Merge pull request #233 from kgoldfeld/232-functions-used-in-formula=…

…-argument-in-defdata-not-available-for-functions-defined-out-of-global-namespace

232 functions used in formula= argument in defdata not available for functions defined out of global namespace

CITATION.cff

@@ -8,8 +8,13 @@ message: 'To cite package "simstudy" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'simstudy: Simulation of Study Data'
-version: 0.7.1.9000
+version: 0.8.0.9000
 doi: 10.21105/joss.02763
+identifiers:
+- type: doi
+  value: 10.32614/CRAN.package.simstudy
+- type: url
+  value: https://kgoldfeld.github.io/simstudy/dev/
 abstract: Simulates data sets in order to explore modeling techniques or better understand
   data generating processes. The user specifies a set of relationships between covariates,
   and generates data based on these specifications. The final data sets can represent
@@ -49,7 +54,7 @@ preferred-citation:
 repository: https://CRAN.R-project.org/package=simstudy
 repository-code: https://github.com/kgoldfeld/simstudy
 url: https://kgoldfeld.github.io/simstudy/
-date-released: '2024-05-10'
+date-released: '2024-07-19'
 contact:
 - family-names: Goldfeld
   given-names: Keith
@@ -97,6 +102,7 @@ references:
     given-names: Toby
     orcid: https://orcid.org/0000-0002-3146-0865
   year: '2024'
+  doi: 10.32614/CRAN.package.data.table
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
@@ -112,6 +118,7 @@ references:
     email: jenny@posit.co
     orcid: https://orcid.org/0000-0002-6983-2759
   year: '2024'
+  doi: 10.32614/CRAN.package.glue
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -122,6 +129,7 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
+  doi: 10.32614/CRAN.package.methods
 - type: software
   title: mvnfast
   abstract: 'mvnfast: Fast Multivariate Normal and Student''s t Methods'
@@ -133,6 +141,7 @@ references:
     given-names: Matteo
     email: matteo.fasiolo@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.mvnfast
 - type: software
   title: Rcpp
   abstract: 'Rcpp: Seamless R and C++ Integration'
@@ -159,6 +168,7 @@ references:
   - family-names: Chambers
     given-names: John
   year: '2024'
+  doi: 10.32614/CRAN.package.Rcpp
 - type: software
   title: backports
   abstract: 'backports: Reimplementations of Functions Introduced Since R-3.0.0'
@@ -170,8 +180,12 @@ references:
     given-names: Michel
     email: michellang@gmail.com
     orcid: https://orcid.org/0000-0001-9754-0393
+  - family-names: Murdoch
+    given-names: Duncan
+    email: murdoch.duncan@gmail.com
   - name: R Core Team
   year: '2024'
+  doi: 10.32614/CRAN.package.backports
 - type: software
   title: fastglm
   abstract: 'fastglm: Fast and Stable Fitting of Generalized Linear Models using ''RcppEigen'''
@@ -183,6 +197,7 @@ references:
     given-names: Jared
     email: jaredhuling@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.fastglm
 - type: software
   title: covr
   abstract: 'covr: Test Coverage for Packages'
@@ -194,6 +209,7 @@ references:
     given-names: Jim
     email: james.f.hester@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.covr
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -218,6 +234,7 @@ references:
     email: davis@posit.co
     orcid: https://orcid.org/0000-0003-4777-038X
   year: '2024'
+  doi: 10.32614/CRAN.package.dplyr
 - type: software
   title: formatR
   abstract: 'formatR: Format R Code Automatically'
@@ -230,6 +247,7 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+  doi: 10.32614/CRAN.package.formatR
 - type: software
   title: gee
   abstract: 'gee: Generalized Estimation Equation Solver'
@@ -239,6 +257,7 @@ references:
   - family-names: Carey
     given-names: Vincent J
   year: '2024'
+  doi: 10.32614/CRAN.package.gee
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
@@ -278,6 +297,7 @@ references:
     name-particle: van den
     orcid: https://orcid.org/0000-0002-9335-7468
   year: '2024'
+  doi: 10.32614/CRAN.package.ggplot2
 - type: software
   title: grid
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -288,6 +308,7 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
+  doi: 10.32614/CRAN.package.grid
 - type: software
   title: gridExtra
   abstract: 'gridExtra: Miscellaneous Functions for "Grid" Graphics'
@@ -298,6 +319,7 @@ references:
     given-names: Baptiste
     email: baptiste.auguie@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.gridExtra
 - type: software
   title: hedgehog
   abstract: 'hedgehog: Property-Based Testing'
@@ -309,6 +331,7 @@ references:
     given-names: Huw
     email: huw.campbell@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.hedgehog
