BGC-Argo pH Data
Pasqualina Vonlanthen & Jens Daniel Müller
11 May, 2022
Last updated: 2022-05-11
Checks: 7 0
Knit directory: bgc_argo_r_argodata/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 6a6e874 | pasqualina-vonlanthendinenna | 2022-04-29 | Build site. |
| html | 2d44f8a | pasqualina-vonlanthendinenna | 2022-04-29 | Build site. |
| html | e61c08e | pasqualina-vonlanthendinenna | 2022-04-27 | Build site. |
| Rmd | 9664e0e | pasqualina-vonlanthendinenna | 2022-04-27 | added temp data page, changed double extremes |
| html | 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 | Build site. |
| Rmd | 3e1ac14 | pasqualina-vonlanthendinenna | 2022-04-26 | separated loading data pages, added mayot biomes, switched to pH and temp flag A |
| html | c03dd24 | pasqualina-vonlanthendinenna | 2022-04-20 | Build site. |
| html | 8805f99 | pasqualina-vonlanthendinenna | 2022-04-11 | Build site. |
| html | 905d82f | pasqualina-vonlanthendinenna | 2022-02-15 | Build site. |
| html | b8a6482 | pasqualina-vonlanthendinenna | 2022-01-03 | Build site. |
| html | 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 | Build site. |
| Rmd | c4cce1a | pasqualina-vonlanthendinenna | 2021-12-17 | updated cache data |
| html | 123e5db | pasqualina-vonlanthendinenna | 2021-12-07 | Build site. |
| Rmd | f8abe59 | pasqualina-vonlanthendinenna | 2021-12-07 | suppressed output messages and updated plots |
| html | 6a5024e | pasqualina-vonlanthendinenna | 2021-12-02 | Build site. |
| Rmd | 65e4748 | pasqualina-vonlanthendinenna | 2021-12-02 | updated offsets between Argo and OceanSODA |
| html | 3dc093a | pasqualina-vonlanthendinenna | 2021-11-30 | Build site. |
| Rmd | 4b89d69 | pasqualina-vonlanthendinenna | 2021-11-30 | added Argo plots to OceanSODA page |
| html | 930ea26 | pasqualina-vonlanthendinenna | 2021-11-26 | Build site. |
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| html | 5e2b8a5 | pasqualina-vonlanthendinenna | 2021-11-26 | Build site. |
| html | 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 | Build site. |
| Rmd | 9b5df99 | pasqualina-vonlanthendinenna | 2021-11-26 | added oceanSODA page |
| Rmd | f43074c | pasqualina-vonlanthendinenna | 2021-11-23 | switched reccap biomes to loading data |
| html | d3f9eb5 | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | b1706c9 | pasqualina-vonlanthendinenna | 2021-11-22 | updated timeseries plots |
| html | 105630e | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | 82f09d0 | pasqualina-vonlanthendinenna | 2021-11-22 | separated Southern Ocean regions |
| html | e96cc7f | pasqualina-vonlanthendinenna | 2021-11-22 | Build site. |
| Rmd | 2c5f2e5 | pasqualina-vonlanthendinenna | 2021-11-22 | corrected offset plot |
| Rmd | fb2fb74 | pasqualina-vonlanthendinenna | 2021-11-19 | corrected offset plot |
| html | 13df4f5 | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | fd6ef5a | pasqualina-vonlanthendinenna | 2021-11-19 | changed offset plot |
| html | 578ae8c | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | ae64132 | pasqualina-vonlanthendinenna | 2021-11-19 | added offset pH plot |
| html | ab70649 | pasqualina-vonlanthendinenna | 2021-11-19 | Build site. |
| Rmd | 171aa37 | pasqualina-vonlanthendinenna | 2021-11-19 | updated loading pH data and color palettes |
| Rmd | c696726 | pasqualina-vonlanthendinenna | 2021-11-17 | updated loading pH data and color palettes |
| html | 9824928 | pasqualina-vonlanthendinenna | 2021-11-16 | Build site. |
| Rmd | 383aa57 | pasqualina-vonlanthendinenna | 2021-11-16 | updated |
| html | b6a26a1 | pasqualina-vonlanthendinenna | 2021-11-16 | Build site. |
| Rmd | b473f72 | pasqualina-vonlanthendinenna | 2021-11-16 | added ggOceanMap for pH |
| html | 0dce554 | pasqualina-vonlanthendinenna | 2021-11-15 | Build site. |
| Rmd | 2c20367 | pasqualina-vonlanthendinenna | 2021-11-15 | added ggOceanMap for pH |
| html | 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 | Build site. |
