Results publication
Jens Daniel Müller
21 January, 2022
Last updated: 2022-01-21
Checks: 7 0
Knit directory: emlr_obs_analysis/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2c3fa75 | jens-daniel-mueller | 2022-01-21 | cleaned alluvial plots |
| html | 1a35f1f | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | e58f510 | jens-daniel-mueller | 2022-01-20 | added relative changes to alluvial plots |
| html | b503ae1 | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | 2eb2567 | jens-daniel-mueller | 2022-01-20 | added relative changes to alluvial plots |
| html | cc31f4b | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | 416e107 | jens-daniel-mueller | 2022-01-20 | added delta dcant map |
| html | 11a800b | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | 81a40d5 | jens-daniel-mueller | 2022-01-20 | updated alluvial plots |
| html | 3087804 | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | 2ae5966 | jens-daniel-mueller | 2022-01-20 | updated alluvial plots |
| html | 6d566d5 | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | 4901b0f | jens-daniel-mueller | 2022-01-20 | updated alluvial plots |
| html | 44796b1 | jens-daniel-mueller | 2022-01-20 | Build site. |
| Rmd | cdbd92c | jens-daniel-mueller | 2022-01-20 | created alluvial plots |
| html | 48ec4c6 | jens-daniel-mueller | 2022-01-19 | Build site. |
| Rmd | 0fb2ae5 | jens-daniel-mueller | 2022-01-19 | printed column inv from AIP standard runs |
| html | f347cd7 | jens-daniel-mueller | 2022-01-18 | Build site. |
| Rmd | 86b711c | jens-daniel-mueller | 2022-01-18 | plot hemisphere budgets and publication results |
1 Read files
version_id_pattern <- "103"
# identify required version IDs
Version_IDs_1 <- list.files(path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
pattern = paste0("v_1", version_id_pattern))
Version_IDs_2 <- list.files(path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
pattern = paste0("v_2", version_id_pattern))
Version_IDs_3 <- list.files(path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
pattern = paste0("v_3", version_id_pattern))
Version_IDs <- c(Version_IDs_1, Version_IDs_2, Version_IDs_3)
print(Version_IDs)[1] "v_1103" "v_2103" "v_3103"for (i_Version_IDs in Version_IDs) {
# i_Version_IDs <- Version_IDs[1]
print(i_Version_IDs)
path_version_data <-
paste(path_observations,
i_Version_IDs,
"/data/",
sep = "")
# load and join data files
dcant_inv <-
read_csv(paste(path_version_data,
"dcant_inv.csv",
sep = ""))
dcant_inv_mod_truth <-
read_csv(paste(path_version_data,
"dcant_inv_mod_truth.csv",
sep = "")) %>%
filter(method == "total") %>%
select(-method)
dcant_inv_bias <-
read_csv(paste(path_version_data,
"dcant_inv_bias.csv",
sep = "")) %>%
mutate(Version_ID = i_Version_IDs)
dcant_inv <- bind_rows(dcant_inv,
dcant_inv_mod_truth) %>%
mutate(Version_ID = i_Version_IDs)
dcant_budget_lat_grid <-
read_csv(paste(path_version_data,
"dcant_budget_lat_grid.csv",
sep = "")) %>%
mutate(Version_ID = i_Version_IDs)
dcant_budget_lon_grid <-
read_csv(paste(path_version_data,
"dcant_budget_lon_grid.csv",
sep = "")) %>%
mutate(Version_ID = i_Version_IDs)
params_local <-
read_rds(paste(path_version_data,
"params_local.rds",
sep = ""))
params_local <- bind_cols(
Version_ID = i_Version_IDs,
# {{config}} := str_c(params_local${{config}}, collapse = "|"),
tref1 = params_local$tref1,
tref2 = params_local$tref2)
tref <- read_csv(paste(path_version_data,
"tref.csv",
sep = ""))
params_local <- params_local %>%
mutate(