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -321,6 +344,7 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+  doi: 10.32614/CRAN.package.knitr
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
@@ -335,6 +359,7 @@ references:
     given-names: Hadley
     email: hadley@rstudio.com
   year: '2024'
+  doi: 10.32614/CRAN.package.magrittr
 - type: software
   title: Matrix
   abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
@@ -353,6 +378,7 @@ references:
     given-names: Mikael
     orcid: https://orcid.org/0000-0002-3542-2938
   year: '2024'
+  doi: 10.32614/CRAN.package.Matrix
 - type: software
   title: mgcv
   abstract: 'mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation'
@@ -363,6 +389,7 @@ references:
     given-names: Simon
     email: simon.wood@r-project.org
   year: '2024'
+  doi: 10.32614/CRAN.package.mgcv
 - type: software
   title: ordinal
   abstract: 'ordinal: Regression Models for Ordinal Data'
@@ -374,6 +401,7 @@ references:
     given-names: Rune Haubo Bojesen
     email: rune.haubo@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.ordinal
 - type: software
   title: pracma
   abstract: 'pracma: Practical Numerical Math Functions'
@@ -384,6 +412,7 @@ references:
     given-names: Hans W.
     email: hwborchers@googlemail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.pracma
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -427,6 +456,7 @@ references:
     email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2024'
+  doi: 10.32614/CRAN.package.rmarkdown
 - type: software
   title: scales
   abstract: 'scales: Scale Functions for Visualization'
@@ -444,6 +474,7 @@ references:
   - family-names: Seidel
     given-names: Dana
   year: '2024'
+  doi: 10.32614/CRAN.package.scales
 - type: software
   title: splines
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -454,6 +485,7 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
+  doi: 10.32614/CRAN.package.splines
 - type: software
   title: survival
   abstract: 'survival: Survival Analysis'
@@ -465,6 +497,7 @@ references:
     given-names: Terry M
     email: therneau.terry@mayo.edu
   year: '2024'
+  doi: 10.32614/CRAN.package.survival
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -476,6 +509,7 @@ references:
     given-names: Hadley
     email: hadley@posit.co
   year: '2024'
+  doi: 10.32614/CRAN.package.testthat
 - type: software
   title: gtsummary
   abstract: 'gtsummary: Presentation-Ready Data Summary and Analytic Result Tables'
@@ -503,6 +537,24 @@ references:
     given-names: Emily C.
     orcid: https://orcid.org/0000-0002-1402-4498
   year: '2024'
+  doi: 10.32614/CRAN.package.gtsummary
+- type: software
+  title: broom.helpers
+  abstract: 'broom.helpers: Helpers for Model Coefficients Tibbles'
+  notes: Suggests
+  url: https://larmarange.github.io/broom.helpers/
+  repository: https://CRAN.R-project.org/package=broom.helpers
+  authors:
+  - family-names: Larmarange
+    given-names: Joseph
+    email: joseph@larmarange.net
+    orcid: https://orcid.org/0000-0001-7097-700X
+  - family-names: Sjoberg
+    given-names: Daniel D.
+    email: danield.sjoberg@gmail.com
+    orcid: https://orcid.org/0000-0003-0862-2018
+  year: '2024'
+  doi: 10.32614/CRAN.package.broom.helpers
 - type: software
   title: survminer
   abstract: 'survminer: Drawing Survival Curves using ''ggplot2'''
@@ -520,6 +572,7 @@ references:
     given-names: Przemyslaw
     email: przemyslaw.biecek@gmail.com
   year: '2024'
+  doi: 10.32614/CRAN.package.survminer
 - type: software
   title: katex
   abstract: 'katex: Rendering Math to HTML, ''MathML'', or R-Documentation Format'
@@ -532,6 +585,7 @@ references:
     email: jeroen@berkeley.edu
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2024'
+  doi: 10.32614/CRAN.package.katex
 - type: software
   title: dirmult
   abstract: 'dirmult: Estimation in Dirichlet-Multinomial Distribution'
@@ -542,6 +596,7 @@ references:
     given-names: Torben
     email: tvede@math.aau.dk
   year: '2024'
+  doi: 10.32614/CRAN.package.dirmult
 - type: software
   title: rms
   abstract: 'rms: Regression Modeling Strategies'
@@ -553,6 +608,7 @@ references:
     given-names: Frank E
     email: fh@fharrell.com
   year: '2024'
+  doi: 10.32614/CRAN.package.rms
 - type: software
   title: pbv
   abstract: 'pbv: Probabilities for Bivariate Normal Distribution'
@@ -564,8 +620,6 @@ references:
     given-names: Alexander
     orcid: https://orcid.org/0000-0002-8226-3132
   year: '2024'
+  doi: 10.32614/CRAN.package.pbv
   version: '>= 0.4-22'
-identifiers:
-- type: url
-  value: https://kgoldfeld.github.io/simstudy/dev/
 