| Rmd | 59073c1 | pasqualina-vonlanthendinenna | 2021-11-12 | added NE Pacific oxygen |
| html | 273ed2c | pasqualina-vonlanthendinenna | 2021-11-12 | Build site. |
| Rmd | 06b6be7 | pasqualina-vonlanthendinenna | 2021-11-12 | added NE Pacific oxygen |
| html | 284003d | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| Rmd | f7807db | pasqualina-vonlanthendinenna | 2021-11-11 | added oxygen data page |
| html | 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 | Build site. |
| Rmd | 8baed53 | pasqualina-vonlanthendinenna | 2021-11-11 | added pH data page |
Task
Explore BGC-Argo pH data through timeseries and monthly climatological maps
path_argo <- '/nfs/kryo/work/updata/bgc_argo_r_argodata'
path_emlr_utilities <- "/nfs/kryo/work/jenmueller/emlr_cant/utilities/files/"
path_basin_mask <- "/nfs/kryo/work/updata/reccap2/"
path_argo_preprocessed <- paste0(path_argo, "/preprocessed_bgc_data")Load pH data
Load in delayed-mode adjusted pH data from the data files created in Loading Data
# keep only pH data and associated CTD variables
# load in surface pH data
# ph_surface_2x2 <- read_rds(file = paste0(path_argo_preprocessed, '/ph_surface_2x2.rds'))
#
# ph_surface_1x1 <- read_rds(file = paste0(path_argo_preprocessed, "/ph_surface_1x1.rds"))
ph_surface <- read_rds(file = paste0(path_argo_preprocessed, "/bgc_merge_flag_A.rds")) %>%
filter(between(depth, 0, 20)) %>%
mutate(year = year(date),
month = month(date))
# region_masks_all_seamask_2x2 <- read_rds(file = paste0(
# path_argo_preprocessed, "/region_masks_all_seamask_2x2.rds"))
#
# region_masks_all_2x2 <- read_rds(file = paste0(path_argo_preprocessed, "/region_masks_all_2x2.rds"))
nm_biomes <- read_rds(file = paste0(path_argo_preprocessed, "/nm_biomes.rds"))Southern Ocean surface pH
The focus here is on surface pH (in the top 20 m of the watercolumn), in the region south of 30ºS
ph_surface_SO <- ph_surface %>%
filter(lat <= - 30)
# check the correct latitudes, QC flags, and depth levels have been filtered
#max(ph_surface_SO$lat)
#min(ph_surface_SO$lat)
# table(ph_surface_SO$ph_in_situ_total_adjusted_qc)
# max(ph_surface_SO$depth)
# min(ph_surface_SO$date)
# max(ph_surface_SO$date)pH offset with depth
Plot the difference between in-situ observed pH and the profile-mean surface pH for the upper 20 m. This difference represents the variability of the surface pH values with respect to the mean surface pH of the upper 20 m.
# calculate the mean pH for each surface profile
mean_profile_ph <- ph_surface_SO %>%
group_by(platform_number, cycle_number) %>%
mutate(mean_prof_ph = mean(ph_in_situ_total_adjusted, na.rm = TRUE),
.before = depth) %>%
ungroup() %>%
mutate(offset = ph_in_situ_total_adjusted-mean_prof_ph,
.after = mean_prof_ph) # subtract the mean profile pH from the measured in situ pH
mean_profile_ph %>%
ggplot()+
geom_point(aes(x = offset, y = depth, col = as.character(year)), size = 0.3, pch = 19) +
scale_y_reverse()+
geom_vline(xintercept = 0, col = 'red', size = 0.6)+
labs(x = 'offset (pH units)',
y = 'depth (m)',
col = 'year',
title = 'in situ pH - mean profile pH')
| Version | Author | Date |
|---|---|---|
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 105630e | pasqualina-vonlanthendinenna | 2021-11-22 |
| e96cc7f | pasqualina-vonlanthendinenna | 2021-11-22 |
| 13df4f5 | pasqualina-vonlanthendinenna | 2021-11-19 |
| 578ae8c | pasqualina-vonlanthendinenna | 2021-11-19 |
Bin the pH data into 2m-depth intervals and calculate the offset for each pH observation in each depth interval relative to the profile-mean pH
# bin the ph values into 2m bins and calculate the offset for each 2m bin
mean_profile_ph_binned <- ph_surface_SO %>%
mutate(depth = cut(depth, seq(0, 20, 2), seq(1, 19, 2)),
depth = as.numeric(as.character(depth))) %>%
group_by(platform_number, cycle_number) %>%
mutate(mean_prof_ph = mean(ph_in_situ_total_adjusted, na.rm = TRUE),
.before = depth) %>%
ungroup() %>%