median_year_1 = sort(tref$median_year)[1],
median_year_2 = sort(tref$median_year)[2],
duration = median_year_2 - median_year_1,
period = paste(median_year_1, "-", median_year_2)
)
if (exists("dcant_inv_all")) {
dcant_inv_all <- bind_rows(dcant_inv_all, dcant_inv)
}
if (!exists("dcant_inv_all")) {
dcant_inv_all <- dcant_inv
}
if (exists("dcant_inv_bias_all")) {
dcant_inv_bias_all <- bind_rows(dcant_inv_bias_all, dcant_inv_bias)
}
if (!exists("dcant_inv_bias_all")) {
dcant_inv_bias_all <- dcant_inv_bias
}
if (exists("dcant_budget_lat_grid_all")) {
dcant_budget_lat_grid_all <- bind_rows(dcant_budget_lat_grid_all, dcant_budget_lat_grid)
}
if (!exists("dcant_budget_lat_grid_all")) {
dcant_budget_lat_grid_all <- dcant_budget_lat_grid
}
if (exists("dcant_budget_lon_grid_all")) {
dcant_budget_lon_grid_all <- bind_rows(dcant_budget_lon_grid_all, dcant_budget_lon_grid)
}
if (!exists("dcant_budget_lon_grid_all")) {
dcant_budget_lon_grid_all <- dcant_budget_lon_grid
}
if (exists("params_local_all")) {
params_local_all <- bind_rows(params_local_all, params_local)
}
if (!exists("params_local_all")) {
params_local_all <- params_local
}
}[1] "v_1103"
[1] "v_2103"
[1] "v_3103"rm(dcant_inv,
dcant_inv_bias,
dcant_inv_mod_truth,
dcant_budget_lat_grid,
dcant_budget_lon_grid,
params_local,
tref)
# params_local_all <-
# params_local_all %>%
# mutate(period = factor(period, c("1994 - 2004", "2004 - 2014", "1994 - 2014")))dcant_inv_all <- dcant_inv_all %>%
filter(inv_depth == params_global$inventory_depth_standard)
dcant_budget_lat_grid_all <- dcant_budget_lat_grid_all %>%
filter(inv_depth == params_global$inventory_depth_standard)
dcant_budget_lon_grid_all <- dcant_budget_lon_grid_all %>%
filter(inv_depth == params_global$inventory_depth_standard)dcant_budget_lat_grid_all <- dcant_budget_lat_grid_all %>%
pivot_wider(names_from = estimate,
values_from = value) %>%
filter(period != "1994 - 2014",
method == "total")
dcant_budget_lon_grid_all <- dcant_budget_lon_grid_all %>%
pivot_wider(names_from = estimate,
values_from = value) %>%
filter(period != "1994 - 2014",
method == "total")# Version_IDs <- Version_IDs[1:length(Version_IDs)-1]
for (i_Version_IDs in Version_IDs) {
# i_Version_IDs <- Version_IDs[1]
print(i_Version_IDs)
path_version_data <-
paste(path_observations,
i_Version_IDs,
"/data/",
sep = "")
# load and join data files
dcant_budget_basin_MLR <-
read_csv(paste(path_version_data,
"dcant_budget_basin_MLR.csv",
sep = ""))
dcant_budget_basin_MLR_mod_truth <-
read_csv(paste(
path_version_data,
"dcant_budget_basin_MLR_mod_truth.csv",
sep = ""
))
dcant_budget_basin_MLR <- bind_rows(dcant_budget_basin_MLR,
dcant_budget_basin_MLR_mod_truth)
dcant_budget_basin_MLR <- dcant_budget_basin_MLR %>%
mutate(Version_ID = i_Version_IDs)
if (exists("dcant_budget_basin_MLR_all")) {
dcant_budget_basin_MLR_all <-
bind_rows(dcant_budget_basin_MLR_all, dcant_budget_basin_MLR)
}
if (!exists("dcant_budget_basin_MLR_all")) {
dcant_budget_basin_MLR_all <- dcant_budget_basin_MLR
}
}[1] "v_1103"
[1] "v_2103"
[1] "v_3103"rm(
dcant_budget_basin_MLR,
dcant_budget_basin_MLR_mod_truth
)dcant_budget_basin_MLR_all <- dcant_budget_basin_MLR_all %>%
filter(estimate == "dcant",
method == "total") %>%
select(-c(estimate, method)) %>%
rename(dcant = value)
dcant_budget_basin_MLR_all <- dcant_budget_basin_MLR_all %>%
filter(inv_depth == params_global$inventory_depth_standard)dcant_budget <- expression(Delta * C["ant"]~(PgC))2 Individual cases
2.1 Absoulte values
2.1.1 dcant
