Merge pull request #26 from sfcheung/devel

0.0.2.0: Prepare for CRAN

DESCRIPTION

@@ -1,17 +1,36 @@
 Package: betaselectr
-Title: Selective Standardization in Structural Equation Models
-Version: 0.0.1.17
+Title: Betas-Select in Structural Equation Models and Linear Models
+Version: 0.0.2.0
 Authors@R:
     c(person(given = "Shu Fai",
              family = "Cheung",
              role = c("aut", "cre"),
              email = "shufai.cheung@gmail.com",
-             comment = c(ORCID = "0000-0002-9871-9448")))
-Description: It computes Beta_Select, standardization in
-  structural equation models with only selected variables
-  standardized. It supports models with moderation, as well
-  as regression models. It can form confidence intervals
-  that takes into account the standardization appropriately.
+             comment = c(ORCID = "0000-0002-9871-9448")),
+      person(given = "Rong Wei",
+             family = "Sun",
+             role = c("aut"),
+             comment = c(ORCID = "0000-0003-0034-1422")),
+      person(given = "Florbela",
+             family = "Chang",
+             role = c("aut"),
+             comment = c(ORCID = "0009-0003-9931-501X")),
+      person(given = "Wendie",
+             family ="Yang",
+             role = c("ctb"),
+             comment = c(ORCID = "0009-0000-8388-6481")),
+      person(given = "Sing-Hang",
+             family = "Cheung",
+             role = c("aut"),
+             comment = c(ORCID = "0000-0001-5182-0752")))
+Description: It computes betas-select, standardization in
+  structural equation models and regression models with only
+  selected variables standardized. It supports models with
+  moderation, with product terms formed after standardization.
+  It can also form confidence intervals that takes into account
+  the standardization appropriately, such as bootstrap
+  confidence intervals proposed by Cheung, Cheung, Lau, Hui,
+  and Vong (2022) <doi:10.1037/hea0001188>.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,4 +1,4 @@
-# betaselectr 0.0.1.17
+# betaselectr 0.0.1.19
 
 - Added `lm_betaselect()` and related
   methods and helper functions.
@@ -96,4 +96,11 @@
   users. (0.0.1.16)
 
 - Updated the vignettes and the `pkgdown`
-  site. (0.0.1.17)
+  site. (0.0.1.17)
+
+- Proofread the documentation and
+  update meta-data. (0.0.1.18)
+
+- Enabled more tests. (0.0.1.19)
+
+- Prepare for CRAN. (0.0.2.0)

R/coef_lav_betaselect.R

@@ -10,7 +10,7 @@
 #'
 #' @return
 #' A numeric vector: The betas-select
-#' in the object. Names of parameters
+#' in the object. The names of parameters
 #' follow the convention in `lavaan`.
 #'
 #' @param object The output of

R/confint_lav_betaselect.R

@@ -1,13 +1,16 @@
-#' @title Confidence Interval for a
+#' @title Confidence Intervals for a
 #' 'lav_betaselect'-Class Object
 #'
 #' @description Return the confidence
 #' intervals of betas-select in the
 #' output of [lav_betaselect()].
 #'
-#' @details Details
-#' (Include subjects for verbs.)
-#' (Use 3rd person forms for verbs.)
+#' @details
+#' The type of
+#' confidence intervals depends
+#' on the call to [lav_betaselect()].
+#' This function does not recompute
+#' the confidence interval.
 #'
 #' @return
 #' A two-column matrix of the confidence

