #' @field   mix.type        An integer which represents how to mix normal distributions
 #'                          of the components.
 #'
-#'                          The type of the distribution model and the row number of \code{cmp}
-#'                          field will be as follows with this value:
+#'                          The type of the distribution model and the number of rows
+#'                          in \code{cmp} field will be as follows with this value:
 #'                          \itemize{
 #'                              \item \code{0} : Normal distribution.
 #'                                        \code{cmp} has only 1 row.
@@ -389,7 +389,7 @@ GGD$methods(
 #' Clear fields
 #'
 #' Clears all fields. The lengths of all vector fields and the number of rows
-#' in the \code{cmp} field will be \code{0}.
+#' in \code{cmp} field will be \code{0}.
 #' @name    clear
 #' @aliases clear
 #' @aliases \S4method{clear}{GGD}
@@ -417,7 +417,7 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Adjust each row name of the cmp field.
+#' Adjust each row name of cmp
 #'
 #' Sets each row name of \code{cmp} field according to \code{mix.type} field.
 #' Normally, users of this class don't need to call this method directly.
@@ -474,7 +474,7 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Adjust the kind.index field
+#' Adjust kind and kind.index fields
 #'
 #' Sets \code{kind.index} and \code{kind} fields according to
 #' \code{mix.type} and \code{cmp} fields.
@@ -637,7 +637,7 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Index number of the kind of distribution
+#' Index number of the kind
 #'
 #' Gets index numbers which represent the kinds of distributions.
 #' @export
@@ -765,7 +765,7 @@ ggd.kind.index <- function( objs, undef.err = FALSE )
 }
 
 ################################################################################################
-#' String of the kind of distribution
+#' String of the kind
 #'
 #' Gets the strings which represent the kinds of distributions.
 #' @export
@@ -819,7 +819,7 @@ ggd.kind <- function( objs )
 }
 
 ################################################################################################
-#' Get mix.type according to grad
+#' mix.type according to grad
 #'
 #' Gets the value for \code{mix.type} field of \code{GGD} object which is appropriate to
 #' given \code{grad} value.
@@ -895,7 +895,7 @@ ggd.mix.type.for <- function( grad = c( "default", "normal", "h", "v", "v2", "v3
 }
 
 ################################################################################################
-#' Get mix.type according to kind.index
+#' mix.type according to kind.index
 #'
 #' Gets a vector of integers of \code{mix.type}s
 #' which are appropriate to the indicated index numbers of \code{ggd:::kinds}.
@@ -931,7 +931,7 @@ ggd.mix.type.for.kind.index <- function( kind.index )
 }
 
 ################################################################################################
-#' Get number of components according to the grad value and others
+#' Number of components according to grad
 #'
 #' Gets the number of components for \code{cmp} field of \code{GGD} object
 #' which is appropriate to given \code{grad} or \code{mix.type} argument.
@@ -1078,9 +1078,9 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Judge if normal distribution
+#' Judge if normal
 #'
-#' Referring only \code{cmp} field, checks if the distribution is a normal distribution.
+#' Referring \code{cmp} field, checks if the distribution is essentially a normal distribution.
 #' Note, this function does not check \code{kind} and \code{kind.index} fields.
 #' @name    is.normal
 #' @aliases is.normal
@@ -1109,9 +1109,9 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Judge if horizontal gradational distribution
+#' Judge if horizontal
 #'
-#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is constructed as
+#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is essentially
 #' a horizontal gradational distribution.
 #' When \code{mix.type = 4}, if it is essentially a horizontal gradational distribution,
 #' this function returns \code{TRUE}.
@@ -1168,9 +1168,9 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Judge if vertical gradation of 2 normal distributions
+#' Judge if 2-component vertical
 #'
-#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is constructed as
+#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is essentially
 #' a vertical gradation of 2 normal distributions.
 #' Even when \code{cmp} field has 3 rows with \code{mix.type = 3}, if the components of
 #' the left-tail side and the right-tail side are the same, this function returns \code{TRUE},
@@ -1233,9 +1233,9 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Judge if vertical gradation of 3 normal distributions
+#' Judge if 3-component vertical
 #'
-#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is constructed as
+#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is essentially
 #' a vertical gradation of 3 normal distributions.
 #' Note! when \code{mix.type = 4},
 #' if the right-top-side and left-top-side components are the same
@@ -1295,9 +1295,9 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Judge if horizontal-vertical gradation
+#' Judge if horizontal-vertical
 #'
-#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is constructed as
+#' Referring \code{mix.type} and \code{cmp} field, checks if the distribution is essentially
 #' a horizontal-vertical gradation of 4 (2x2) normal distributions.
 #' @name    is.hv
 #' @aliases is.hv
@@ -1349,13 +1349,13 @@ GGD$methods(
         }
         else
         {
-            return ( isTRUE( mix.type == 4 ) && !is.h() && !is.v2() )
+            return ( isTRUE( mix.type == 4 ) )
         }
     }
 )
 