mutate(offset = ph_in_situ_total_adjusted-mean_prof_ph,
.after = mean_prof_ph)
# plot the offset of the depth-binned values
mean_profile_ph_binned %>%
ggplot()+
geom_point(aes(x = offset, y = depth, col = as.character(year)), size = 0.3, pch = 19) +
scale_y_reverse()+
geom_vline(xintercept = 0, col = 'red', size = 0.6)+
labs(x = 'offset (pH units)',
y = 'depth (m)',
col = 'year',
title = 'in situ pH - mean profile pH (2m depth bins)')
Mean offset for each 2m depth bin
# bin the ph values into 2m bins and calculate the offset for each 2m bin
profile_ph_binned_ave <- ph_surface_SO %>%
mutate(depth = cut(depth, seq(0, 20, 2), seq(1, 19, 2)),
depth = as.numeric(as.character(depth))) %>%
group_by(platform_number, cycle_number) %>%
mutate(mean_prof_ph = mean(ph_in_situ_total_adjusted, na.rm = TRUE),
.before = depth) %>%
ungroup() %>%
mutate(offset = ph_in_situ_total_adjusted-mean_prof_ph,
.after = mean_prof_ph) %>%
group_by(depth) %>%
summarise(mean_offset = mean(offset))
# plot the offset of the depth-binned values
profile_ph_binned_ave %>%
ggplot()+
geom_point(aes(x = mean_offset, y = depth), size = 1, pch = 19) +
geom_line(aes(x = mean_offset, y = depth))+
scale_y_reverse()+
geom_vline(xintercept = 0, col = 'red', size = 1)+
labs(x = 'mean offset (pH units)',
y = 'depth (m)',
col = 'year',
title = 'in situ pH - mean profile pH (2m depth bins)')
Monthly climatological map
Create a climatological monthly map of surface pH, in a 2x2º longitude/latitude grid, for the region south of 30ºS (monthly pH averaged over April 2014-December 2021)
# average pH values in the top 20 m for each month in each 2 x 2º longitude/latitude grid
ph_clim_SO <- ph_surface_SO %>%
group_by(lat, lon, month) %>%
summarise(ph_clim_month = mean(ph_in_situ_total_adjusted))
# read in the map from updata
map <-
read_rds(paste(path_emlr_utilities,
"map_landmask_WOA18.rds",
sep = ""))
# map a monthly climatology of pH (April 2014 - December 2021)
map +
geom_tile(data = ph_clim_SO,
aes(lon, lat, fill = ph_clim_month)) +
lims(y = c(-85, -25)) +
scale_fill_viridis_c() +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly climatological \nArgo pH (Apr 2014 - Dec 2021)') +
theme(legend.position = 'right') +
facet_wrap(~month, ncol = 2)
| Version | Author | Date |
|---|---|---|
| e61c08e | pasqualina-vonlanthendinenna | 2022-04-27 |
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
| 8805f99 | pasqualina-vonlanthendinenna | 2022-04-11 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 3dc093a | pasqualina-vonlanthendinenna | 2021-11-30 |
| 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 |
| 105630e | pasqualina-vonlanthendinenna | 2021-11-22 |
| e96cc7f | pasqualina-vonlanthendinenna | 2021-11-22 |
| ab70649 | pasqualina-vonlanthendinenna | 2021-11-19 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
basemap(limits = -32, data = ph_clim_SO) + # change to polar projection
geom_spatial_tile(data = ph_clim_SO,
aes(x = lon,
y = lat,
fill = ph_clim_month),
linejoin = 'mitre',
col = 'transparent',
detail = 60)+
scale_fill_viridis_c()+
theme(legend.position = 'bottom')+
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'monthly climatological \nArgo pH (Apr 2014 - Dec 2021)')+
facet_wrap(~month, ncol = 2)Monthly timeseries
Timeseries of monthly mean pH values, over the three different Southern Ocean regions (separated based on Mayot biomes):
# plot the region separations on a map
map +
geom_raster(data = nm_biomes,
aes(x = lon,
y = lat,
fill = biome_name)) +
labs(title = 'Southern Ocean Mayot biomes',
fill = 'biome')
# plot a timeseries of monthly values over the whole southern ocean south of 30ºS
ph_surface_SO <- inner_join(ph_surface_SO, nm_biomes)
ph_month_SO <- ph_surface_SO %>%
group_by(year, month, biome_name) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))
# timeseries of monthly pH values over 2014-2021 (separate panels for each month)
ph_month_SO %>%
ggplot(aes(x = year,
y = ph_ave,
group = biome_name,