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: simstudy
 Title: Simulation of Study Data
 Version: 0.8.0.9000
-Date: 2024-05-14
+Date: 2024-07-19
 Authors@R: 
     c(person(given = "Keith",
              family = "Goldfeld",
@@ -57,6 +57,7 @@ Suggests:
     survival,
     testthat,
     gtsummary,
+    broom.helpers,
     survminer,
     katex,
     dirmult,

NEWS.md

@@ -6,6 +6,7 @@
 
 ## Minor fix
 * `addCorGen` no longer requires all clusters to have the same size when using the *rho* and *corstr* arguments to define the correlation.
+* Fixed an issue that prevented functions defined outside the global namespace from being referenced in `defData`.
 
 # simstudy 0.8.0
 

R/generate_data.R

@@ -960,6 +960,7 @@ genSpline <- function(dt, newvar, predictor, theta,
 #' @param keepEvents Indicator to retain original "events" columns. Defaults
 #' to FALSE.
 #' @param idName Name of id field in existing data set.
+#' @param envir Optional environment, defaults to current calling environment.
 #' @return Original data table with survival time
 #' @examples
 #' # Baseline data definitions
@@ -996,7 +997,7 @@ genSpline <- function(dt, newvar, predictor, theta,
 #
 genSurv <- function(dtName, survDefs, digits = 3, 
   timeName = NULL, censorName = NULL, eventName = "event", 
-  typeName = "type", keepEvents = FALSE, idName = "id") {
+  typeName = "type", keepEvents = FALSE, idName = "id", envir = parent.frame()) {
 
   # For double-dot notation
 
@@ -1042,13 +1043,13 @@ genSurv <- function(dtName, survDefs, digits = 3,
     subDef <- survDefs[varname == events[i]]
 
     formshape <- subDef[1, shape]
-    shape <- as.vector(.evalWith(formshape, .parseDotVars(formshape,  envir = parent.frame()), dtSurv))
+    shape <- as.vector(.evalWith(formshape, .parseDotVars(formshape,  envir = parent.frame()), dtSurv, envir = envir))
 
     formscale <- subDef[1, scale]
-    scale <- as.vector(.evalWith(formscale, .parseDotVars(formscale, envir = parent.frame()), dtSurv))
+    scale <- as.vector(.evalWith(formscale, .parseDotVars(formscale, envir = parent.frame()), dtSurv, envir = envir))
 
     formulas <- subDef[, formula]
-    form1 <- as.vector(.evalWith(formulas[1], .parseDotVars(formulas[1], envir = parent.frame()), dtSurv))
+    form1 <- as.vector(.evalWith(formulas[1], .parseDotVars(formulas[1], envir = parent.frame()), dtSurv, envir = envir))
 
     if (nrow(subDef) > 1) {
 
@@ -1063,7 +1064,7 @@ genSurv <- function(dtName, survDefs, digits = 3,
       transition <- subDef[2, transition]
       t_adj <- transition ^ (1/shape)
 
-      form2 <- as.vector(.evalWith(formulas[2], .parseDotVars(formulas[2], envir = parent.frame()), dtSurv))
+      form2 <- as.vector(.evalWith(formulas[2], .parseDotVars(formulas[2], envir = parent.frame()), dtSurv, envir = envir))
 
       threshold <- exp(form1) * t_adj
       period <- 1*(nlogu < threshold) + 2*(nlogu >= threshold)