DRS_parameter_percentage.R
shuheimitsutomi
2024-07-29
suppressPackageStartupMessages(library(tidyverse))
devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')## ℹ Loading myUtilitieslibrary(ggupset)## Warning: package 'ggupset' was built under R version 4.3.3Settings
wd <- "~/Google Drive/My Drive/Analysis/METTL2A/"
setwd(wd)
figdir <- paste0(wd, 'Figures/DRS_m3C_sites/Parameters/')
tabledir <- paste0(wd, 'Tables/DRS/Positions/')
theme_set(
theme_classic(base_size = 7) +
theme(legend.position = 'bottom')
)Functions
add_yrange <- function(df) {
new_df <- df |>
mutate(ymax = cumsum(percentage / 100))
new_df$ymin <- c(0, head(new_df$ymax, n = -1))
return(new_df)
}
donutplot <- function(df, var, col) {
df |>
add_yrange() |>
ggplot(aes(
xmin = 2, xmax = 4, ymin = ymin, ymax = ymax,
fill = {{ col }}, colour = {{ col }}
)) +
geom_rect() +
coord_polar(theta = 'y') +
ggrepel::geom_text_repel(
aes(label = {{ var }}, y = (ymin + ymax) / 2), x = 1
) +
xlim(c(-1,4)) +
theme_void()
}Read data
sampcomp_results <-
read_tsv(
paste0(
wd,
'Tables/DRS/Positions/sampcomp_results_joined_2024-04-09.tsv.gz'
)
)## Rows: 5884004 Columns: 67
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (34): transcript_id, transcript_name, ref_kmer, GMM_cov_type_G, cluster_...
## dbl (33): position, GMM_logit_pvalue_G, KS_dwell_pvalue_G, KS_intensity_pval...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.sampcomp_results## # A tibble: 5,884,004 × 67
## transcript_id transcript_name position ref_kmer GMM_logit_pvalue_G
## <chr> <chr> <dbl> <chr> <dbl>
## 1 ENST00000264926.7 RAD18-201 1464 TCACA NA
## 2 ENST00000264926.7 RAD18-201 1465 CACAT 1
## 3 ENST00000264926.7 RAD18-201 1466 ACATA NA
## 4 ENST00000264926.7 RAD18-201 1467 CATAA 1
## 5 ENST00000264926.7 RAD18-201 1468 ATAAA NA
## 6 ENST00000264926.7 RAD18-201 1473 AACGA 1
## 7 ENST00000264926.7 RAD18-201 1475 CGATC NA
## 8 ENST00000264926.7 RAD18-201 1486 ACACA NA
## 9 ENST00000264926.7 RAD18-201 1501 CAAGA 1
## 10 ENST00000264926.7 RAD18-201 1502 AAGAC NA
## # ℹ 5,883,994 more rows
## # ℹ 62 more variables: KS_dwell_pvalue_G <dbl>, KS_intensity_pvalue_G <dbl>,
## # GMM_cov_type_G <chr>, GMM_n_clust_G <dbl>, cluster_counts_G <chr>,
## # Logit_LOR_G <chr>, c1_mean_intensity_G <dbl>, c2_mean_intensity_G <dbl>,
## # c1_median_intensity_G <dbl>, c2_median_intensity_G <dbl>,
## # c1_sd_intensity_G <dbl>, c2_sd_intensity_G <dbl>, c1_mean_dwell_G <dbl>,
## # c2_mean_dwell_G <dbl>, c1_median_dwell_G <dbl>, c2_median_dwell_G <dbl>, …sampcomp_results |> colnames()## [1] "transcript_id" "transcript_name" "position"
## [4] "ref_kmer" "GMM_logit_pvalue_G" "KS_dwell_pvalue_G"
## [7] "KS_intensity_pvalue_G" "GMM_cov_type_G" "GMM_n_clust_G"
## [10] "cluster_counts_G" "Logit_LOR_G" "c1_mean_intensity_G"
## [13] "c2_mean_intensity_G" "c1_median_intensity_G" "c2_median_intensity_G"
## [16] "c1_sd_intensity_G" "c2_sd_intensity_G" "c1_mean_dwell_G"
## [19] "c2_mean_dwell_G" "c1_median_dwell_G" "c2_median_dwell_G"
## [22] "c1_sd_dwell_G" "c2_sd_dwell_G" "intensity_up_G"
## [25] "intensity_down_G" "dwell_up_G" "dwell_down_G"
## [28] "GMM_change_G" "GMM_logit_pvalue_I" "KS_dwell_pvalue_I"
## [31] "KS_intensity_pvalue_I" "GMM_cov_type_I" "GMM_n_clust_I"
## [34] "cluster_counts_I" "Logit_LOR_I" "c1_mean_intensity_I"
## [37] "c2_mean_intensity_I" "c1_median_intensity_I" "c2_median_intensity_I"