dcant_inv_all %>%
filter(data_source %in% c("mod", "obs"),
period != "1994 - 2014") %>%
group_by(data_source) %>%
group_split() %>%
# head(1) %>%
map(
~ p_map_cant_inv(df = .x,
var = "dcant",
subtitle_text = paste("data_source:",
unique(.x$data_source))) +
facet_grid(period ~ .) +
theme(axis.text = element_blank(),
axis.ticks = element_blank())
)[[1]]
| Version | Author | Date |
|---|---|---|
| 48ec4c6 | jens-daniel-mueller | 2022-01-19 |
[[2]]
| Version | Author | Date |
|---|---|---|
| 48ec4c6 | jens-daniel-mueller | 2022-01-19 |
dcant_inv_all %>%
filter(data_source %in% c("mod", "obs"),
period != "1994 - 2014") %>%
select(data_source, lon, lat, basin_AIP, period, dcant) %>%
pivot_wider(names_from = period,
values_from = dcant) %>%
mutate(delta_dcant = `2004 - 2014` - `1994 - 2004`) %>%
group_by(data_source) %>%
group_split() %>%
# head(1) %>%
map(
~ p_map_cant_inv(df = .x,
var = "delta_dcant",
subtitle_text = paste("data_source:",
unique(.x$data_source)),
col = "divergent") +
# facet_grid(period ~ .) +
theme(axis.text = element_blank(),
axis.ticks = element_blank())
)[[1]]
| Version | Author | Date |
|---|---|---|
| cc31f4b | jens-daniel-mueller | 2022-01-20 |
[[2]]
| Version | Author | Date |
|---|---|---|
| cc31f4b | jens-daniel-mueller | 2022-01-20 |
2.1.2 dcant pos
dcant_inv_all %>%
filter(data_source %in% c("mod", "obs"),
period != "1994 - 2014") %>%
group_by(data_source) %>%
group_split() %>%
# head(1) %>%
map(
~ p_map_cant_inv(df = .x,
var = "dcant_pos",
subtitle_text = paste("data_source:",
unique(.x$data_source))) +
facet_grid(period ~ .) +
theme(axis.text = element_blank(),
axis.ticks = element_blank())
)[[1]]
| Version | Author | Date |
|---|---|---|
| cc31f4b | jens-daniel-mueller | 2022-01-20 |
[[2]]
| Version | Author | Date |
|---|---|---|
| cc31f4b | jens-daniel-mueller | 2022-01-20 |
3 Basins hemisphere
3.1 Individual cases
3.1.1 Absoulte values
dcant_budget_basin_MLR_all_plot <- dcant_budget_basin_MLR_all %>%
filter(period != "1994 - 2014",
data_source == "obs") %>%
mutate(
basin = str_replace(basin, "_", ". "),
basin = fct_relevel(
basin,
"N. Pacific",
"S. Pacific",
"N. Atlantic",
"S. Atlantic",
"Indian"
)
)g1 <- dcant_budget_basin_MLR_all_plot %>%
ggplot(aes(
y = dcant,
x = period,
alluvium = basin,
fill = basin,
stratum = basin
)) +
stat_alluvium(decreasing = FALSE) +
stat_stratum(decreasing = FALSE) +
stat_stratum(geom = "text",
decreasing = FALSE,
aes(label = paste(
round(after_stat(max-min),1)
# 100*round(after_stat(prop), 2), "%"
))) +
ggrepel::geom_label_repel(
data = dcant_budget_basin_MLR_all_plot %>% filter(period == "2004 - 2014"),
stat = "stratum",
size = 4,
nudge_x = .5,
point.padding = 3,
aes(fill = basin, label = basin),
decreasing = FALSE
)+
scale_fill_brewer(palette = "Paired", guide = "none") +
scale_y_continuous(limits = c(0, 32), expand = c(0, 0)) +
labs(y = dcant_budget) +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
axis.title.x = element_blank()) +
theme_classic()
newdat <- tibble(layer_data(g1))
change <-
newdat %>%
select(x, alluvium, count) %>%
pivot_wider(names_from = x,
values_from = count) %>%
mutate(dcant_change = round(100*(`2` - `1`) / `1`)) %>%
select(alluvium, dcant_change)
coord <- newdat %>%
filter(x == 2) %>%
select(x, y, alluvium)
new_layer <- full_join(
change,
coord
)
new_layer <- new_layer %>%
mutate(dcant_change = as.character(dcant_change),
dcant_change = if_else(str_detect(dcant_change, "-"),
dcant_change,
paste0("+", dcant_change)),
