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prepare cran submission 0.10.5
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‎DESCRIPTION‎

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Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression
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Version: 0.10.5
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Date: 2024-04-09
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Authors@R:
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c(person(given = "Sahir",
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family = "Bhatnagar",
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role = c("aut", "cre"),
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email = "sahir.bhatnagar@gmail.com",
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comment = "https://sahirbhatnagar.com/"),
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person(given = "Maxime",
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family = "Turgeon",
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role = "aut",
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email = "max.turgeon@umanitoba.ca",
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comment = "https://www.maxturgeon.ca/"),
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person(given = "Jesse",
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family = "Islam",
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role = "aut",
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email = "jesse.islam@mail.mcgill.ca",
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comment = "https://www.jesseislam.com/"),
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person(given = "Olli",
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family = "Saarela",
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role = "aut",
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email = "olli.saarela@utoronto.ca",
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comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"),
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person(given = "James",
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family = "Hanley",
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role = "aut",
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email = "james.hanley@mcgill.ca",
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comment = "https://jhanley.biostat.mcgill.ca/"))
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Authors@R: c(
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person("Sahir", "Bhatnagar", , "sahir.bhatnagar@gmail.com", role = c("aut", "cre"),
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comment = "https://sahirbhatnagar.com/"),
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person("Maxime", "Turgeon", , "max.turgeon@umanitoba.ca", role = "aut",
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comment = "https://www.maxturgeon.ca/"),
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person("Jesse", "Islam", , "jesse.islam@mail.mcgill.ca", role = "aut",
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comment = "https://www.jesseislam.com/"),
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person("Olli", "Saarela", , "olli.saarela@utoronto.ca", role = "aut",
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comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"),
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person("James", "Hanley", , "james.hanley@mcgill.ca", role = "aut",
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comment = "https://jhanley.biostat.mcgill.ca/")
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)
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Description: Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple
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competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms
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of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the
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R (>= 3.5.0)
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Imports:
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data.table,
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ggplot2,
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ggplot2 (>= 3.4.0),
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methods,
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mgcv,
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stats,

‎NEWS.md‎

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* Skip tests when R is compiled against ATLAS BLAS
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* Set seed for reproducible tests
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* Addressed deprecation warning in ggplot2
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# casebase 0.10.4
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* Fix bug with tangled outputs of vignettes.
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* Fixed bug with tangled outputs of vignettes.
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# casebase 0.10.3
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‎R/popTime.R‎

