From fecef524e8d1a52504b4714dbd12352250cd1eab Mon Sep 17 00:00:00 2001 From: Max Turgeon Date: Tue, 9 Apr 2024 16:24:32 -0400 Subject: [PATCH] prepare cran submission 0.10.5 --- DESCRIPTION | 40 ++++------- NEWS.md | 3 +- R/popTime.R | 132 +++++++++++++++++++--------------- cran-comments.md | 2 +- revdep/README.md | 17 +++-- revdep/data.sqlite | Bin 61440 -> 135168 bytes revdep/failures.md | 6 +- tests/testthat/test-fitting.R | 4 +- tests/testthat/test-gam.R | 8 +-- tests/testthat/test-gbm.R | 4 +- 10 files changed, 112 insertions(+), 104 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4995683e..2a0c15dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,32 +3,18 @@ Type: Package Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression Version: 0.10.5 Date: 2024-04-09 -Authors@R: - c(person(given = "Sahir", - family = "Bhatnagar", - role = c("aut", "cre"), - email = "sahir.bhatnagar@gmail.com", - comment = "https://sahirbhatnagar.com/"), - person(given = "Maxime", - family = "Turgeon", - role = "aut", - email = "max.turgeon@umanitoba.ca", - comment = "https://www.maxturgeon.ca/"), - person(given = "Jesse", - family = "Islam", - role = "aut", - email = "jesse.islam@mail.mcgill.ca", - comment = "https://www.jesseislam.com/"), - person(given = "Olli", - family = "Saarela", - role = "aut", - email = "olli.saarela@utoronto.ca", - comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"), - person(given = "James", - family = "Hanley", - role = "aut", - email = "james.hanley@mcgill.ca", - comment = "https://jhanley.biostat.mcgill.ca/")) +Authors@R: c( + person("Sahir", "Bhatnagar", , "sahir.bhatnagar@gmail.com", role = c("aut", "cre"), + comment = "https://sahirbhatnagar.com/"), + person("Maxime", "Turgeon", , "max.turgeon@umanitoba.ca", role = "aut", + comment = "https://www.maxturgeon.ca/"), + person("Jesse", "Islam", , "jesse.islam@mail.mcgill.ca", role = "aut", + comment = "https://www.jesseislam.com/"), + person("Olli", "Saarela", , "olli.saarela@utoronto.ca", role = "aut", + comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"), + person("James", "Hanley", , "james.hanley@mcgill.ca", role = "aut", + comment = "https://jhanley.biostat.mcgill.ca/") + ) Description: Fit 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 @@ -42,7 +28,7 @@ Depends: R (>= 3.5.0) Imports: data.table, - ggplot2, + ggplot2 (>= 3.4.0), methods, mgcv, stats, diff --git a/NEWS.md b/NEWS.md index 380082f0..72f3c6c3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,10 +2,11 @@ * Skip tests when R is compiled against ATLAS BLAS * Set seed for reproducible tests +* Addressed deprecation warning in ggplot2 # casebase 0.10.4 -* Fix bug with tangled outputs of vignettes. +* Fixed bug with tangled outputs of vignettes. # casebase 0.10.3 diff --git a/R/popTime.R b/R/popTime.R index 61eadbdc..3df4ca88 100644 --- a/R/popTime.R +++ b/R/popTime.R @@ -269,62 +269,79 @@ popTime <- function(data, time, event, censored.indicator, #' @importFrom ggplot2 margin element_blank rel %+replace% theme_cb <- function(font_size = 14, font_family = "", line_size = 0.5, rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) { - half_line <- 0.5 * font_size - small_size <- rel_small * font_size - ggplot2::theme_grey(base_size = font_size, base_family = font_family) %+replace% - theme(line = element_line(color = "black", size = line_size, - linetype = 1, lineend = "butt"), rect = element_rect(fill = NA, - color = NA, size = line_size, linetype = 1), text = element_text(family = font_family, - face = "plain", color = "black", size = font_size, - hjust = 0.5, vjust = 0.5, angle = 0, lineheight = 0.9, - margin = margin(), debug = FALSE), axis.line = element_line(color = "black", - size = line_size, lineend = "square"), axis.line.x = NULL, - axis.line.y = NULL, axis.text = element_text(color = "black", - size = small_size), axis.text.x = element_text(margin = margin(t = 0.25 * small_size), - vjust = 1), axis.text.x.top = element_text(margin = margin(b = 0.25 * small_size), - vjust = 0), axis.text.y = element_text(margin = margin(r = 0.25 * small_size), - hjust = 1), axis.text.y.right = element_text(margin = margin(l = 0.25 * small_size), - hjust = 0), axis.ticks = element_line(color = "black", - size = line_size), axis.ticks.length = unit(0.5 * half_line, - "pt"), axis.title.x = element_text(margin = margin(t = 0.5 * half_line), - vjust = 1), axis.title.x.top = element_text(margin = margin(b = 0.5 * half_line), - vjust = 0), axis.title.y = element_text(angle = 90, - margin = margin(r = 0.5 * half_line), - vjust = 1), - axis.title.y.right = element_text(angle = -90, margin = margin(l = 0.5 * half_line), - vjust = 0), legend.background = element_blank(), - legend.spacing = unit(font_size, "pt"), legend.spacing.x = NULL, - legend.spacing.y = NULL, legend.margin = margin(0, - 0, 0, 0), legend.key = element_blank(), legend.key.size = unit(1.1 * - font_size, "pt"), legend.key.height = NULL, - legend.key.width = NULL, legend.text = element_text(size = rel(rel_small)), - legend.text.align = NULL, legend.title = element_text(hjust = 0), - legend.title.align = NULL, legend.position = "right", - legend.direction = NULL, legend.justification = c("left", - "center"), legend.box = NULL, legend.box.margin = margin(0, - 0, 0, 0), legend.box.background = element_blank(), - legend.box.spacing = unit(font_size, "pt"), panel.background = element_blank(), - panel.border = element_blank(), panel.grid = element_blank(), - panel.grid.major = NULL, panel.grid.minor = NULL, - panel.grid.major.x = NULL, panel.grid.major.y = NULL, - panel.grid.minor.x = NULL, panel.grid.minor.y = NULL, - panel.spacing = unit(half_line, "pt"), panel.spacing.x = NULL, - panel.spacing.y = NULL, panel.ontop = FALSE, strip.background = element_rect(fill = "grey80"), - strip.text = element_text(size = rel(rel_small), - margin = margin(0.5 * half_line, 0.5 * half_line, 0.5 * half_line, - 0.5 * half_line)), strip.text.x = NULL, strip.text.y = element_text(angle = -90), - strip.placement = "inside", strip.placement.x = NULL, - strip.placement.y = NULL, strip.switch.pad.grid = unit(0.5 * half_line, - "pt"), strip.switch.pad.wrap = unit(0.5 * half_line, - "pt"), plot.background = element_blank(), plot.title = element_text(face = "bold", - size = rel(rel_large), hjust = 0, vjust = 1, - margin = margin(b = half_line)), plot.subtitle = element_text(size = rel(rel_small), - hjust = 0, vjust = 1, margin = margin(b = half_line)), - plot.caption = element_text(size = rel(rel_tiny), - hjust = 1, vjust = 1, margin = margin(t = half_line)), - plot.tag = element_text(face = "bold", hjust = 0, - vjust = 0.7), plot.tag.position = c(0, 1), plot.margin = margin(half_line, - half_line, half_line, half_line), complete = TRUE) + half_line <- 0.5 * font_size + small_size <- rel_small * font_size + ggplot2::theme_grey(base_size = font_size, base_family = font_family) %+replace% + theme(line = element_line(color = "black", linewidth = line_size, + linetype = 1, lineend = "butt"), + rect = element_rect(fill = NA, color = NA, linewidth = line_size, + linetype = 1), + text = element_text(family = font_family, + face = "plain", color = "black", size = font_size, + hjust = 0.5, vjust = 0.5, angle = 0, lineheight = 0.9, + margin = margin(), debug = FALSE), + axis.line = element_line(color = "black", + linewidth = line_size, + lineend = "square"), + axis.line.x = NULL, + axis.line.y = NULL, + axis.text = element_text(color = "black", size = small_size), + axis.text.x = element_text(margin = margin(t = 0.25 * small_size), + vjust = 1), + axis.text.x.top = element_text(margin = margin(b = 0.25 * small_size), + vjust = 0), + axis.text.y = element_text(margin = margin(r = 0.25 * small_size), + hjust = 1), + axis.text.y.right = element_text(margin = margin(l = 0.25 * small_size), + hjust = 0), + axis.ticks = element_line(color = "black", linewidth = line_size), + axis.ticks.length = unit(0.5 * half_line, "pt"), + axis.title.x = element_text(margin = margin(t = 0.5 * half_line), + vjust = 1), + axis.title.x.top = element_text(margin = margin(b = 0.5 * half_line), + vjust = 0), + axis.title.y = element_text(angle = 90, + margin = margin(r = 0.5 * half_line), + vjust = 1), + axis.title.y.right = element_text(angle = -90, margin = margin(l = 0.5 * half_line), + vjust = 0), legend.background = element_blank(), + legend.spacing = unit(font_size, "pt"), legend.spacing.x = NULL, + legend.spacing.y = NULL, + legend.margin = margin(0, 0, 0, 0), + legend.key = element_blank(), + legend.key.size = unit(1.1 * font_size, "pt"), legend.key.height = NULL, + legend.key.width = NULL, legend.text = element_text(size = rel(rel_small)), + legend.text.align = NULL, legend.title = element_text(hjust = 0), + legend.title.align = NULL, legend.position = "right", + legend.direction = NULL, + legend.justification = c("left", "center"), + legend.box = NULL, + legend.box.margin = margin(0, 0, 0, 0), legend.box.background = element_blank(), + legend.box.spacing = unit(font_size, "pt"), panel.background = element_blank(), + panel.border = element_blank(), panel.grid = element_blank(), + panel.grid.major = NULL, panel.grid.minor = NULL, + panel.grid.major.x = NULL, panel.grid.major.y = NULL, + panel.grid.minor.x = NULL, panel.grid.minor.y = NULL, + panel.spacing = unit(half_line, "pt"), panel.spacing.x = NULL, + panel.spacing.y = NULL, panel.ontop = FALSE, + strip.background = element_rect(fill = "grey80"), + strip.text = element_text(size = rel(rel_small), + margin = margin(0.5 * half_line, 0.5 * half_line, 0.5 * half_line, + 0.5 * half_line)), + strip.text.x = NULL, strip.text.y = element_text(angle = -90), + strip.placement = "inside", strip.placement.x = NULL, + strip.placement.y = NULL, + strip.switch.pad.grid = unit(0.5 * half_line, "pt"), + strip.switch.pad.wrap = unit(0.5 * half_line, "pt"), + plot.background = element_blank(), + plot.title = element_text(face = "bold", size = rel(rel_large), hjust = 0, vjust = 1, margin = margin(b = half_line)), + plot.subtitle = element_text(size = rel(rel_small), hjust = 0, vjust = 1, margin = margin(b = half_line)), + plot.caption = element_text(size = rel(rel_tiny), + hjust = 1, vjust = 1, margin = margin(t = half_line)), + plot.tag = element_text(face = "bold", hjust = 0, + vjust = 0.7), plot.tag.position = c(0, 1), + plot.margin = margin(half_line, half_line, half_line, half_line), + complete = TRUE) } @@ -341,6 +358,7 @@ panelBorder <- function(color = "grey85", size = 1, linetype = 1, } theme(panel.border = element_rect( color = color, fill = NA, - linetype = linetype, size = size + linetype = linetype, + linewidth = size )) } diff --git a/cran-comments.md b/cran-comments.md index 4e91bc0e..f861092c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,7 +4,7 @@ There were no ERRORs or WARNINGs ## Test environments -* local macOS 14.3, R 4.3.2 +* local macOS 14.4, R 4.3.2 * ubuntu 22.04 (on GH-Actions), R-release, R-devel, R-oldrelease * Windows Server 2022 x64 (on GH-Actions), R-release * macOS 12.7 (on GH-Actions), R-release diff --git a/revdep/README.md b/revdep/README.md index e5fd6cad..9a802144 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -3,23 +3,26 @@ |field |value | |:--------|:-----------------------------------| |version |R version 4.3.2 (2023-10-31) | -|os |macOS Sonoma 14.3 | +|os |macOS Sonoma 14.4.1 | |system |aarch64, darwin20 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/Toronto | -|date |2024-02-01 | -|rstudio |2023.12.0+369 Ocean Storm (desktop) | +|date |2024-04-09 | +|rstudio |2023.12.1+402 Ocean Storm (desktop) | |pandoc |2.19 @ /opt/homebrew/bin/pandoc | # Dependencies -|package |old |new |Δ | -|:----------|:------|:------|:--| -|casebase |0.10.3 |0.10.4 |* | -|data.table |NA |1.15.0 |* | +|package |old |new |Δ | +|:----------|:---|:------|:--| +|casebase |NA |0.10.5 |* | +|data.table |NA |1.15.4 |* | +|ggplot2 |NA |3.5.0 |* | +|munsell |NA |0.5.1 |* | +|VGAM |NA |1.1-10 |* | # Revdeps diff --git a/revdep/data.sqlite b/revdep/data.sqlite index 669a0cba0e17d09342a9e313ea034a35374e41fb..7cf0d2cad6c163923cade04ad13cdc95fd9a1526 100644 GIT binary patch literal 135168 zcmeHwTa(<#mEKUJo%KqdoxON=Y|HYdD#Bv-3=4JX3%hH?