Initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^\_config\.yml$
+^\.github$
+^CONTRIBUTING\.md$
+^NEWS\.md$
+^_pkgdown\.yml$
+pkgdown/
+.DS_Store
+.Rhistory
+.gitignore
+^codecov\.yml$
+vignettes/models-survival-check.Rmd

.github/.gitignore

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+*.html

.github/workflows/check.yml

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+# This workflow file is from https://github.com/stan-dev/cmdstanr/blob/master/.github/workflows
+# under the BSD 3-Clause License: https://github.com/stan-dev/cmdstanr/blob/master/LICENSE.md.
+#
+# BSD 3-Clause License
+# Copyright (c) 2019, Stan Developers and their Assignees
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice,
+# this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+# this list of conditions and the following disclaimer in the documentation
+# and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors
+# may be used to endorse or promote products derived from this software without
+# specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+# BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+# OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+# OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+# EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+name: check
+
+jobs:
+  check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release', rtools: '42'}
+          - {os: ubuntu-latest,   r: 'release', rtools: ''}
+
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NOT_CRAN: true
+
+    steps:
+      - name: cmdstan env vars
+        run: |
+          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
+        shell: bash
+
+      - uses: actions/checkout@v3
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libglpk-dev libglpk40 libcurl4-openssl-dev openmpi-bin openmpi-common libopenmpi-dev || true
+
+      - uses: r-lib/actions/[email protected]
+        with:
+          r-version: ${{ matrix.config.r }}
+          rtools-version: ${{ matrix.config.rtools }}
+
+      - uses: r-lib/actions/[email protected]
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

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+*.Rproj.user
+*.Rhistory
+*.RData
+*.Ruserdata
+*.DS_Store
+*.exe
+*.so
+*.o
+*.dll
+docs/
+*.html
+*_cache/
+*_files/
+.Rproj.user
+inst/doc

DESCRIPTION

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+Package: sfgp
+Type: Package
+Title: Additive semiparametric modeling
+Version: 0.3.0
+Author: Juho Timonen.
+Maintainer: Juho Timonen <[email protected]>
+Description: Additive semiparametric regression modeling with joint longitudinal
+    and time-to-event models.
+    The additive components of the longitudinal part can be for example 
+    Stein-Fojo or approximate Gaussian process functions.
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.1
+Depends: 
+    R (>= 3.5.0)
+SystemRequirements: CmdStan >= 2.33.0
+Remotes:
+  stan-dev/cmdstanr,
+Imports: 
+    methods,
+    cmdstanr (>= 0.4.0),
+    checkmate (>= 2.0.0),
+    posterior (>= 1.1.0),
+    R6 (>= 2.4.0),
+    ggplot2 (>= 3.3.5),
+    ggdist (>= 3.3.1),
+    processx (>= 3.5.2),
+    stringr (>= 1.5.0),
+    ggpubr (>= 0.6.0),
+    dplyr (>= 1.1.4),
+    magrittr(>= 2.0.3)
+Suggests:
+    covr,
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Config/testthat/edition: 3
+License: file LICENSE

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Generable
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method("+",FunctionDraws)
+S3method("-",FunctionDraws)
+export("%>%")
+export(FunctionDraws)
+export(JointModel)
+export(JointModelFit)
+export(StanModelFit)
+export(TSModel)
+export(TSModelFit)
+export(TTEModel)
+export(TermList)
+export(WeibullHazard)
+export(add_sff_input)
+export(create_jm_grid)
+export(example)
+export(example2)
+export(extend_df)
+export(extend_df2)
+export(new_draws)
+export(plot_metric)
+export(predict_new_subjects)
+export(prior_sigma_informed)
+export(sample_subjects)
+export(sfsim)
+export(stancode_ts)
+export(term_to_code)
+export(trajectory_metrics)
+export(treatment_effect)
+import(ggplot2)
+import(stats)
+importFrom(R6,R6Class)
+importFrom(magrittr,"%>%")
+importFrom(posterior,as_draws_rvars)