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#' @importFrom ggplot2 margin element_blank rel %+replace%
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theme_cb <- function(font_size = 14, font_family = "", line_size = 0.5,
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rel_small = 12/14, rel_tiny = 11/14, rel_large = 16/14) {
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half_line <- 0.5 * font_size
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small_size <- rel_small * font_size
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ggplot2::theme_grey(base_size = font_size, base_family = font_family) %+replace%
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theme(line = element_line(color = "black", size = line_size,
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linetype = 1, lineend = "butt"), rect = element_rect(fill = NA,
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color = NA, size = line_size, linetype = 1), text = element_text(family = font_family,
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face = "plain", color = "black", size = font_size,
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hjust = 0.5, vjust = 0.5, angle = 0, lineheight = 0.9,
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margin = margin(), debug = FALSE), axis.line = element_line(color = "black",
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size = line_size, lineend = "square"), axis.line.x = NULL,
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axis.line.y = NULL, axis.text = element_text(color = "black",
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size = small_size), axis.text.x = element_text(margin = margin(t = 0.25 * small_size),
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vjust = 1), axis.text.x.top = element_text(margin = margin(b = 0.25 * small_size),
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vjust = 0), axis.text.y = element_text(margin = margin(r = 0.25 * small_size),
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hjust = 1), axis.text.y.right = element_text(margin = margin(l = 0.25 * small_size),
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hjust = 0), axis.ticks = element_line(color = "black",
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size = line_size), axis.ticks.length = unit(0.5 * half_line,
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"pt"), axis.title.x = element_text(margin = margin(t = 0.5 * half_line),
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vjust = 1), axis.title.x.top = element_text(margin = margin(b = 0.5 * half_line),
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vjust = 0), axis.title.y = element_text(angle = 90,
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margin = margin(r = 0.5 * half_line),
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vjust = 1),
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axis.title.y.right = element_text(angle = -90, margin = margin(l = 0.5 * half_line),
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vjust = 0), legend.background = element_blank(),
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legend.spacing = unit(font_size, "pt"), legend.spacing.x = NULL,
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legend.spacing.y = NULL, legend.margin = margin(0,
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0, 0, 0), legend.key = element_blank(), legend.key.size = unit(1.1 *
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font_size, "pt"), legend.key.height = NULL,
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legend.key.width = NULL, legend.text = element_text(size = rel(rel_small)),
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legend.text.align = NULL, legend.title = element_text(hjust = 0),
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legend.title.align = NULL, legend.position = "right",
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legend.direction = NULL, legend.justification = c("left",
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"center"), legend.box = NULL, legend.box.margin = margin(0,
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0, 0, 0), legend.box.background = element_blank(),
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legend.box.spacing = unit(font_size, "pt"), panel.background = element_blank(),
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panel.border = element_blank(), panel.grid = element_blank(),
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panel.grid.major = NULL, panel.grid.minor = NULL,
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panel.grid.major.x = NULL, panel.grid.major.y = NULL,
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panel.grid.minor.x = NULL, panel.grid.minor.y = NULL,
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panel.spacing = unit(half_line, "pt"), panel.spacing.x = NULL,
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panel.spacing.y = NULL, panel.ontop = FALSE, strip.background = element_rect(fill = "grey80"),
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strip.text = element_text(size = rel(rel_small),
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margin = margin(0.5 * half_line, 0.5 * half_line, 0.5 * half_line,
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0.5 * half_line)), strip.text.x = NULL, strip.text.y = element_text(angle = -90),
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strip.placement = "inside", strip.placement.x = NULL,
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strip.placement.y = NULL, strip.switch.pad.grid = unit(0.5 * half_line,
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"pt"), strip.switch.pad.wrap = unit(0.5 * half_line,
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"pt"), plot.background = element_blank(), plot.title = element_text(face = "bold",
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size = rel(rel_large), hjust = 0, vjust = 1,
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margin = margin(b = half_line)), plot.subtitle = element_text(size = rel(rel_small),
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hjust = 0, vjust = 1, margin = margin(b = half_line)),
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plot.caption = element_text(size = rel(rel_tiny),
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hjust = 1, vjust = 1, margin = margin(t = half_line)),
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plot.tag = element_text(face = "bold", hjust = 0,
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vjust = 0.7), plot.tag.position = c(0, 1), plot.margin = margin(half_line,
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half_line, half_line, half_line), complete = TRUE)
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half_line <- 0.5 * font_size
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small_size <- rel_small * font_size
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ggplot2::theme_grey(base_size = font_size, base_family = font_family) %+replace%
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theme(line = element_line(color = "black", linewidth = line_size,
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linetype = 1, lineend = "butt"),
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rect = element_rect(fill = NA, color = NA, linewidth = line_size,
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linetype = 1),
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text = element_text(family = font_family,
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face = "plain", color = "black", size = font_size,
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hjust = 0.5, vjust = 0.5, angle = 0, lineheight = 0.9,
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margin = margin(), debug = FALSE),
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axis.line = element_line(color = "black",
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linewidth = line_size,
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lineend = "square"),
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axis.line.x = NULL,
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axis.line.y = NULL,
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axis.text = element_text(color = "black", size = small_size),
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axis.text.x = element_text(margin = margin(t = 0.25 * small_size),
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vjust = 1),
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axis.text.x.top = element_text(margin = margin(b = 0.25 * small_size),
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vjust = 0),
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axis.text.y = element_text(margin = margin(r = 0.25 * small_size),
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hjust = 1),
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axis.text.y.right = element_text(margin = margin(l = 0.25 * small_size),
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hjust = 0),
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axis.ticks = element_line(color = "black", linewidth = line_size),
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axis.ticks.length = unit(0.5 * half_line, "pt"),
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axis.title.x = element_text(margin = margin(t = 0.5 * half_line),
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vjust = 1),
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axis.title.x.top = element_text(margin = margin(b = 0.5 * half_line),
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vjust = 0),
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axis.title.y = element_text(angle = 90,
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margin = margin(r = 0.5 * half_line),
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vjust = 1),
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axis.title.y.right = element_text(angle = -90, margin = margin(l = 0.5 * half_line),
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vjust = 0), legend.background = element_blank(),
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legend.spacing = unit(font_size, "pt"), legend.spacing.x = NULL,
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legend.spacing.y = NULL,
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legend.margin = margin(0, 0, 0, 0),
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legend.key = element_blank(),
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legend.key.size = unit(1.1 * font_size, "pt"), legend.key.height = NULL,
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legend.key.width = NULL, legend.text = element_text(size = rel(rel_small)),
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legend.text.align = NULL, legend.title = element_text(hjust = 0),
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legend.title.align = NULL, legend.position = "right",
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legend.direction = NULL,
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legend.justification = c("left", "center"),
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legend.box = NULL,
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legend.box.margin = margin(0, 0, 0, 0), legend.box.background = element_blank(),
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legend.box.spacing = unit(font_size, "pt"), panel.background = element_blank(),
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panel.border = element_blank(), panel.grid = element_blank(),
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panel.grid.major = NULL, panel.grid.minor = NULL,
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panel.grid.major.x = NULL, panel.grid.major.y = NULL,
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panel.grid.minor.x = NULL, panel.grid.minor.y = NULL,
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panel.spacing = unit(half_line, "pt"), panel.spacing.x = NULL,
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panel.spacing.y = NULL, panel.ontop = FALSE,
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strip.background = element_rect(fill = "grey80"),
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strip.text = element_text(size = rel(rel_small),
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margin = margin(0.5 * half_line, 0.5 * half_line, 0.5 * half_line,
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0.5 * half_line)),
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strip.text.x = NULL, strip.text.y = element_text(angle = -90),
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strip.placement = "inside", strip.placement.x = NULL,
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strip.placement.y = NULL,
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strip.switch.pad.grid = unit(0.5 * half_line, "pt"),
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strip.switch.pad.wrap = unit(0.5 * half_line, "pt"),
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plot.background = element_blank(),
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plot.title = element_text(face = "bold", size = rel(rel_large), hjust = 0, vjust = 1, margin = margin(b = half_line)),
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plot.subtitle = element_text(size = rel(rel_small), hjust = 0, vjust = 1, margin = margin(b = half_line)),
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plot.caption = element_text(size = rel(rel_tiny),
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hjust = 1, vjust = 1, margin = margin(t = half_line)),
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plot.tag = element_text(face = "bold", hjust = 0,
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vjust = 0.7), plot.tag.position = c(0, 1),
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plot.margin = margin(half_line, half_line, half_line, half_line),
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complete = TRUE)
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}
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}
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theme(panel.border = element_rect(
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color = color, fill = NA,
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linetype = linetype, size = size
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linetype = linetype,
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linewidth = size
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))
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}