 ################################################################################################
-#' Judge if symmetric distribution
+#' Judge if symmetric
 #'
 #' Referring \code{mix.type} and \code{cmp} field,
 #' checks if the probability density function is symmetric about the mean.

diff --git a/R/ggd.apply.R b/R/ggd.apply.R
@@ -10,7 +10,7 @@
 #  Functions
 
 ################################################################################################
-#' Apply functions to elements of cmp
+#' Apply functions to cmp
 #'
 #' Applies a function to each element in the \code{cmp} field.
 #' Different functions can be applied to \code{mean} column and \code{sd} column.
@@ -58,7 +58,7 @@
 #'      (e.g., \code{\link[ggd]{adjust.cmp}}, \code{\link[ggd]{round.cmp}}, etc.)
 #'      for the object of the 2nd argument, since they may update the values of the fields.
 #'
-#'      This function does not change the number of rows of the \code{cmp} field,
+#'      This function does not change the number of rows in \code{cmp} field,
 #'      no matter what results are obtained.
 #' @examples
 #'  a <- ggd.set.cmp( data.frame( mean = c( -0.5, 0, 0.5 ), sd = c( 1, 0.8, 1.2 ) ) )
@@ -137,12 +137,12 @@ apply.cmp.sub <- function( f, values, obj )
 }
 
 ################################################################################################
-#' Rounding of numbers in cmp
+#' Rounding values in cmp
 #'
 #' Rounds the values of all elements in the \code{cmp} field and adjusts other fields
 #' accordingly.
 #' \code{\link[base]{round}} and \code{\link[base]{signif}} functions can apply.
-#' These functions does not change the number of rows of \code{cmp} field,
+#' These functions does not change the number of rows in \code{cmp} field,
 #' no matter what results are obtained.
 #' If an error occurs, these functions do not clear the object, but retains the values of
 #' all fields.

diff --git a/R/ggd.file.R b/R/ggd.file.R
@@ -10,7 +10,7 @@
 #  Functions
 
 ################################################################################################
-#' Read a composition from a CSV file
+#' Read a composition
 #'
 #' Reads a CSV file recorded the composition of a \code{\link[ggd]{GGD}} object
 #' and generates a \code{\link[ggd]{GGD}} object.
@@ -132,7 +132,7 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Write the composition to a CSV file
+#' Write the composition
 #'
 #' Writes the composition of a \code{\link[ggd]{GGD}} object as a CSV file.
 #' Mean values and standard deviations of the components are recorded to a maximum length of

diff --git a/R/ggd.mean.sd.R b/R/ggd.mean.sd.R
@@ -499,7 +499,7 @@ calc.v.t4.via.integrate <- function( means, sds, mean = calc.mean( 4, means, sds
 }
 
 ################################################################################################
-#' Adjust the median, mean and sd fields
+#' Adjust median, mean and sd fields
 #'
 #' Calculates the median, the mean and the standard deviation of the distribution model and
 #' sets those values into the fields.

diff --git a/R/ggd.nls.freq.R b/R/ggd.nls.freq.R
@@ -301,7 +301,7 @@
 #'      You know a standard deviation must be a non-zero positive value.
 #'      But if you use standard deviations directly in the formula for \code{\link[stats]{nls}},
 #'      they will sometimes drop into negative values while the Gauss-Newton algorithm is running
-#'      and the algorithm will fail, even if it can reach to convergence if done better.
+#'      and the algorithm will fail, even if it can reach convergence if done better.
 #'
 #'      So, to avoid such failures, we use square roots of standard deviations and
 #'      take squares of them in the formula for \code{\link[stats]{nls}}.
@@ -1123,7 +1123,7 @@ extract.freq.data <- function( data, x, freq )
     data.ext <- extract.complete.x.y( data, x, freq, "freq" )
     if ( nrow( data.ext ) < 3 )
     {
-        stop( "Error: The row number of data is too small." )
+        stop( "Error: Too few rows for data." )
     }
 
     # Check if rows are sorted.
@@ -1298,14 +1298,14 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
     #       but closer to mean of the frequency distribution than "means".
     #       These are used when we do not want the initial mean values to be dispersed.
     #
-    #   sqrt.sd.mid:
+    #   sqrt.sds.mid:
     #       Global or local standard deviation corresponding to around center of the range of
     #       the frequency distribution.
     if ( is.na( start.level ) )
     {
         # Level NA: all parameters are NA.
         means.mid <- means <- rep( NA_real_, 4 )
-        sqrt.sd.mid <- sqrt.sds <- rep( NA_real_, 4 )
+        sqrt.sds.mid <- sqrt.sds <- rep( NA_real_, 4 )
 
         mean.lower <- mean.upper <- mean.inner <- mean.outer <- NA_real_
         sqrt.sd.lower <- sqrt.sd.upper <- sqrt.sd.inner <- sqrt.sd.outer <- NA_real_
@@ -1320,7 +1320,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
         sqrt.sd.lower <- sqrt.sd.upper <- sqrt.sd.inner <- sqrt.sd.outer <- sqrt( data.sd )
 