col = biome_name)) +
facet_wrap(~month) +
geom_line() +
geom_point() +
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'monthly mean Argo pH (Apr 2014-Dec 2021, Southern Ocean)',
col = 'region')
| Version | Author | Date |
|---|---|---|
| e61c08e | pasqualina-vonlanthendinenna | 2022-04-27 |
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 |
| 105630e | pasqualina-vonlanthendinenna | 2021-11-22 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 284003d | pasqualina-vonlanthendinenna | 2021-11-11 |
#all months on one plot in different colors (not very nice plot)
# ph_month_SO %>%
# ggplot(aes(x = year, y = ph_ave, group = month, col = as.character(month))) +
# geom_line() +
# geom_point() +
# labs(x = 'year', y = 'pH in situ (total scale)', title = 'monthly mean pH (Apr 2014-Aug 2021)')Plot the monthly average pH, per year (from Jan 2015 - Dec 2020), for each Southern Ocean RECCAP region (1, 2, 3)
# timeseries of monthly pH values for each year (separate years on the same plot)
ph_month_SO %>%
# filter(year != 2014) %>% # remove the year that is missing data
ggplot(aes(x = month,
y = ph_ave,
group = year,
col = as.character(year)))+
geom_line()+
geom_point()+
scale_x_continuous(breaks = seq(1, 12, 2))+
facet_wrap(~biome_name)+
labs(x = 'month',
y = 'pH in situ (total scale)',
title = 'monthly mean Argo pH (Jan 2015-Dec 2021, Southern Ocean regions)',
col = 'year')
| Version | Author | Date |
|---|---|---|
| e61c08e | pasqualina-vonlanthendinenna | 2022-04-27 |
| 10036ed | pasqualina-vonlanthendinenna | 2022-04-26 |
| 7f3cfe7 | pasqualina-vonlanthendinenna | 2021-12-17 |
| 3df4daf | pasqualina-vonlanthendinenna | 2021-11-26 |
| 105630e | pasqualina-vonlanthendinenna | 2021-11-22 |
| 7a01367 | pasqualina-vonlanthendinenna | 2021-11-12 |
| 6276d6c | pasqualina-vonlanthendinenna | 2021-11-11 |
# calculate a yearly average ph (one ph value per year, for the whole domain)
ph_year_SO <- ph_surface_SO %>%
group_by(year, biome_name) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))
# plot a timeseries of the yearly average pH value (one value per year)
ph_year_SO %>%
ggplot(aes(x = year, y = ph_ave, group = biome_name, col = biome_name))+
geom_line()+
geom_point()+
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'yearly mean Argo pH (Apr 2014-Aug 2021, south of 30ºS)',
col = 'region')Northeast Pacific surface pH
Focus on surface pH in the northeast Pacific Ocean (10ºN - 70ºN, -190ºE - -140ºE)
# select only pH databetween 10 and 70ºN, and 190 and 140ºW, for the top 20 m of the watercolumn
ph_nepacific <- ph_surface %>%
filter(between(lat, 10, 70),
between(lon, 190, 240))
# longitudes larger than -180ºE are lon-380Monthly climatological map
Create a map of climatological monthly surface pH values, in the north-west Pacific ocean (10ºN - 70ºN, -190ºE, -140ºE), for
# average pH values in the top 20 m for each month in each 2 x 2º longitude/latitude grid
ph_mean_nepacific <- ph_nepacific %>%
group_by(lat, lon, month) %>%
summarise(ph_ave_month = mean(ph_in_situ_total_adjusted))
# map a monthly climatology of surface pH (Jan 2013 - August 2021)
map +
geom_tile(data = ph_mean_nepacific,
aes(lon, lat, fill = ph_ave_month)) +
lims(y = c(5, 60),
x = c(180, 250)) +
scale_fill_viridis_c() +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly average pH (Jan 2013-Aug 2021)') +
theme(legend.position = 'right')+
facet_wrap(~month)# using the ggOceanMaps package
basemap(limits = c(-180, -110, 7, 60), data = ph_mean_nepacific) +
geom_spatial_tile(data = ph_mean_nepacific,
aes(x = lon,
y = lat,
fill = ph_ave_month))+
scale_fill_viridis_c()+
facet_wrap(~month) +
labs(x = 'lon',
y = 'lat',
fill = 'pH',
title = 'Monthly average pH (Jan 2013-Aug 2021)')
# haven't figured out why the data isn't being plotted Monthly timeseries
Timeseries of monthly mean pH, averaged over the whole NE-Pacific region (10ºN - 70ºN, -190ºE - -140ºE), in the upper 20 m of the watercolumn.