‎cran-comments.md‎

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## Test environments
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* local macOS 14.3, R 4.3.2
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* local macOS 14.4, R 4.3.2
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* ubuntu 22.04 (on GH-Actions), R-release, R-devel, R-oldrelease
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* Windows Server 2022 x64 (on GH-Actions), R-release
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* macOS 12.7 (on GH-Actions), R-release

‎revdep/README.md‎

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|field |value |
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|:--------|:-----------------------------------|
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|version |R version 4.3.2 (2023-10-31) |
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|os |macOS Sonoma 14.3 |
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|os |macOS Sonoma 14.4.1 |
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|system |aarch64, darwin20 |
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|ui |RStudio |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/Toronto |
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|date |2024-02-01 |
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|rstudio |2023.12.0+369 Ocean Storm (desktop) |
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|date |2024-04-09 |
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|rstudio |2023.12.1+402 Ocean Storm (desktop) |
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|pandoc |2.19 @ /opt/homebrew/bin/pandoc |
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# Dependencies
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|package |old |new |Δ |
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|:----------|:------|:------|:--|
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|casebase |0.10.3 |0.10.4 |* |
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|data.table |NA |1.15.0 |* |
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|package |old |new |Δ |
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|:----------|:---|:------|:--|
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|casebase |NA |0.10.5 |* |
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|data.table |NA |1.15.4 |* |
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|ggplot2 |NA |3.5.0 |* |
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|munsell |NA |0.5.1 |* |
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|VGAM |NA |1.1-10 |* |
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# Revdeps
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‎revdep/data.sqlite‎

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