From 606ef9ad6cae0ddfae6db6b90deb03f81140e46f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Nov 2020 05:14:57 +0100 Subject: Digits for summary methods, print.saem.mmkin --- NAMESPACE | 1 + R/nlme.mmkin.R | 7 +-- R/saemix.R | 30 ++++++++++++ R/summary.nlme.mmkin.R | 14 +++--- R/summary.saem.mmkin.R | 16 +++---- docs/dev/news/index.html | 3 +- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/nlme.mmkin.html | 35 +++++++------- docs/dev/reference/saem.html | 95 +++++++++++++++++++++----------------- man/nlme.mmkin.Rd | 7 +-- man/saem.Rd | 7 +++ 12 files changed, 137 insertions(+), 82 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index a7aa9eeb..e85f8311 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -25,6 +25,7 @@ S3method(print,mkinmod) S3method(print,mmkin) S3method(print,nafta) S3method(print,nlme.mmkin) +S3method(print,saem.mmkin) S3method(print,summary.mkinfit) S3method(print,summary.nlme.mmkin) S3method(print,summary.saem.mmkin) 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){ diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c068b8a4..3a868426 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -146,7 +146,8 @@ mkin 0.9.50.4 (unreleased) Unreleased