---
title: "R Packages: Timeline of Updates"
subtitle: "Packages published in CRAN that I maintain "
author: "Pedro J. Aphalo"
date: "2024-07-13"
date-modified: today
categories: [R packages]
keywords: [R, photobiology, data visualization, computations]
freeze: false
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.retina = 3,
out.width = "100%"
)
library(lubridate)
library(ggplot2)
library(ggpp)
```
```{r, echo=FALSE, include=FALSE}
# protect against date change while script is running
today <- lubridate::today()
# download info from CRAN
# cache the data based on R session and date
if (!exists("all_pkgs.df") ||
is.null(attr(all_pkgs.df, "download.date")) || # not strictly needed
attr(all_pkgs.df, "download.date") != today) {
all_pkgs.df <- tools::CRAN_package_db() |>
tibble::as_tibble()
attr(all_pkgs.df, "download.date") <- lubridate::today()
}
dim(all_pkgs.df)
all_pkgs.df |>
janitor::clean_names() |>
dplyr::filter(grepl("Aphalo", author)) -> my_pkgs.df
dim(my_pkgs.df)
my_pkgs.df |>
dplyr::filter(package != "ggrepel") |>
dplyr::select(Package = package, Title = title, Version = version, Date = published, doi) -> my_pkgs_condensed.df
dim(my_pkgs_condensed.df)
```
```{r, echo = FALSE}
# Prepare data for plotting
packages <- my_pkgs_condensed.df[["Package"]]
# we download package history only once per session if possible
if (!exists("pkgs_hist.ls") ||
length(packages) != length(names(pkgs_hist.ls)) ||
length(setdiff(packages, names(pkgs_hist.ls)))) {
pkgs_hist.ls <- list() # will collect one member per package
for (package in packages) {
pkgs_hist.ls[[package]] <-
packageRank::packageHistory(package, check.package = TRUE)
}
}
dates.vec <- lubridate::Date() #
packages.vec <- character()
for (package in packages) {
temp <- pkgs_hist.ls[[package]]
dates.vec <- c(dates.vec, temp[["Date"]])
packages.vec <- c(packages.vec, rep(package, length(temp[["Date"]])))
}
ordering <- order(dates.vec)
dates.vec <- dates.vec[ordering]
packages.vec <- packages.vec[ordering]
earliest.date <- dates.vec[1]
latest.date <- dates.vec[length(dates.vec)]
```
The sources of the R packages I have published are in public Git repositories at [GitHub}(https://github.com/aphalo). Out of the packages that I have authored and maintain, `r length(packages)` are currently available through [CRAN](https://cran.r-project.org/). The total number of packages submissions to CRAN (mostly updates) as author and maintainer is `r length(dates.vec)` since `r format.Date(earliest.date)`.
The most recent of these updates was published in CRAN on `r format.Date(latest.date)`.
```{r 'cran-packages-plot', echo = FALSE, fig.width=6, fig.height=5}
cran_releases.df <-
data.frame(Package = factor(packages.vec),
CRAN.dates = dates.vec,
ones = rep(1, length(dates.vec)))
# combined plot
ggplot(cran_releases.df, aes(CRAN.dates, Package, colour = Package)) +
geom_point(shape = "|", size = 6, alpha = 0.8) +
scale_x_date(name = "Date of Publication in CRAN",
date_breaks = "year", date_labels = "%Y") +
theme_minimal(12) + theme(legend.position = "none")
```
```{r, results='asis', echo = FALSE}
#| label: tbl-packages
#| tbl-cap: List of packages available at CRAN-with the most recently updated one at the top. Package names are linked to their pages in CRAN. Titles are linked to their HTML documentation at this site.
my_pkgs_condensed.df |>
dplyr::transmute("Package (CRAN)" = paste("[", Package, "](", "https://doi.org/", doi, ")", sep = ""),
"Title (documentation)" = paste("[", Title, "](", "https://docs.r4photobiology.info/", package, "/)", sep = ""),
Version = Version,
Date = Date) |>
dplyr::arrange(desc(Date)) |>
knitr::kable()
```
Updates under development are published at [R-Universe](https://aphalo.r-universe.dev/builds) as soon as merged or commited into the main branch in the repositories at GitHub. Two packages that depend on a commercial closed-source driver, but usable with a free runtime of the driver, are published only at R-Universe. Some new, still unstable packages, are also only at R-Universe.
R-Universe profile: [https://aphalo.r-universe.dev](https://aphalo.r-universe.dev).
[](https://aphalo.r-universe.dev/)
[](https://aphalo.r-universe.dev/packages)