         means.mid <- rep( data.mean, 4 )
-        sqrt.sd.mid <- sqrt( data.sd )
+        sqrt.sds.mid <- sqrt( data.sd )
     }
     else if ( start.level == 1 )
     {
@@ -1352,7 +1352,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
         }, 0 )
 
         means.mid <- rep( data.mean, 4 )
-        sqrt.sd.mid <- sqrt( data.sd )
+        sqrt.sds.mid <- sqrt( data.sd )
     }
     else if ( start.level >= 2 )
     {
@@ -1381,7 +1381,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
         sqrt.sd.outer <- sqrt( ( ms[[1]]$sd + ms[[4]]$sd ) / 2 )
 
         means.mid <- rep( data.mean, 4 )
-        sqrt.sd.mid <- sqrt( data.sd )
+        sqrt.sds.mid <- sqrt( data.sd )
 
         if ( start.level == 3 )
         {
@@ -1393,7 +1393,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                                   c( sep$data[[1]][lengths[1]], sep$data[[4]][1] ) )
 
                 means.mid <- rep( ms$mean, 4 )
-                sqrt.sd.mid <- sqrt( ms$sd )
+                sqrt.sds.mid <- sqrt( ms$sd )
             }
             else
             {
@@ -1437,7 +1437,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                     {
                         means.mid <- means <- obj$cmp$mean[c( 1, 2, 4, 3 )]
                         sqrt.sds <- sqrt( obj$cmp$sd[c( 1, 2, 4, 3 )] )
-                        sqrt.sd.mid <- ( sqrt.sds[2] + sqrt.sds[3] ) / 2
+                        sqrt.sds.mid <- ( sqrt.sds[2] + sqrt.sds[3] ) / 2
                     }
                     else
                     {
@@ -1454,7 +1454,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                         sqrt.sd.inner <- sqrt.sds[2]
                         sqrt.sd.outer <- sqrt.sds[1]
 
-                        sqrt.sd.mid <- sqrt.sds[2]
+                        sqrt.sds.mid <- sqrt.sds[2]
                     }
                 }
             }
@@ -1466,7 +1466,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
         # via Normal Distribution
         fm <- d ~ dnorm( x, mean, sqrt.sd^2 )
 
-        start <- list( mean = means.mid[1], sqrt.sd = sqrt.sd.mid )
+        start <- list( mean = means.mid[1], sqrt.sd = sqrt.sds.mid )
     }
     else
     {
@@ -1478,7 +1478,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                 fm <- d ~ ( dnorm( x, mean.1, sqrt.sd^2 ) + dnorm( x, mean.2, sqrt.sd^2 ) ) / 2
                 start <- list( mean.1 = mean.lower,
                                mean.2 = mean.upper,
-                               sqrt.sd = sqrt.sd.mid )
+                               sqrt.sd = sqrt.sds.mid )
             }
             else if ( eq.mean )
             {
@@ -1507,7 +1507,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
 
                 start <- list( mean.1 = mean.lower,
                                mean.2 = mean.upper,
-                               sqrt.sd  = sqrt.sd.mid )
+                               sqrt.sd  = sqrt.sds.mid )
             }
             else if ( eq.mean )
             {
@@ -1543,7 +1543,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
 
                     start <- list( mean.1 = mean.outer,
                                    mean.2 = mean.inner,
-                                   sqrt.sd = sqrt.sd.mid )
+                                   sqrt.sd = sqrt.sds.mid )
                 }
                 else if ( eq.mean )
                 {
@@ -1576,7 +1576,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                     start <- list( mean.1 = means[1],
                                    mean.2 = mean.inner,
                                    mean.3 = means[4],
-                                   sqrt.sd = sqrt.sd.mid )
+                                   sqrt.sd = sqrt.sds.mid )
                 }
                 else if ( eq.mean )
                 {
@@ -1620,7 +1620,7 @@ get.nls.params <- function( x, freq, total, mix.type, grad, eq.mean, eq.sd, star
                                mean.1.2 = means[2],
                                mean.2.1 = means[4],
                                mean.2.2 = means[3],
-                               sqrt.sd = sqrt.sd.mid )
+                               sqrt.sd = sqrt.sds.mid )
             }
             else if ( eq.mean )
             {

diff --git a/R/ggd.set.cmp.R b/R/ggd.set.cmp.R
@@ -396,7 +396,7 @@ GGD$methods(
 )
 
 ################################################################################################
-#' Adjust the cmp field
+#' Adjust cmp field
 #'
 #' Simplifies the components in \code{cmp} field with retaining
 #' the substance of the distribution. Also, you can make \code{cmp} field redundant inversely.

diff --git a/R/ggd.trace.q.R b/R/ggd.trace.q.R
@@ -581,7 +581,7 @@ GGD$methods(
                     mix.type.seq <- c( mix.type,
                                        mix.type.seq[mix.type.seq != mix.type] )
 
-                    # In order to attempt to retain number of rows of cmp field when mix.type = 3,
+                    # In order to attempt to retain number of rows in cmp field when mix.type = 3,
                     # make sequences of values to set grad values.
                     if ( mix.type == 3 && nrow( cmp ) == 2 )
                     {