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lcolladotor/incar.R

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incar.R
## From https://docs.google.com/document/d/1CSCPUfHGMoa_QTDf6EUsFMYVTiA5GP8OyeIGCyTVbLI/edit?usp=sharing
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_cran(
c(
"tidyverse", "gganimate", "maps", "knitr", "kableExtra",
"scales", "lubridate", "RColorBrewer"
)
)
## Get data from GitHub directly
prison_raw <- readr::read_csv("https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2019/2019-01-22/prison_population.csv")
## Download the data through the tidytuesdayR package
## https://github.com/thebioengineer/tidytuesdayR
remotes::install_github("thebioengineer/tidytuesdayR")
tt_data <- tidytuesdayR::tt_load("2019-01-22")
prison_raw2 <- tt_data$prison_population
stopifnot(identical(prison_raw, prison_raw2))
# Loading useful packages
library(tidyverse)
library(gganimate)
library(maps)
library(knitr)
library(kableExtra)
# Loading data from GitHub
raw_data <- read_csv("https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2019/2019-01-22/prison_population.csv")
map_data("county") %>%
tbl_df() %>%
ggplot(aes(x = long, y = lat, group = group)) +
geom_polygon() +
coord_map()
pdf("test_map.pdf")
map_data("county") %>%
tbl_df() %>%
ggplot(aes(x = long, y = lat, group = group)) +
geom_polygon() +
coord_map()
dev.off()
state_missing_data <- raw_data %>%
filter(pop_category == "Total") %>%
group_by(year, state) %>%
summarise(missing_data = round(100*mean(is.na(prison_population)), 2)) %>%
ungroup()
anim <- state_missing_data %>%
mutate(region = str_to_lower(state.name[match(state, state.abb)])) %>% # Cool trick!
right_join(map_data("state"), by = "region") %>%
ggplot(aes(x = long, y = lat, group = group, fill = missing_data)) +
geom_polygon() +
ggthemes::theme_map() +
coord_map() +
scale_fill_viridis_c(guide = guide_legend(title = "Percent")) +
transition_manual(year) +
labs(title = "Percentage of counties with missing data (per state)",
subtitle = "Year: {current_frame}") +
theme(legend.position = "right",
plot.title = element_text(hjust = 0.5, face = "bold"),
plot.subtitle = element_text(hjust = 0.5))
anim_save(
"test.mp4",
anim,
renderer = ffmpeg_renderer(format = ".mp4"),
fps = 10
)
library("sessioninfo")
options(width = 120)
session_info()
####################### WINDOWS LAPTOP
# - Session info -------------------------------------------------------------------------------------------------------
# setting value
# version R version 4.0.0 (2020-04-24)
# os Windows 10 x64
# system x86_64, mingw32
# ui RStudio
# language (EN)
# collate English_United States.1252
# ctype English_United States.1252
# tz America/New_York
# date 2020-06-26
#
# - Packages -----------------------------------------------------------------------------------------------------------
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
# backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)
# blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
# broom 0.5.6 2020-04-20 [1] CRAN (R 4.0.0)
# cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
# cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
# colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
# curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
# DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
# dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.0)
# digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
# dplyr * 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
# ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
# evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
# farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
# forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
# fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
# generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
# gganimate * 1.0.5 2020-02-09 [1] CRAN (R 4.0.0)
# ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
# ggthemes 4.2.0 2019-05-13 [1] CRAN (R 4.0.0)
# glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
# gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
# haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.0)
# highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
# hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
# htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.0)
# httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
# jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0)
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# knitr * 1.29 2020-06-23 [1] CRAN (R 4.0.0)
# labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
# lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
# lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
# lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2)
# magick 2.4.0 2020-06-23 [1] CRAN (R 4.0.0)
# magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
# mapproj 1.2.7 2020-02-03 [1] CRAN (R 4.0.0)
# maps * 3.3.0 2018-04-03 [1] CRAN (R 4.0.0)
# modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.0)
# munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
# nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.0)
# pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
# plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
# progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0)
# purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
# R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
# Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
# readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
# readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
# remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
# reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.0)
# rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
# rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.0)
# rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
# rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0)
# scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
# stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
# stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
# tibble * 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
# tidyr * 1.1.0 2020-05-20 [1] CRAN (R 4.0.0)
# tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
# tidytuesdayR 1.0.0 2020-06-26 [1] Github (thebioengineer/tidytuesdayR@e04ebea)
# tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2)
# tweenr 1.0.1 2018-12-14 [1] CRAN (R 4.0.0)
# utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)
# vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.2)
# viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
# webshot 0.5.2 2019-11-22 [1] CRAN (R 4.0.0)
# withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
# xfun 0.15 2020-06-21 [1] CRAN (R 4.0.2)
# xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0)
#
# [1] D:/R/R-4.0.0/library
#### macOS laptop
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.0.0 (2020-04-24)
# os macOS Catalina 10.15.4
# system x86_64, darwin17.0
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/New_York
# date 2020-06-26
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# ! package * version date lib source
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
# available 1.0.4 2019-07-19 [1] CRAN (R 4.0.0)
# backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
# Biobase 2.48.0 2020-04-27 [1] Bioconductor
# BiocFileCache 1.12.0 2020-04-27 [1] Bioconductor
# BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
# BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
# BiocParallel 1.22.0 2020-04-27 [1] Bioconductor
# biocthis 0.99.0 2020-05-27 [1] Github (lcolladotor/biocthis@3b96da1)
# Biostrings 2.56.0 2020-04-27 [1] Bioconductor
# bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
# bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
# bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
# blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
# broom 0.5.6 2020-04-20 [1] CRAN (R 4.0.0)
# callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
# cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
# cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
# colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681)
# colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
# curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
# data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
# DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
# dbplyr 1.4.3 2020-04-19 [1] CRAN (R 4.0.0)
# DelayedArray 0.14.0 2020-04-27 [1] Bioconductor
# desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
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# digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
# dplyr * 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
# V ellipsis 0.3.0 2020-05-15 [1] CRAN (R 4.0.0)
# evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
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# forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
# fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
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# GenomeInfoDbData 1.2.3 2020-04-16 [1] Bioconductor
# GenomicAlignments 1.24.0 2020-04-27 [1] Bioconductor
# GenomicRanges 1.40.0 2020-04-27 [1] Bioconductor
# gganimate * 1.0.5 2020-02-09 [1] CRAN (R 4.0.0)
# ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
# ggthemes 4.2.0 2019-05-13 [1] CRAN (R 4.0.0)
# V glue 1.4.0 2020-05-13 [1] CRAN (R 4.0.0)
# gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
# haven 2.2.0 2019-11-08 [1] CRAN (R 4.0.0)
# hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
# htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
# httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
# IRanges 2.22.1 2020-04-28 [1] Bioconductor
# V jsonlite 1.6.1 2020-06-25 [1] CRAN (R 4.0.0)
# kableExtra * 1.1.0 2019-03-16 [1] CRAN (R 4.0.0)
# knitr * 1.29 2020-06-23 [1] CRAN (R 4.0.0)
# labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
# lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
# lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
# lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.0)
# magick 2.3 2020-01-24 [1] CRAN (R 4.0.0)
# magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
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# maps * 3.3.0 2018-04-03 [1] CRAN (R 4.0.0)
# MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.0)
# Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
# matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
# memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
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# pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
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# purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
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# rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.0.0)
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# rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0)
# S4Vectors 0.26.0 2020-04-27 [1] Bioconductor
# scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
# selectr 0.4-2 2019-11-20 [1] CRAN (R 4.0.0)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
# stringdist 0.9.5.5 2019-10-21 [1] CRAN (R 4.0.0)
# stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
# stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
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# SummarizedExperiment 1.18.1 2020-04-30 [1] Bioconductor
# testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
# tibble * 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
# tidyr * 1.0.3 2020-05-07 [1] CRAN (R 4.0.0)
# tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
# tidytuesdayR 1.0.0 2020-06-26 [1] Github (thebioengineer/tidytuesdayR@e04ebea)
# tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
# tweenr 1.0.1 2018-12-14 [1] CRAN (R 4.0.0)
# usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
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# zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
#
# [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
#
# V ── Loaded and on-disk version mismatch.
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