## [40] "c1_sd_intensity_I" "c2_sd_intensity_I" "c1_mean_dwell_I"
## [43] "c2_mean_dwell_I" "c1_median_dwell_I" "c2_median_dwell_I"
## [46] "c1_sd_dwell_I" "c2_sd_dwell_I" "intensity_up_I"
## [49] "intensity_down_I" "dwell_up_I" "dwell_down_I"
## [52] "GMM_change_I" "intensity_up" "intensity_down"
## [55] "dwell_up" "dwell_down" "GMM_change"
## [58] "middle_base" "middle_isC" "have_CC_middle"
## [61] "have_C3_middle" "middleC_info" "transcript_type"
## [64] "gene_id" "gene_type" "gene_name"
## [67] "seqname"sampcomp_sig_positions <-
sampcomp_results |>
select(
transcript_id, transcript_name, position, ref_kmer, middle_isC,
intensity_up, intensity_down, dwell_up, dwell_down, GMM_change
) |>
pivot_longer(
cols = c(intensity_up:GMM_change),
names_to = 'parameter', values_to = 'significant'
) |>
filter(significant == 'common')
sampcomp_sig_positions## # A tibble: 671 × 7
## transcript_id transcript_name position ref_kmer middle_isC parameter
## <chr> <chr> <dbl> <chr> <chr> <chr>
## 1 ENST00000429711.7 RPL32-204 422 GCCCA C intensity_up
## 2 ENST00000647248.2 RPL35A-211 380 ACCCC C intensity_up
## 3 ENST00000647248.2 RPL35A-211 381 CCCCT C intensity_up
## 4 ENST00000389680.2 MT-RNR1-201 43 ACACA others intensity_up
## 5 ENST00000389680.2 MT-RNR1-201 57 CCCCG C intensity_up
## 6 ENST00000389680.2 MT-RNR1-201 71 GTTCA others intensity_up
## 7 ENST00000389680.2 MT-RNR1-201 73 TCACC others intensity_up
## 8 ENST00000389680.2 MT-RNR1-201 75 ACCCT C intensity_up
## 9 ENST00000389680.2 MT-RNR1-201 93 ATCAA C intensity_up
## 10 ENST00000389680.2 MT-RNR1-201 138 GCTTA others intensity_up
## # ℹ 661 more rows
## # ℹ 1 more variable: significant <chr>sampcomp_sig_positions |>
group_by(parameter) |>
reframe(n = n()) |>
mutate(percent = 100 * n / sum(n))## # A tibble: 5 × 3
## parameter n percent
## <chr> <int> <dbl>
## 1 GMM_change 32 4.77
## 2 dwell_down 7 1.04
## 3 dwell_up 6 0.894
## 4 intensity_down 21 3.13
## 5 intensity_up 605 90.2sampcomp_sig_positions |>
export_tsv(outdir = tabledir)##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/DRS/Positions/sampcomp_sig_positions_2024-07-29.tsv## # A tibble: 671 × 7
## transcript_id transcript_name position ref_kmer middle_isC parameter
## <chr> <chr> <dbl> <chr> <chr> <chr>
## 1 ENST00000429711.7 RPL32-204 422 GCCCA C intensity_up
## 2 ENST00000647248.2 RPL35A-211 380 ACCCC C intensity_up
## 3 ENST00000647248.2 RPL35A-211 381 CCCCT C intensity_up
## 4 ENST00000389680.2 MT-RNR1-201 43 ACACA others intensity_up
## 5 ENST00000389680.2 MT-RNR1-201 57 CCCCG C intensity_up
## 6 ENST00000389680.2 MT-RNR1-201 71 GTTCA others intensity_up
## 7 ENST00000389680.2 MT-RNR1-201 73 TCACC others intensity_up
## 8 ENST00000389680.2 MT-RNR1-201 75 ACCCT C intensity_up
## 9 ENST00000389680.2 MT-RNR1-201 93 ATCAA C intensity_up
## 10 ENST00000389680.2 MT-RNR1-201 138 GCTTA others intensity_up
## # ℹ 661 more rows
## # ℹ 1 more variable: significant <chr>sampcomp_sig_positions_summarised <-
sampcomp_sig_positions |>
group_by(transcript_id, position, transcript_name, ref_kmer, middle_isC) |>
summarise(parameters = list(parameter)) |>
ungroup()## `summarise()` has grouped output by 'transcript_id', 'position',
