review before bump to 0.1.0

mightymetrika · Apr 28, 2024 · 31d24b4 · 31d24b4
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,3 +3,4 @@
 ^LICENSE\.md$
 ^data-raw$
 ^README\.Rmd$
+^cran-comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: scdtb
-Title: Tools for Analyzing Data from Single Case Designs
+Title: Single Case Design Tools
 Version: 0.0.0.9000
 Authors@R: c(
     person("Mackson", "Ncube", , "[email protected]", role = c("aut", "cre")),
@@ -15,7 +15,9 @@ Description: In some situations where researchers would like to demonstrate
     Works Clearinghouse (2022) <https://ies.ed.gov/ncee/wwc/Handbooks>. The
     package also offers the mixed_model_analysis() and cross_lagged() functions
     which implement mixed effects models and cross lagged analyses as described
-    in Maric & van der Werff <2020, ISBN:9780429273872>. The scdtb() 'shiny'
+    in Maric & van der Werff (2020) <doi:10.4324/9780429273872-9>. The
+    randomization_test() function implements randomization tests based on methods
+    presented in Onghena (2020) <doi:10.4324/9780429273872-8>. The scdtb() 'shiny'
     application can be used to upload single case design data and access various
     'scdtb' tools for plotting and analysis.
 License: MIT + file LICENSE

diff --git a/NEWS.md b/NEWS.md
diff --git a/R/cross_lagged.R b/R/cross_lagged.R
@@ -25,7 +25,7 @@
 #' @examples
 #' # Creating a sample dataset
 #' reversal_withdrawal <- data.frame(
-#'   phase = c(rep("baseline1", 6), rep("teratment1", 5), rep("baseline2", 5), rep("teratment2", 5)),
+#'   phase = c(rep("baseline1", 6), rep("treatment1", 5), rep("baseline2", 5), rep("treatment2", 5)),
 #'   time = 1:21,
 #'   extbehavs = c(15, 10, 14, 17, 13, 12, 2, 1, 1, 0, 0, 9, 9, 11, 15, 20, 1, 0, 4, 0, 1)
 #' )

diff --git a/R/data.R b/R/data.R
@@ -41,7 +41,7 @@
 #' Designs in Clinical Intervention Research. In R. van de Schoot & M. Miocevic
 #' (Eds.), Small Sample Size Solutions: A Guide for Applied Researchers and
 #' Practitioners (1st ed., pp. 10). Routledge.
-#' https://doi.org/10.4324/9780429273872
+#' <doi:10.4324/9780429273872-9>
 #'
 #' @format ## `efficacy_of_CBT`
 #' A data frame with 10 rows and 4 columns:
@@ -51,7 +51,7 @@
 #'   \item{Anxious}{Outcome measure}
 #'   \item{CATS_N}{Outcome measure}
 #' }
-#' @source <https://doi.org/10.4324/9780429273872>
+#' @source <doi:10.4324/9780429273872-9>
 "efficacy_of_CBT"
 
 #' Sleeping Pills and Dizziness Example
@@ -61,7 +61,7 @@
 #' @references Onghena, P. (2020). One by one: The design and analysis of
 #' replicated randomized single-case experiments. In R. van de Schoot & M. Miocevic
 #' (Eds.), Small sample size solutions: A guide for applied researchers and
-#' practitioners (1st ed., pp. 15). Routledge. https://doi.org/10.4324/9780429273872
+#' practitioners (1st ed., pp. 15). Routledge. <doi:10.4324/9780429273872-8>
 #'
 #' @format ## `sleeping_pills`
 #' A data frame with 14 rows and 3 columns:
@@ -70,7 +70,7 @@
 #'   \item{treatment}{E, Experimental; C, Control}
 #'   \item{sever_compl}{Severity of complaints}
 #' }
-#' @source <https://doi.org/10.4324/9780429273872>
+#' @source <doi:10.4324/9780429273872-8>
 "sleeping_pills"
 
