Merge branch 'main' into 929_readme_news@main

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.8.2.9000
-Date: 2023-05-03
+Version: 0.8.2.9001
+Date: 2023-05-25
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),

NAMESPACE

@@ -285,11 +285,8 @@ importFrom(grid,drawDetails)
 importFrom(grid,heightDetails)
 importFrom(grid,validDetails)
 importFrom(grid,widthDetails)
-importFrom(lifecycle,badge)
 importFrom(magrittr,"%>%")
 importFrom(methods,new)
-importFrom(rlang,"!!")
-importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(stats,pchisq)
 importFrom(survival,Surv)

NEWS.md

@@ -1,4 +1,4 @@
-# tern 0.8.2.9000
+# tern 0.8.2.9001
 
 ### Miscellaneous
 * Updated README to include installation instructions for CRAN.

R/estimate_proportion.R

@@ -238,7 +238,7 @@ prop_wilson <- function(rsp, conf_level, correct = FALSE) {
 #'   [stats::prop.test()].
 #'
 #' @references
-#' - \insertRef{Yan2010-jt}{tern}
+#' \insertRef{Yan2010-jt}{tern}
 #'
 #' @examples
 #' # Stratified Wilson confidence interval with unequal probabilities

R/package.R

@@ -7,11 +7,10 @@
 #' @import rtables ggplot2
 #' @importFrom broom tidy
 #' @importFrom formatters propose_column_widths
-#' @importFrom lifecycle badge
-#' @importFrom methods new
 #' @importFrom magrittr %>%
+#' @importFrom methods new
 #' @importFrom Rdpack reprompt
-#' @importFrom rlang .data := !!
+#' @importFrom rlang .data
 #' @importFrom survival coxph strata Surv
 #' @importFrom stats pchisq
 NULL

R/prop_diff.R

@@ -533,7 +533,7 @@ prop_diff_cmh <- function(rsp,
 #'   and directs the way weights are estimated.
 #'
 #' @references
-#' - \insertRef{Yan2010-jt}{tern}
+#' \insertRef{Yan2010-jt}{tern}
 #'
 #' @examples
 #' # Stratified Newcombe confidence interval

inst/REFERENCES.bib

@@ -1,63 +1,5 @@
 % Encoding: UTF-8
 
-@inproceedings{KimWon2013,
-  title = {Adjusted proportion difference and confidence interval in stratified randomized trials},
-  author = {Kim Y., Won S.},
-  url = {https://www.pharmasug.org/proceedings/2013/SP/PharmaSUG-2013-SP04.pdf},
-  crossref = {SUG2013}
-}
-
-@Manual{Hughes2020,
-  title  = {Tables, Listings and Graphs Specifications for Parallel-Group Studies(Part 1 of 3) Version: June 2020},
-  author = {Hughes, Claire},
-  month  = jun,
-  year   = {2020},
-}
-
-@InBook{Hughes2020a,
-  author    = {Hughes, Claire},
-  editor    = {Roche},
-  chapter   = {COXT01: Cox-Regression Model With Treatment And Individual Covariates Table Programming Notes},
-  pages     = {25--27},
-  publisher = {GDSR},
-  title     = {Tables, Listings and GraphsSpecifications for Parallel-GroupStudies(Part 2 of 3)},
-  year      = {2020},
-  edition   = {GDSR - Efficacy Standard Tables},
-  month     = sep,
-}
-
-@Manual{STREAM2020,
-  title     = {Deaths (DTHT01)},
-  author    = {STREAM},
-  note      = {v2.9},
-  year      = {2020},
-  timestamp = {2020-09-08},
-}
-
-@Manual{STREAM_LBT02,
-  title  = {Laboratory Test Results by Visit (LBT02)},
-  author = {STREAM},
-  year   = {2020},
-}
-
-@proceedings{SUG2013,
-  title = "PharmaSUG 2013 Conference Proceedings",
-  year  = {2013},
-  url = {https://www.pharmasug.org/2013-proceedings.html}
-}
-
-@Article{Schouten1980,
-  author    = {Schouten, HJA and Molenaar, IW and Van Strik, R and Boomsma, A},
-  journal   = {Biometrical Journal},
-  title     = {Comparing two independent binomial proportions by a modified chi square test},
-  year      = {1980},
-  number    = {3},
-  pages     = {241--248},
-  volume    = {22},
-  doi       = {10.1002/bimj.4710220305},
-  publisher = {Wiley Online Library},
-}
-
 @ARTICLE{Yan2010-jt,
   title     = "Stratified Wilson and Newcombe Confidence Intervals for Multiple
                Binomial Proportions",
@@ -83,14 +25,3 @@ @ARTICLE{Yan2010-jt
   month     =  aug,
   year      =  2010
 }
-
-
-@InBook{NESTTeam2020,
-  author    = {{NEST Team}},
-  chapter   = {4.4 Cox Proportional Hazards Model},
-  publisher = {NEST Roche},
-  title     = {Statistical Analysis of Clinical Trials Data with R},
-  year      = {2020},
-}
-
-@Comment{jabref-meta: databaseType:bibtex;}