Digits for summary methods, print.saem.mmkin

4 files changed, 49 insertions, 18 deletions

diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index d26b86ac..a9e1694f 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -210,7 +210,8 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
 #' @export
 #' @rdname nlme.mmkin
 #' @param x An nlme.mmkin object to print
-print.nlme.mmkin <- function(x, ...) {
+#' @param digits Number of digits to use for printing
+print.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
   cat( "Kinetic nonlinear mixed-effects model fit by " )
   cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n")
   cat("\nStructural model:\n")
@@ -230,9 +231,9 @@ print.nlme.mmkin <- function(x, ...) {
     x$call$fixed
   else
     lapply(fixF, function(el) as.name(deparse(el)))), "\n")
-  print(fixef(x), ...)
+  print(fixef(x), digits = digits, ...)
   cat("\n")
-  print(summary(x$modelStruct), sigma = x$sigma, ...)
+  print(summary(x$modelStruct), sigma = x$sigma, digits = digits, ...)
   invisible(x)
 }
 
diff --git a/R/saemix.R b/R/saemix.R
index 8955aa54..68bbd233 100644
--- a/R/saemix.R
+++ b/R/saemix.R
@@ -139,6 +139,36 @@ saem.mmkin <- function(object,
   return(result)
 }
 
+#' @export
+#' @rdname saem
+#' @param x An saem.mmkin object to print
+#' @param digits Number of digits to use for printing
+print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
+  cat( "Kinetic nonlinear mixed-effects model fit by SAEM" )
+  cat("\nStructural model:\n")
+  diffs <- x$mmkin[[1]]$mkinmod$diffs
+  nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
+  writeLines(strwrap(nice_diffs, exdent = 11))
+  cat("\nData:\n")
+  cat(nrow(x$data), "observations of",
+    length(unique(x$data$name)), "variable(s) grouped in",
+    length(unique(x$data$ds)), "datasets\n")
+
+  cat("\nLikelihood computed by importance sampling\n")
+  print(data.frame(
+      AIC = AIC(x$so, type = "is"),
+      BIC = BIC(x$so, type = "is"),
+      logLik = logLik(x$so, type = "is"),
+      row.names = " "), digits = digits)
+
+  cat("\nFitted parameters:\n")
+  conf.int <- x$so@results@conf.int[c("estimate", "lower", "upper")]
+  rownames(conf.int) <- x$so@results@conf.int[["name"]]
+  print(conf.int, digits = digits)
+
+  invisible(x)
+}
+
 #' @rdname saem
 #' @return An [saemix::SaemixModel] object.
 #' @export
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index ad730f9a..42326b39 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -191,10 +191,10 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
 
   cat("\nResults:\n\n")
   print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
-      row.names = " "))
+      row.names = " "), ...)
 
   cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
-  print(x$confint_trans)
+  print(x$confint_trans, digits = digits, ...)
 
   if (nrow(x$confint_trans) > 1) {
     corr <- x$corFixed
@@ -204,28 +204,28 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
 
   cat("\n") # Random effects
   print(summary(x$modelStruct), sigma = x$sigma,
-        reEstimates = x$coef$random, verbose = verbose, ...)
+        reEstimates = x$coef$random, digits = digits, verbose = verbose, ...)
 
   cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
-  print(x$confint_back)
+  print(x$confint_back, digits = digits, ...)
 
 
   printSFORB <- !is.null(x$SFORB)
   if(printSFORB){
     cat("\nEstimated Eigenvalues of SFORB model(s):\n")
-    print(x$SFORB, digits=digits,...)
+    print(x$SFORB, digits = digits,...)
   }
 
   printff <- !is.null(x$ff)
   if(printff){
     cat("\nResulting formation fractions:\n")
-    print(data.frame(ff = x$ff), digits=digits,...)
+    print(data.frame(ff = x$ff), ...)
   }
 
   printdistimes <- !is.null(x$distimes)
   if(printdistimes){
     cat("\nEstimated disappearance times:\n")
-    print(x$distimes, digits=digits,...)
+    print(x$distimes, digits = digits, ...)
   }
 
   if (x$print_data){
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 75fdb045..337120b2 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -213,10 +213,10 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
   cat("\nResults:\n\n")
   cat("Likelihood computed by importance sampling\n")
   print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
-      row.names = " "))
+      row.names = " "), digits = digits)
 
   cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
-  print(x$confint_trans)
+  print(x$confint_trans, digits = digits)
 
   if (nrow(x$confint_trans) > 1) {
     corr <- x$corFixed
@@ -225,30 +225,30 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
   }
 
   cat("\nRandom effects:\n")
-  print(x$confint_ranef)
+  print(x$confint_ranef, digits = digits)
 
   cat("\nVariance model:\n")
-  print(x$confint_errmod)
+  print(x$confint_errmod, digits = digits)
 
   cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
-  print(x$confint_back)
+  print(x$confint_back, digits = digits)
 
   printSFORB <- !is.null(x$SFORB)
   if(printSFORB){
     cat("\nEstimated Eigenvalues of SFORB model(s):\n")
-    print(x$SFORB, digits=digits,...)
+    print(x$SFORB, digits = digits,...)
   }
 
   printff <- !is.null(x$ff)
   if(printff){
     cat("\nResulting formation fractions:\n")
-    print(data.frame(ff = x$ff), digits=digits,...)
+    print(data.frame(ff = x$ff), digits = digits,...)
   }
 
   printdistimes <- !is.null(x$distimes)
   if(printdistimes){
     cat("\nEstimated disappearance times:\n")
-    print(x$distimes, digits=digits,...)
+    print(x$distimes, digits = digits,...)
   }
 
   if (x$print_data){