R/lav_betaselect.R

@@ -1,4 +1,4 @@
-#' @title Standardize Coefficients in a 'lavaan'-Model
+#' @title Betas-Select in a 'lavaan'-Model
 #'
 #' @description Can standardize selected
 #' variables in a `lavaan` model without
@@ -19,26 +19,28 @@
 #'
 #' - It does not standardize product
 #' term, which is incorrect. Instead,
-#' it compute the product term with
-#' its component variables standardized.
+#' it computes the product term with
+#' its component variables standardized
+#' first.
 #'
 #' - It can be used to generate bootstrap
 #' confidence intervals for the
-#' standardized solution. Bootstrap
+#' standardized solution (Falk, 2018). Bootstrap
 #' confidence interval is better than
 #' doing standardization *before* fitting
 #' a model because it correctly takes
 #' into account the sampling variance
 #' of the standard deviations. It is
-#' also better than delta method
+#' also better than delta-method
 #' confidence interval because it takes
 #' into account the usually asymmetric
 #' distribution of parameters after
-#' standardization.
+#' standardization, such as standardized
+#' loadings and correlations.
 #'
 #' - For comparison, it can also report
-#' delta method standard errors and
-#' confidence intervals.
+#' delta-method standard errors and
+#' confidence intervals if requested.
 #'
 #' ## Problems With Common Approaches
 #'
@@ -50,7 +52,7 @@
 #' or misleading in these conditions:
 #'
 #' - Dummy variables are standardized
-#' and can not be interpreted as the
+#' and their coefficients cannot be interpreted as the
 #' difference between two groups on the
 #' outcome variables.
 #'
@@ -66,14 +68,14 @@
 #' they are standardized (e.g., age).
 #'
 #' Moreover, the delta method is usually
-#' used, which is suboptimal for
+#' used in standardization, which is suboptimal for
 #' standardization unless the sample
-#' size is large. For example, the
+#' size is large (Falk, 2018). For example, the
 #' covariance with variables standardized
 #' is a correlation, and its sampling
 #' distribution is skewed unless its
 #' population value is zero. However,
-#' delta method confidence interval
+#' delta-method confidence interval
 #' for the correlation is necessarily
 #' symmetric around the point estimate.
 #'
@@ -92,7 +94,8 @@
 #' - Intercepts not supported.
 #'
 #' @return
-#' A data frame storing the parameter
+#' A `lav_betaselect`-class object,
+#' which is a data frame storing the parameter
 #' estimates, similar in form to the
 #' output of [lavaan::parameterEstimates()].
 #'
@@ -103,9 +106,9 @@
 #' @param to_standardize A string vector,
 #' which should be the names of the
 #' variables to be standardized.
-#' Default is `".all"`, indicating all
+#' Default is `".all."`, indicating all
 #' variables are to be standardized
-#' (but see `skip_categorical`).
+#' (but see `skip_categorical_x`).
 #'
 #' @param not_to_standardize A string
 #' vector, which should be the names
@@ -127,14 +130,15 @@
 #' `to_standardize`. That is, a
 #' categorical predictor will not be
 #' standardized even if listed in
-#' `to_standardize`, unless uses set
+#' `to_standardize`, unless users set
 #' this argument to `FALSE`.
 #'
 #' @param output The format of the
 #' output. Not used because the format
-#' of the print out is now controlled
+#' of the printout is now controlled
 #' by the `print`-method of the output
-#' of this function.
+#' of this function. Kept for backward
+#' compatibility.
 #'
 #' @param std_se String. If set to `"none"`,
 #' the default, standard errors will not
@@ -193,7 +197,7 @@
 #' output.
 #'
 #' @param delta_method The method used
-#' to compute delta method standard
+#' to compute delta-method standard
 #' errors. For internal use and should
 #' not be changed.
 #'
@@ -308,6 +312,13 @@
 #' (2022) Improving an old way to measure moderation effect in standardized
 #' units. *Health Psychology*, *41*(7), 502-505.
 #' \doi{10.1037/hea0001188}
+#'
+#' Falk, C. F. (2018). Are robust standard errors the best approach
+#' for interval estimation with nonnormal data in structural equation
+#' modeling?
+#' *Structural Equation Modeling: A Multidisciplinary Journal, 25*(2)
+#'  244-266. \doi{10.1080/10705511.2017.1367254}
+
 #'
 #' @seealso [print.lav_betaselect()] for its print method.
 #'