# plot a timeseries of monthly values over the whole southern ocean south of 30ºS
ph_month_nepacific <- ph_nepacific %>%
group_by(year, month) %>%
summarise(ph_ave = mean(ph_in_situ_total_adjusted))
# timeseries of monthly pH values over 2014-2021 (separate panels for each month)
ph_month_nepacific %>%
ggplot(aes(x = year, y = ph_ave)) +
facet_wrap(~month) +
scale_x_continuous(breaks = seq(2013, 2021, 2)) +
geom_line() +
geom_point() +
labs(x = 'year',
y = 'pH in situ (total scale)',
title = 'monthly mean pH (Jan 2013-Aug 2021, NE Pacific)')Monthly average pH, per year, over the NE Pacific region
# timeseries of monthly pH values for each year (separate years on the same plot)
ph_month_nepacific %>%
ggplot(aes(x = month, y = ph_ave, group = year, col = as.character(year)))+
geom_line()+
geom_point()+
scale_x_continuous(breaks = seq(1, 12, 1))+
labs(x = 'month',
y = 'pH in situ (total scale)',
title = 'monthly mean pH (Jan 2013-Dec 2020, NE Pacific)',
col = 'year')
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3
Matrix products: default
BLAS: /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggOceanMaps_1.2.6 ggspatial_1.1.5 oce_1.5-0 gsw_1.0-6
[5] lubridate_1.8.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[9] purrr_0.3.4 readr_2.1.1 tidyr_1.1.4 tibble_3.1.6
[13] ggplot2_3.3.5 tidyverse_1.3.1 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] fs_1.5.2 sf_1.0-5 httr_1.4.2 rprojroot_2.0.2
[5] tools_4.1.2 backports_1.4.1 bslib_0.3.1 rgdal_1.5-28
[9] utf8_1.2.2 R6_2.5.1 KernSmooth_2.23-20 rgeos_0.5-9
[13] DBI_1.1.2 colorspace_2.0-2 raster_3.5-11 withr_2.4.3
[17] sp_1.4-6 tidyselect_1.1.1 processx_3.5.2 compiler_4.1.2
[21] git2r_0.29.0 cli_3.1.1 rvest_1.0.2 xml2_1.3.3
[25] labeling_0.4.2 sass_0.4.0 scales_1.1.1 classInt_0.4-3
[29] callr_3.7.0 proxy_0.4-26 digest_0.6.29 rmarkdown_2.11
[33] pkgconfig_2.0.3 htmltools_0.5.2 highr_0.9 dbplyr_2.1.1
[37] fastmap_1.1.0 rlang_1.0.2 readxl_1.3.1 rstudioapi_0.13
[41] farver_2.1.0 jquerylib_0.1.4 generics_0.1.1 jsonlite_1.7.3
[45] magrittr_2.0.1 Rcpp_1.0.8 munsell_0.5.0 fansi_1.0.2
[49] lifecycle_1.0.1 terra_1.5-12 stringi_1.7.6 whisker_0.4
[53] yaml_2.2.1 grid_4.1.2 parallel_4.1.2 promises_1.2.0.1
[57] crayon_1.4.2 lattice_0.20-45 haven_2.4.3 hms_1.1.1
[61] knitr_1.37 ps_1.6.0 pillar_1.6.4 codetools_0.2-18
[65] reprex_2.0.1 glue_1.6.0 evaluate_0.14 getPass_0.2-2
[69] modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0 httpuv_1.6.5
[73] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.29
[77] broom_0.7.11 e1071_1.7-9 later_1.3.0 viridisLite_0.4.0
[81] class_7.3-20 units_0.7-2 ellipsis_0.3.2