## 'transcript_name', 'ref_kmer'. You can override using the `.groups` argument.sampcomp_sig_positions_summarised## # A tibble: 644 × 6
## transcript_id position transcript_name ref_kmer middle_isC parameters
## <chr> <dbl> <chr> <chr> <chr> <list>
## 1 ENST00000009589.8 290 RPS20-201 GCCTA C <chr [1]>
## 2 ENST00000199764.7 1697 CEACAM6-201 TTCAG C <chr [1]>
## 3 ENST00000202773.14 326 RPL6-201 GTACC others <chr [1]>
## 4 ENST00000202773.14 328 RPL6-201 ACCCG C <chr [1]>
## 5 ENST00000202773.14 381 RPL6-201 GCCTC C <chr [1]>
## 6 ENST00000215754.8 78 MIF-201 GTCCT C <chr [1]>
## 7 ENST00000215754.8 179 MIF-201 GCCAC C <chr [1]>
## 8 ENST00000215754.8 190 MIF-201 GCCCC C <chr [1]>
## 9 ENST00000215754.8 483 MIF-201 ACCCG C <chr [1]>
## 10 ENST00000224237.9 1193 VIM-201 ACTTT others <chr [1]>
## # ℹ 634 more rowssampcomp_sig_positions_summarised |>
ggplot(aes(x = parameters)) +
geom_bar() +
geom_text(stat = 'count', aes(label = after_stat(count)), vjust = -1) +
ggupset::scale_x_upset(scale_name = 'parameter')
sampcomp_sig_positions_summarised |>
filter(parameters == 'intensity_up') |>
group_by(middle_isC) |>
reframe(n = n()) |>
mutate(percent = 100 * n / sum(n))## # A tibble: 2 × 3
## middle_isC n percent
## <chr> <int> <dbl>
## 1 C 481 81.9
## 2 others 106 18.1sampcomp_sig_positions_summarised2 <-
sampcomp_sig_positions_summarised |>
group_by(parameters) |>
reframe(n = n()) |>
ungroup()
sampcomp_sig_positions_summarised2 |>
export_tsv(outdir = tabledir)##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/DRS/Positions/sampcomp_sig_positions_summarised2_2024-07-29.tsv## # A tibble: 12 × 2
## parameters n
## <list> <int>
## 1 <chr [1]> 587
## 2 <chr [1]> 9
## 3 <chr [2]> 14
## 4 <chr [3]> 2
## 5 <chr [2]> 2
## 6 <chr [1]> 19
## 7 <chr [1]> 2
## 8 <chr [2]> 2
## 9 <chr [1]> 3
## 10 <chr [2]> 1
## 11 <chr [2]> 2
## 12 <chr [3]> 1sampcomp_sig_positions_summarised2$parameters <-
sapply(
sampcomp_sig_positions_summarised2$parameters,
function(x) paste(unlist(x), collapse = ',')
)
sampcomp_sig_positions_summarised2 |>
mutate(percent = 100 * n / sum(n)) |>
filter(!grepl('intensity_up', parameters)) |>
mutate(sum(n))## # A tibble: 7 × 4
## parameters n percent `sum(n)`
## <chr> <int> <dbl> <int>
## 1 GMM_change 9 1.40 39
## 2 dwell_up,GMM_change 2 0.311 39
## 3 intensity_down 19 2.95 39
## 4 dwell_up 2 0.311 39
## 5 dwell_down,GMM_change 2 0.311 39
## 6 dwell_down 3 0.466 39
## 7 intensity_down,GMM_change 2 0.311 39Plot
color_palette <- c('#04D2D9', '#64FFFF', '#AFB1B2')
sampcomp_sig_positions_parameter_donut <-
sampcomp_sig_positions_summarised2 |>
arrange(parameters |> fct_rev()) |>
mutate(
percentage = 100 * n / sum(n),
color = case_when(
'intensity_up' == parameters ~ color_palette[1],
grepl('intensity_up,', parameters) ~ color_palette[2],
.default = color_palette[3]
)
) |>
donutplot(parameters, color) +
scale_fill_manual(values = color_palette) +
scale_color_manual(values = color_palette)
sampcomp_sig_positions_parameter_donut |>
ggsave_multiple_formats(
width = 5, height = 5, fontsize = 7, outdir = figdir
)## Warning: ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
## ggrepel: 11 unlabeled data points (too many overlaps). Consider increasing max.overlaps
# sampcomp_sig_positions_summarised |>
# rowwise() |>
# mutate(
# include_intensityup = 'intensity_up' %in% parameters
# ) |>
# group_by(include_intensityup) |>
# reframe(n = n()) |>
# mutate(percent = 100 * n /sum(n))Sesison info
sessioninfo::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.3.1 (2023-06-16)
## os macOS Sonoma 14.5
## system aarch64, darwin20
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Asia/Tokyo