R/lm_betaselect.R

@@ -1,4 +1,4 @@
-#' @title Standardize Coefficients in a
+#' @title Betas-Select in a
 #' Regression Model
 #'
 #' @description Can fit a linear regression
@@ -63,7 +63,7 @@
 #' or misleading in these conditions:
 #'
 #' - Dummy variables are standardized
-#' and cannot be interpreted as the
+#' and their coefficients cannot be interpreted as the
 #' difference between two groups on the
 #' outcome variables.
 #'
@@ -226,8 +226,7 @@
 #' which should be the names of the
 #' variables to be standardized.
 #' Default is `NULL`, indicating all
-#' variables are to be standardized
-#' (but see `skip_categorical`).
+#' variables are to be standardized.
 #'
 #' @param not_to_standardize A string
 #' vector, which should be the names
@@ -270,7 +269,7 @@
 #' parallel processing will be used to
 #' do bootstrapping. Default is `FALSE`
 #' because bootstrapping for models fitted
-#' by [lm()] or [glm()] is rarely slow.
+#' by [stats::lm()] or [stats::glm()] is rarely slow.
 #' Actually, if both `parallel` and
 #' `progress` are set to `TRUE`, the
 #' speed may even be slower than serial
@@ -546,7 +545,8 @@ glm_betaselect <- function(...,
 #' object.
 #'
 #' @details This is a helper functions
-#' to be used by [lm_betaselect()]. It
+#' to be used by [lm_betaselect()]
+#' and [glm_betaselect()]. It
 #' assumes that the variables selected
 #' has been checked whether they are
 #' numeric.

R/lm_betaselect_methods.R

@@ -11,11 +11,11 @@
 #' selected variables have been
 #' standardized. If requested, it can
 #' also return the regression
-#' coefficients *without*
+#' coefficients *before*
 #' standardization.
 #'
 #' @return
-#' A scalar vector: The estimate of
+#' A numeric vector: The estimate of
 #' regression coefficients.
 #'
 #' @param object The output of
@@ -288,13 +288,11 @@ vcov.glm_betaselect <- vcov.lm_betaselect
 #' was requested, by default it returns
 #' the percentile bootstrap confidence
 #' intervals. Otherwise, it returns the
-#' default confidence intervals
-#' and raises a warning for the
-#' standardized solution.
+#' default confidence intervals.
 #'
 #' Support for other type of
-#' confidence intervals will be
-#' added.
+#' confidence intervals may be
+#' added in the future.
 #'
 #' @return
 #' A *p* by 2 matrix of the confidence

R/print_std_selected_lavaan.R

@@ -1,6 +1,6 @@
 #' @title Print a 'lav_betaselect' Object
 #'
-#' @description Print method for an
+#' @description Print method for a
 #' 'lav_betaselect' object, which
 #' is the output of
 #' [lav_betaselect()].
@@ -23,8 +23,9 @@
 #' which is compact but not easy to
 #' read.
 #'
-#' @param x Object of the class
-#' `std_solution_boot`.
+#' @param x A `lav_betaselect`-class
+#' object, such as the output of
+#' [lav_betaselect()].
 #'
 #' @param ... Optional arguments to be
 #' passed to [print()] methods.
@@ -39,43 +40,43 @@
 #' printed in a format similar to
 #' the printout of the output of
 #' the `summary`-method of a
-#' `lavaan-class` object.
+#' 'lavaan'-class object.
 #' If set to `"table"`, the results are
 #' printed in a table
 #' format similar to that of
 #' [lavaan::parameterEstimates()]
 #' with `output` set to `"data.frame"`.
 #'
 #' @param standardized_only Logical.
-#' If `TRUE`, only the
+#' If `TRUE`, the default, only the
 #' results for the standardized solution
 #' will be printed. If `FALSE`,
-#' the default, then
+#' then
 #' the standardized solution is printed
 #' alongside the unstandardized solution,
 #' as in the printout of the output
-#' of [summary()] of a [lavaan-class]
+#' of [summary()] of a 'lavaan'-class
 #' object.
 #'
 #' @param show_Bs.by Logical. If `TRUE`
 #' and `output` is `"lavaan.printer"`, then the
 #' column `"Bs.by"` is shown,
 #' indicating, for each parameter, the
-#' variables standardized. Otherwise,
-#' this column is not shown if `output`
+#' variables standardized.
+#' This column is not shown if `output`
 #' is not `"lavaan.printer"`.
 #'
 #' @param by_group If `TRUE`, the
 #' default, and the model has more than
-#' one groups, sections will be grouped
+#' one group, sections will be grouped
 #' by groups first, as in the print
 #' out of `summary()` in `lavaan`.
 #' If `FALSE`, then the sections will
 #' be grouped by sections first.
 #'
 #' @param na_str The string to be used
-#' for cells with `NA``. Default is
-#' `" "``, a white space.
+#' for cells with `NA`. Default is
+#' `" "`, a whitespace.
 #'
 #' @param sig_stars If `TRUE`, the
 #' default, symbols such as asterisks