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prepare cran submission 0.10.5
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@turgeonmaxime
turgeonmaxime committed Apr 9, 2024
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40 changes: 13 additions & 27 deletions DESCRIPTION
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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 = "[email protected]",
comment = "https://sahirbhatnagar.com/"),
person(given = "Maxime",
family = "Turgeon",
role = "aut",
email = "[email protected]",
comment = "https://www.maxturgeon.ca/"),
person(given = "Jesse",
family = "Islam",
role = "aut",
email = "[email protected]",
comment = "https://www.jesseislam.com/"),
person(given = "Olli",
family = "Saarela",
role = "aut",
email = "[email protected]",
comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"),
person(given = "James",
family = "Hanley",
role = "aut",
email = "[email protected]",
comment = "https://jhanley.biostat.mcgill.ca/"))
Authors@R: c(
person("Sahir", "Bhatnagar", , "[email protected]", role = c("aut", "cre"),
comment = "https://sahirbhatnagar.com/"),
person("Maxime", "Turgeon", , "[email protected]", role = "aut",
comment = "https://www.maxturgeon.ca/"),
person("Jesse", "Islam", , "[email protected]", role = "aut",
comment = "https://www.jesseislam.com/"),
person("Olli", "Saarela", , "[email protected]", role = "aut",
comment = "https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/"),
person("James", "Hanley", , "[email protected]", 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
Expand All @@ -42,7 +28,7 @@ Depends:
R (>= 3.5.0)
Imports:
data.table,
ggplot2,
ggplot2 (>= 3.4.0),
methods,
mgcv,
stats,
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3 changes: 2 additions & 1 deletion NEWS.md
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Expand Up @@ -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

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132 changes: 75 additions & 57 deletions R/popTime.R
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Expand Up @@ -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)
}


Expand All @@ -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
))
}
2 changes: 1 addition & 1 deletion cran-comments.md
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Expand Up @@ -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
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17 changes: 10 additions & 7 deletions revdep/README.md
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Expand Up @@ -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

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