Fix CRAN issues, add test suite, and fix correctness bugs

.Rbuildignore

@@ -9,3 +9,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^.*\.Rhistory$
+^_scratch$
+^Rplots\.pdf$

.gitignore

@@ -3,7 +3,11 @@ inst/doc/
 *.Rcheck/
 *.tar.gz
 *.md
+!README.md
+!NEWS.md
+!cran-comments.md
 figure/
+Rplots.pdf
 
 # R user files
 .Rhistory

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: svyTable1
 Title: Create Survey-Weighted Descriptive Statistics and Diagnostic Tables
-Version: 0.14.1
+Version: 0.14.1.9000
 Authors@R: c(person("Ehsan", "Karim",
                  email = "ehsan.karim@gmail.com",
                  role = c("aut", "cre")),
@@ -10,20 +10,28 @@ Authors@R: c(person("Ehsan", "Karim",
              person("Kevin", "Hu",
                  role = "ctb",
                  comment = "Reported a scoping bug in the svycoxph_CE function regarding survey design objects created via pipes."))
-Description: A tool to create publication-ready tables from complex 
-    survey data, including descriptive summaries and multi-panel 
-    interaction reports. It also provides a suite of functions to 
-    evaluate survey-weighted regression models and survey-weighted 
-    survival plots, including coefficient diagnostics, 
-    goodness-of-fit tests, design-correct AUC calculations,
-    proportional hazards assumption testing, and visualization 
-    of interaction effects.
+Description: A teaching toolkit for graduate epidemiology students analyzing
+    complex survey data such as 'NHANES'. It builds survey-weighted "Table 1"
+    summaries with reliability suppression, fits and diagnoses survey-weighted
+    regression and survival models, computes additive interaction measures, and
+    pools multiply-imputed analyses. Methods are described in Lumley (2004)
+    <doi:10.18637/jss.v009.i08> for survey-weighted estimation, Archer and
+    Lemeshow (2006) <doi:10.1177/1536867X0600600106> for survey
+    goodness-of-fit, Parker et al. (2017)
+    <https://www.cdc.gov/nchs/data/series/sr_02/sr02_175.pdf> for the National
+    Center for Health Statistics data-presentation reliability standards,
+    VanderWeele and Knol (2014) <doi:10.1515/em-2013-0005> and Hosmer and
+    Lemeshow (1992) <doi:10.1097/00001648-199209000-00012> for additive
+    interaction, van Buuren and Groothuis-Oudshoorn (2011)
+    <doi:10.18637/jss.v045.i03> and Rubin (1987, ISBN:9780471087052) for
+    multiple imputation, and Westreich and Greenland (2013)
+    <doi:10.1093/aje/kws412> for interpreting adjusted estimates.
 License: MIT + file LICENSE
-URL: https://ehsanx.github.io/svyTable1, https://github.com/ehsanx/svyTable1
+URL: https://ehsanx.github.io/svyTable1/, https://github.com/ehsanx/svyTable1
 BugReports: https://github.com/ehsanx/svyTable1/issues
 Encoding: UTF-8
 RoxygenNote: 7.3.3
-Imports: 
+Imports:
     dplyr,
     emmeans,
     ggplot2,
@@ -48,12 +56,12 @@ Imports:
     utils,
     WeightedROC,
     broom
-Suggests: 
+Suggests:
     NHANES,
     mitools,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-Depends: 
+Depends:
     R (>= 3.5)
 LazyData: true

NAMESPACE

@@ -88,7 +88,9 @@ importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,plogis)
 importFrom(stats,pnorm)
+importFrom(stats,qlogis)
 importFrom(stats,qnorm)
+importFrom(stats,qt)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(stats,terms)