 
diff --git a/R/mixed_model_analysis.R b/R/mixed_model_analysis.R
@@ -35,7 +35,7 @@
 #' Designs in Clinical Intervention Research. In R. van de Schoot & M. Miocevic
 #' (Eds.), Small Sample Size Solutions: A Guide for Applied Researchers and
 #' Practitioners (1st ed., pp. 10). Routledge.
-#' https://doi.org/10.4324/9780429273872
+#' <doi:10.4324/9780429273872-9>
 #'
 #' @examples
 #' res <- mixed_model_analysis(efficacy_of_CBT, .dv = "Anxious", .time = "time",
@@ -119,7 +119,7 @@ mixed_model_analysis <- function(.df, .dv, .time, .phase, .participant = NULL,
   mod <- nlme::gls(model       = mod_form,
                    data        = .df,
                    method      = "REML",
-                   correlation = nlme::corAR1(, form=re_form),
+                   correlation = nlme::corAR1(form=re_form),
                    ...)
 
   # Get predicted values
@@ -176,4 +176,3 @@ mixed_model_analysis <- function(.df, .dv, .time, .phase, .participant = NULL,
               plot = ggp))
 
 }
-
diff --git a/R/randomization_test.R b/R/randomization_test.R
@@ -50,7 +50,7 @@
 #' Onghena, P. (2020). One by One: The design and analysis of replicated randomized
 #' single-case experiments.In R. van de Schoot & M. Mioecvic (Eds.), Small Sample
 #' Size Solutions: A Guide for Applied Researchers and Practitioners (1st ed., pp.
-#' 15). Routledge. https://doi.org/10.4324/9780429273872
+#' 15). Routledge. <doi:10.4324/9780429273872-8>
 #'
 #' @export
 randomization_test <- function(.df, .out, .cond, .time, num_permutations = NULL,

diff --git a/R/scdtb.R b/R/scdtb.R
@@ -17,7 +17,7 @@
 #' Maric, M., & van der Werff, V. (2020). Single-Case ExperimentalDesigns in
 #' Clinical Intervention Research. In R. van de Schoot & M. Miocevic (Eds.),
 #' Small Sample Size Solutions: A Guide for Applied Researchers and Practitioners
-#' (1st ed., pp. 10). Routledge. https://doi.org/10.4324/9780429273872
+#' (1st ed., pp. 10). Routledge. <doi:10.4324/9780429273872-9>
 #'
 #' What Works Clearinghouse. (2022). What Works Clearinghouse procedures and
 #' standards handbook, version 5.0. U.S. Department of Education, Institute of
@@ -28,7 +28,7 @@
 #' Onghena, P. (2020). One by One: The design and analysis of replicated randomized
 #' single-case experiments.In R. van de Schoot & M. Mioecvic (Eds.), Small Sample
 #' Size Solutions: A Guide for Applied Researchers and Practitioners (1st ed., pp.
-#' 15). Routledge. https://doi.org/10.4324/9780429273872
+#' 15). Routledge. <doi:10.4324/9780429273872-8>
 #'
 #' @export
 scdtb <- function(){

diff --git a/README.Rmd b/README.Rmd
@@ -22,6 +22,12 @@ The goal of 'scdtb' is to provide tools for the analysis of single case design d
 
 ## Installation
 
+You can install the released version of 'scdtb' from [CRAN](https://CRAN.R-project.org):
+
+```{r eval=FALSE}
+install.packages("scdtb")
+```
+
 To install the development version of 'scdtb' from GitHub, use the [devtools](https://devtools.r-lib.org/) package:
 
 ```{r, eval=FALSE}

diff --git a/README.md b/README.md
@@ -11,6 +11,13 @@ design data.
 
 ## Installation
 
+You can install the released version of ‘scdtb’ from
+[CRAN](https://CRAN.R-project.org):
+
+``` r
+install.packages("scdtb")
+```
+
 To install the development version of ‘scdtb’ from GitHub, use the
 [devtools](https://devtools.r-lib.org/) package:
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
diff --git a/man/cross_lagged.Rd b/man/cross_lagged.Rd
diff --git a/man/efficacy_of_CBT.Rd b/man/efficacy_of_CBT.Rd
diff --git a/man/mixed_model_analysis.Rd b/man/mixed_model_analysis.Rd
diff --git a/man/randomization_test.Rd b/man/randomization_test.Rd
diff --git a/man/scdtb.Rd b/man/scdtb.Rd
diff --git a/man/sleeping_pills.Rd b/man/sleeping_pills.Rd