*=aVLR7+%&s%}cNo*K1K 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zlUYEaF`09&=j5(`MxyaW`Q=JhN=2E)*+Hr4MXANbnfZCsx5_j6G4f2_uN?&s899U# fWqFZY$BWH%e5kJDC+Ip4Zm>m@f6Xo>&6(Z+bQ`I@ diff --git a/revdep/failures.md b/revdep/failures.md index 98b529b3..3768e352 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -6,7 +6,7 @@ * GitHub: https://github.com/tagteam/riskRegression * Source code: https://github.com/cran/riskRegression * Date/Publication: 2023-12-19 17:00:02 UTC -* Number of recursive dependencies: 188 +* Number of recursive dependencies: 186 Run `revdepcheck::revdep_details(, "riskRegression")` for more info @@ -30,7 +30,7 @@ Run `revdepcheck::revdep_details(, "riskRegression")` for more info ** using staged installation ** libs using C++ compiler: ‘Homebrew clang version 14.0.6’ -using SDK: ‘MacOSX14.2.sdk’ +using SDK: ‘MacOSX14.4.sdk’ /opt/homebrew/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/Rcpp/include' -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include' -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o In file included from IC-Nelson-Aalen-cens-time.cpp:2: In file included from ./IC-Nelson-Aalen-cens-time.h:1: @@ -57,7 +57,7 @@ ERROR: compilation failed for package ‘riskRegression’ ** using staged installation ** libs using C++ compiler: ‘Homebrew clang version 14.0.6’ -using SDK: ‘MacOSX14.2.sdk’ +using SDK: ‘MacOSX14.4.sdk’ /opt/homebrew/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/Rcpp/include' -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include' -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o In file included from IC-Nelson-Aalen-cens-time.cpp:2: In file included from ./IC-Nelson-Aalen-cens-time.h:1: diff --git a/tests/testthat/test-fitting.R b/tests/testthat/test-fitting.R index 2519b802..efcabedf 100644 --- a/tests/testthat/test-fitting.R +++ b/tests/testthat/test-fitting.R @@ -61,9 +61,9 @@ test_that("no error in summary method for gam", { fitDT <- try(fitSmoothHazard(event ~ Z, data = DT, time = "ftime"), silent = TRUE) - sumDF <- try(print(summary(fitDF)), + sumDF <- try(summary(fitDF), silent = TRUE) - sumDT <- try(print(summary(fitDT)), + sumDT <- try(summary(fitDT), silent = TRUE) expect_false(inherits(sumDF, "try-error")) diff --git a/tests/testthat/test-gam.R b/tests/testthat/test-gam.R index 632071d5..d18ee3f6 100644 --- a/tests/testthat/test-gam.R +++ b/tests/testthat/test-gam.R @@ -105,10 +105,10 @@ test_that("output probabilities", { # Summary method test_that("no error in summary method for gam", { - sumDF <- try(print(summary(fitDF_gam)), - silent = TRUE) - sumDT <- try(print(summary(fitDT_gam)), - silent = TRUE) + sumDF <- try(summary(fitDF_gam), + silent = TRUE) + sumDT <- try(summary(fitDT_gam), + silent = TRUE) expect_false(inherits(sumDF, "try-error")) expect_false(inherits(sumDT, "try-error")) diff --git a/tests/testthat/test-gbm.R b/tests/testthat/test-gbm.R index c155929c..aef58403 100644 --- a/tests/testthat/test-gbm.R +++ b/tests/testthat/test-gbm.R @@ -130,9 +130,9 @@ test_that("output probabilities", { # Summary method test_that("no error in summary method for gbm", { - sumDF <- try(print(summary(fitDF_gbm)), + sumDF <- try(summary(fitDF_gbm), silent = TRUE) - sumDT <- try(print(summary(fitDT_gbm)), + sumDT <- try(summary(fitDT_gbm), silent = TRUE) expect_false(inherits(sumDF, "try-error"))