## date 2024-07-29
## pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
## backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0)
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
## broom 1.0.5 2023-06-09 [1] CRAN (R 4.3.0)
## bslib 0.5.1 2023-08-11 [1] CRAN (R 4.3.0)
## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
## car 3.1-2 2023-03-30 [1] CRAN (R 4.3.0)
## carData 3.0-5 2022-01-06 [1] CRAN (R 4.3.0)
## class 7.3-22 2023-05-03 [1] CRAN (R 4.3.1)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
## codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
## colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
## crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
## data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
## desc 1.4.2 2022-09-08 [1] CRAN (R 4.3.0)
## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
## dials 1.2.0 2023-04-03 [1] CRAN (R 4.3.0)
## DiceDesign 1.9 2021-02-13 [1] CRAN (R 4.3.0)
## digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
## dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
## evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0)
## fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
## farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
## forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.3.0)
## foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
## fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
## furrr 0.3.1 2022-08-15 [1] CRAN (R 4.3.0)
## future 1.33.0 2023-07-01 [1] CRAN (R 4.3.0)
## future.apply 1.11.0 2023-05-21 [1] CRAN (R 4.3.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
## ggforce 0.4.1 2022-10-04 [1] CRAN (R 4.3.0)
## ggplot2 * 3.4.3 2023-08-14 [1] CRAN (R 4.3.0)
## ggpubr 0.6.0 2023-02-10 [1] CRAN (R 4.3.0)
## ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.3.0)
## ggsignif 0.6.4 2022-10-13 [1] CRAN (R 4.3.0)
## ggupset * 0.4.0 2024-06-24 [1] CRAN (R 4.3.3)
## globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
## gower 1.0.1 2022-12-22 [1] CRAN (R 4.3.0)
## GPfit 1.0-8 2019-02-08 [1] CRAN (R 4.3.0)
## gprofiler2 0.2.3 2024-02-23 [1] CRAN (R 4.3.1)
## gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
## hardhat 1.3.0 2023-03-30 [1] CRAN (R 4.3.0)
## highr 0.10 2022-12-22 [1] CRAN (R 4.3.0)
## hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
## htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.0)
## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
## httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
## httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
## ipred 0.9-14 2023-03-09 [1] CRAN (R 4.3.0)
## iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
## jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.0)
## knitr 1.43 2023-05-25 [1] CRAN (R 4.3.0)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.3.0)
## later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
## lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.1)
## lava 1.7.2.1 2023-02-27 [1] CRAN (R 4.3.0)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
## lhs 1.1.6 2022-12-17 [1] CRAN (R 4.3.0)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
## listenv 0.9.0 2022-12-16 [1] CRAN (R 4.3.0)
## lubridate * 1.9.2 2023-02-10 [1] CRAN (R 4.3.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
## MASS 7.3-60 2023-05-04 [1] CRAN (R 4.3.1)
## Matrix 1.6-1 2023-08-14 [1] CRAN (R 4.3.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
## mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
## miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
## R myUtilities * 0.0.0.9000 <NA> [?] <NA>
## nnet 7.3-19 2023-05-03 [1] CRAN (R 4.3.1)
## parallelly 1.36.0 2023-05-26 [1] CRAN (R 4.3.0)
## parsnip 1.1.1 2023-08-17 [1] CRAN (R 4.3.0)
## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
## pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
## pkgload 1.3.2.1 2023-07-08 [1] CRAN (R 4.3.0)
## plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.1)
## polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.3.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
## processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0)
## prodlim 2023.08.28 2023-08-28 [1] CRAN (R 4.3.0)
## profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
## promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
## ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
## purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
## ragg 1.2.5 2023-01-12 [1] CRAN (R 4.3.0)
## Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
## readr * 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
## recipes 1.0.8 2023-08-25 [1] CRAN (R 4.3.0)
## remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
## rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
## rmarkdown 2.24 2023-08-14 [1] CRAN (R 4.3.0)
## rpart 4.1.19 2022-10-21 [1] CRAN (R 4.3.1)
## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.3.0)
## rsample 1.2.0 2023-08-23 [1] CRAN (R 4.3.0)
## rstatix 0.7.2 2023-02-01 [1] CRAN (R 4.3.0)
## rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
## sass 0.4.7 2023-07-15 [1] CRAN (R 4.3.0)
## scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
## shiny 1.7.5 2023-08-12 [1] CRAN (R 4.3.0)
## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
## stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
## survival 3.5-5 2023-03-12 [1] CRAN (R 4.3.1)
## svglite 2.1.1 2023-01-10 [1] CRAN (R 4.3.0)
## systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.3.0)
## textshaping 0.3.6 2021-10-13 [1] CRAN (R 4.3.0)
## tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
## tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
## tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.3.0)
## timechange 0.2.0 2023-01-11 [1] CRAN (R 4.3.0)
## timeDate 4022.108 2023-01-07 [1] CRAN (R 4.3.0)
## tune 1.1.2 2023-08-23 [1] CRAN (R 4.3.0)
## tweenr 2.0.2 2022-09-06 [1] CRAN (R 4.3.0)
## tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
## usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.0)
## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
## vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0)
## viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
## vroom 1.6.3 2023-04-28 [1] CRAN (R 4.3.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0)
## workflows 1.1.3 2023-02-22 [1] CRAN (R 4.3.0)
## xfun 0.40 2023-08-09 [1] CRAN (R 4.3.0)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
## yardstick 1.2.0 2023-04-21 [1] CRAN (R 4.3.0)
##
## [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
##
## R ── Package was removed from disk.
##
## ──────────────────────────────────────────────────────────────────────────────