Correcting documentation in nobs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: defm
 Type: Package
 Title: Estimation and Simulation of Multi-Binary Response Models
-Version: 0.1-0
+Version: 0.1-1
 Authors@R: c(
     person("George", "Vega Yon", role=c("aut", "cre"),
     email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844")),

Makefile

@@ -26,3 +26,7 @@ README.md: README.Rmd
 	Rscript --vanilla -e 'rmarkdown::render("README.Rmd")'
 
 .PHONY: build update clean
+
+inst/NEWS: NEWS.md
+	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')" && \
+		head -n 80 inst/NEWS

NAMESPACE

@@ -3,6 +3,7 @@
 S3method("+",DEFM)
 S3method(as.data.frame,defm_motif_census)
 S3method(names,defm_motif_census)
+S3method(nobs,DEFM)
 S3method(print,DEFM)
 S3method(print,defm_motif_census)
 export(defm_mle)
@@ -17,7 +18,6 @@ export(motif_census)
 export(ncol_defm_x)
 export(ncol_defm_y)
 export(new_defm)
-export(nobs.DEFM)
 export(nobs_defm)
 export(nrow_defm)
 export(nterms_defm)
@@ -32,5 +32,10 @@ export(term_defm_transition)
 export(term_defm_transition_formula)
 import(stats4)
 importFrom(Rcpp,sourceCpp)
+importFrom(stats,AIC)
+importFrom(stats,BIC)
+importFrom(stats,coef)
+importFrom(stats,nobs)
 importFrom(stats,pnorm)
+importFrom(stats,vcov)
 useDynLib(defm, .registration = TRUE)

NEWS.md

@@ -0,0 +1,6 @@
+# defm 0.1-1
+
+* Added a `NEWS.md` file to track changes to the package.
+
+* Change how `nobs.DEFM` is documented (per CRAN)
+

R/defm-package.R

@@ -81,11 +81,13 @@ new_defm <- function(
 
 }
 
-#' @export
 #' @rdname DEFM
 #' @param object An object of class [DEFM].
 #' @return - `nobs` is an alias for `nobs_defm()`.
 #' @param ... Not used.
+#' @importFrom stats nobs
+#' @export
+#' @exportS3Method stats4::nobs
 nobs.DEFM <- function(object, ...) {
   nobs_defm(object)
 }

R/defm_mle.R

@@ -111,8 +111,7 @@ defm_mle <- function(
 }
 
 pval_calc <- function(obj) {
-  pvals <- -abs(coef(obj)/sqrt(diag(vcov(obj)))) |> pnorm()
-  pvals * 2
+  stats::pnorm(-abs(stats::coef(obj)/sqrt(diag(vcov(obj))))) * 2
 }
 
 #' @export
@@ -121,15 +120,16 @@ pval_calc <- function(obj) {
 #' with the estimates, se, and pvalues. If `as_texreg = TRUE`, then it will
 #' return a texreg object.
 #' @rdname defm_mle
+#' @importFrom stats AIC BIC coef vcov
 summary_table <- function(object, as_texreg = FALSE, ...) {
 
   # Generating the output table
   tab <- list(
-    coef.names  = names(coef(object)),
-    coef        = coef(object),
-    se          = sqrt(diag(vcov(object))),
+    coef.names  = names(stats::coef(object)),
+    coef        = stats::coef(object),
+    se          = sqrt(diag(stats::vcov(object))),
     gof.names   = c("AIC", "BIC", "N"),
-    gof         = c(AIC(object), BIC(object), nobs(object)),
+    gof         = c(stats::AIC(object), stats::BIC(object), stats::nobs(object)),
     gof.decimal = c(T,T,F),
     pvalues     = pval_calc(object)
   )

inst/NEWS

@@ -0,0 +1,5 @@
+defm 0.1-1
+
+-   Added a NEWS.md file to track changes to the package.
+
+-   Change how nobs.DEFM is documented (per CRAN)