diff --git a/DESCRIPTION b/DESCRIPTION index add0aeda..81faf9b6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: casebase Type: Package Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression Version: 0.9.1 -Date: 2021-02-05 +Date: 2021-02-06 Authors@R: c( person("Sahir", "Bhatnagar", email = "sahir.bhatnagar@gmail.com", role = c("aut", "cre"), comment = "http://sahirbhatnagar.com/"), diff --git a/README.Rmd b/README.Rmd index 27861fbd..208aa5a8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,9 +18,9 @@ knitr::opts_chunk$set( # casebase -[![Build Status](https://travis-ci.org/sahirbhatnagar/casebase.svg?branch=master)](https://travis-ci.org/sahirbhatnagar/casebase) [![Coverage Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://codecov.io/github/sahirbhatnagar/casebase?branch=master) [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase) [![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase) +[![Build Status](https://api.travis-ci.org/sahirbhatnagar/casebase.svg?branch=master)](https://travis-ci.org/github/sahirbhatnagar/casebase) [![Coverage Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://codecov.io/github/sahirbhatnagar/casebase?branch=master) [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase) [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/sahirbhatnagar/casebase?branch=master&svg=true)](https://ci.appveyor.com/project/sahirbhatnagar/casebase) -[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) `casebase` is an R package for fitting flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. diff --git a/README.md b/README.md index 993084d8..f940ba53 100644 --- a/README.md +++ b/README.md @@ -6,15 +6,15 @@ [![Build -Status](https://travis-ci.org/sahirbhatnagar/casebase.svg?branch=master)](https://travis-ci.org/sahirbhatnagar/casebase) +Status](https://api.travis-ci.org/sahirbhatnagar/casebase.svg?branch=master)](https://travis-ci.org/github/sahirbhatnagar/casebase) [![Coverage Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://codecov.io/github/sahirbhatnagar/casebase?branch=master) [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase) -[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase) +[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/sahirbhatnagar/casebase?branch=master&svg=true)](https://ci.appveyor.com/project/sahirbhatnagar/casebase) [![Lifecycle: -maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) `casebase` is an R package for fitting flexible and fully parametric @@ -128,26 +128,26 @@ summary(fit) #> #> Deviance Residuals: #> Min 1Q Median 3Q Max -#> -0.2579 -0.1481 -0.1377 -0.1273 3.1543 +#> -0.2479 -0.1482 -0.1373 -0.1268 3.1490 #> #> Coefficients: #> Estimate Std. Error z value Pr(>|z|) -#> (Intercept) -5.8423 0.3007 -19.431 < 2e-16 *** -#> treatmentestPro 0.6382 0.3772 1.692 0.0907 . -#> ns(time, df = 3)1 -0.4667 0.3611 -1.292 0.1963 -#> ns(time, df = 3)2 0.7903 0.7331 1.078 0.2811 -#> ns(time, df = 3)3 1.4514 0.3431 4.230 2.34e-05 *** -#> treatmentestPro:ns(time, df = 3)1 0.1975 0.4880 0.405 0.6857 -#> treatmentestPro:ns(time, df = 3)2 -1.4337 0.9385 -1.528 0.1266 -#> treatmentestPro:ns(time, df = 3)3 -1.1912 0.4844 -2.459 0.0139 * +#> (Intercept) -5.85621 0.30013 -19.512 < 2e-16 *** +#> treatmentestPro 0.66414 0.37783 1.758 0.0788 . +#> ns(time, df = 3)1 -0.41110 0.35944 -1.144 0.2527 +#> ns(time, df = 3)2 0.77792 0.73254 1.062 0.2883 +#> ns(time, df = 3)3 1.37771 0.34131 4.036 5.43e-05 *** +#> treatmentestPro:ns(time, df = 3)1 0.07468 0.48613 0.154 0.8779 +#> treatmentestPro:ns(time, df = 3)2 -1.40359 0.94189 -1.490 0.1362 +#> treatmentestPro:ns(time, df = 3)3 -1.06823 0.48634 -2.196 0.0281 * #> --- #> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> #> (Dispersion parameter for binomial family taken to be 1) #> #> Null deviance: 3635.4 on 32723 degrees of freedom -#> Residual deviance: 3612.7 on 32716 degrees of freedom -#> AIC: 3628.7 +#> Residual deviance: 3613.4 on 32716 degrees of freedom +#> AIC: 3629.4 #> #> Number of Fisher Scoring iterations: 7 ``` diff --git a/cran-comments.md b/cran-comments.md index dbbe739a..76224f8d 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,8 @@ +## Resubmission +This is a resubmission. In this version I have: + +* Fixed redirected URL. + ## Test environments * local macOS 10.16, R 4.0.2 diff --git a/man/figures/README-plot-mason-1.png b/man/figures/README-plot-mason-1.png index 16c39ce2..a37e0959 100644 Binary files a/man/figures/README-plot-mason-1.png and b/man/figures/README-plot-mason-1.png differ diff --git a/man/figures/README-unnamed-chunk-2-1.png b/man/figures/README-unnamed-chunk-2-1.png index 13edebdc..151a83d1 100644 Binary files a/man/figures/README-unnamed-chunk-2-1.png and b/man/figures/README-unnamed-chunk-2-1.png differ diff --git a/man/figures/README-unnamed-chunk-3-1.png b/man/figures/README-unnamed-chunk-3-1.png index eabcfc79..3d4f527e 100644 Binary files a/man/figures/README-unnamed-chunk-3-1.png and b/man/figures/README-unnamed-chunk-3-1.png differ diff --git a/man/figures/README-unnamed-chunk-4-1.png b/man/figures/README-unnamed-chunk-4-1.png index c99dd732..aa6ef89a 100644 Binary files a/man/figures/README-unnamed-chunk-4-1.png and b/man/figures/README-unnamed-chunk-4-1.png differ