R/aaa.R

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+# MAIN DOCUMENTATION PAGE -------------------------------------------------
+
+#' The 'sfgp' package.
+#'
+#' @description SF+GP modeling using 'Stan'.
+#' @author Juho Timonen (first.last at iki.fi)
+#' @keywords tumor GP Stan Bayesian
+#'
+#' @section Getting started:
+#' See the following \code{R6} classes.
+#' \itemize{
+#'  \item \code{\link{TSModel}}: Main model class.
+#'  \item \code{\link{TSModelFit}}: Fit class.
+#'  \item \code{\link{JointModel}}: Main model class.
+#'  \item \code{\link{JointModelFit}}: Fit class.
+#'  \item \code{\link{TermList}}: Class describing model terms.
+#'  \item \code{\link{FunctionDraws}}: Class to hold fitted function
+#'  distributions.
+#' }
+#'
+#' @section Data:
+#' The data that you wish to analyze with 'sfgp' should be in an \R
+#' \code{data.frame} where columns correspond to measured variables and rows
+#' correspond to observations. Categorical variables should be \code{factor}s
+#' and continuous ones should be \code{numeric}.
+#'
+#' @name sfgp-package
+#' @aliases sfgp
+#' @import ggplot2 stats
+#' @importFrom R6 R6Class
+#' @importFrom posterior as_draws_rvars
+#'
+#'
+"_PACKAGE"
+
+
+#' Run an example
+#'
+#' @description Fits a model to simple simulated data.
+#' @export
+#' @param num_bf Number of basis functions.
+#' @param scale_bf Basis function domain scale.
+#' @param formula The model formula.
+#' @param ... Other arguments to the \code{$fit()} method of
+#' \code{\link{TSModel}}.
+#' @return An \code{\link{TSModelFit}} object.
+example <- function(num_bf = 32, scale_bf = 1.5, formula = "y ~ gp(x)",
+                    ...) {
+  form <- stats::as.formula(formula)
+  m <- TSModel$new(form)
+  xx <- seq(1, 10, by = 0.15)
+  ff <- 20 + 5 * sin(xx) + 2 * sin(5 * xx) + xx
+  yy <- ff + stats::rnorm(n = length(xx), mean = 0, sd = 1)
+  a <- data.frame(x = xx, y = yy)
+  tc1 <- list(num_bf = num_bf, scale_bf = scale_bf)
+  tc <- list(f_gp_x = tc1)
+  m$fit(data = a, term_confs = tc, ...)
+}
+
+#' Run an example
+#'
+#' @description Fits a model to \code{testdata}.
+#' @export
+#' @param num_bf Number of basis functions.
+#' @param scale_bf Basis function domain scale.
+#' @param formula The model formula.
+#' @param ... Other arguments to the \code{$fit()} method of
+#' \code{\link{TSModel}}.
+#' @return An \code{\link{TSModelFit}} object.
+example2 <- function(num_bf = 24, scale_bf = 1.5,
+                     formula = "y ~ gp(time) + gp(time,arm) + gp(time,id)",
+                     ...) {
+  form <- stats::as.formula(formula)
+  dat <- testdata
+  m <- TSModel$new(form)
+  dat <- add_sff_input(dat, m)
+  tc1 <- list(num_bf = num_bf, scale_bf = scale_bf)
+  tc <- list(gp_x = tc1)
+  m$fit(data = dat, term_confs = tc, ...)
+}

R/data.R

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+#' Simulated longitudinal test data
+#'
+#'
+#' @format
+#' A data frame with 176 rows and 7 columns:
+#' \describe{
+#'   \item{id}{Subject id, factor}
+#'   \item{arm}{Trial arm, factor}
+#'   \item{sex}{Sex, factor}
+#'   \item{time}{Measurement time, numeric}
+#'   \item{weight}{Weight, numeric}
+#'   \item{y}{Response variable, numeric}
+#'   \item{f_true}{True signal}
+#' }
+#' @family built-in datasets
+"testdata"
+
+#' Simulated joint longitudinal and time-to-event test data
+#'
+#'
+#' @format
+#' A list of two data frames \code{lon} (longitudinal data) and
+#' \code{tte} (time-to-event data). Generated using \code{simjm}.
+#' @family built-in datasets
+"example_data_jm"