dcant_change = paste(dcant_change, "%"))
g1 +
geom_text(data = new_layer,
aes(
x = x - 0.3,
y = y,
label = dcant_change
),
inherit.aes = FALSE)
g2 <- dcant_budget_basin_MLR_all_plot %>%
ggplot(aes(
y = dcant,
x = period,
alluvium = basin,
fill = basin,
stratum = basin,
label = basin
)) +
geom_alluvium() +
geom_stratum() +
stat_stratum(geom = "text",
aes(label = paste(
round(after_stat(count),1)
# 100*round(after_stat(prop), 2), "%"
))) +
ggrepel::geom_label_repel(
data = dcant_budget_basin_MLR_all_plot %>% filter(period == "2004 - 2014"),
stat = "stratum",
size = 4,
nudge_x = .5,
point.padding = 3,
aes(fill = basin)
)+
scale_fill_brewer(palette = "Paired", guide = "none") +
scale_color_brewer(palette = "Paired", guide = "none") +
scale_y_continuous(limits = c(0, 32.5), expand = c(0, 0)) +
guides(y = "none") +
labs(title = dcant_budget) +
theme_classic() +
theme(axis.text.x = element_text(angle = 45, hjust = 1),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
plot.title = element_text(hjust = 0.5))
newdat <- tibble(layer_data(g2))
change_basin <-
newdat %>%
select(x, alluvium, count) %>%
pivot_wider(names_from = x,
values_from = count) %>%
mutate(dcant_change = round(100*(`2` - `1`) / `1`)) %>%
select(alluvium, dcant_change)
coord_basin <- newdat %>%
filter(x == 2) %>%
select(x, y, alluvium)
new_layer_basin <- full_join(
change_basin,
coord_basin
)
new_layer_basin <- new_layer_basin %>%
mutate(dcant_change = as.character(dcant_change),
dcant_change = if_else(str_detect(dcant_change, "-"),
dcant_change,
paste0("+", dcant_change)),
dcant_change = paste(dcant_change, "%"))
new_layer_total <-
newdat %>%
select(x, alluvium, count) %>%
group_by(x) %>%
summarise(dcant_change = sum(count)) %>%
ungroup()
new_layer_total <- new_layer_total %>%
mutate(y = dcant_change,
dcant_change = as.character(round(dcant_change,1)),
dcant_change = paste("global:",dcant_change))
g2 +
geom_text(data = new_layer_basin,
aes(
x = x - 0.3,
y = y,
label = dcant_change
),
inherit.aes = FALSE) +
geom_label(data = new_layer_total,
aes(
x = x,
y = y + 1,
label = dcant_change
),
inherit.aes = FALSE)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3
Matrix products: default
BLAS: /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/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] ggalluvial_0.12.3 ggforce_0.3.3 metR_0.9.0 scico_1.2.0
[5] patchwork_1.1.1 collapse_1.5.0 forcats_0.5.0 stringr_1.4.0
[9] dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[13] tibble_3.1.3 ggplot2_3.3.5 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 viridisLite_0.3.0 jsonlite_1.7.1
[4] modelr_0.1.8 assertthat_0.2.1 highr_0.8
[7] blob_1.2.1 cellranger_1.1.0 ggrepel_0.8.2
[10] yaml_2.2.1 pillar_1.6.2 backports_1.1.10
[13] lattice_0.20-41 glue_1.4.2 RcppEigen_0.3.3.7.0
[16] digest_0.6.27 RColorBrewer_1.1-2 promises_1.1.1
[19] polyclip_1.10-0 checkmate_2.0.0 rvest_0.3.6
[22] colorspace_2.0-2 htmltools_0.5.0 httpuv_1.5.4
[25] Matrix_1.2-18 pkgconfig_2.0.3 broom_0.7.9
[28] haven_2.3.1 scales_1.1.1 tweenr_1.0.2
[31] whisker_0.4 later_1.2.0 git2r_0.27.1
[34] generics_0.1.0 farver_2.0.3 ellipsis_0.3.2
[37] withr_2.3.0 cli_3.0.1 magrittr_1.5
[40] crayon_1.3.4 readxl_1.3.1 evaluate_0.14
[43] fs_1.5.0 fansi_0.4.1 MASS_7.3-53
[46] xml2_1.3.2 RcppArmadillo_0.10.1.0.0 tools_4.0.3
[49] data.table_1.14.0 hms_0.5.3 lifecycle_1.0.0
[52] munsell_0.5.0 reprex_0.3.0 compiler_4.0.3
[55] rlang_0.4.10 grid_4.0.3 rstudioapi_0.13
[58] labeling_0.4.2 rmarkdown_2.10 gtable_0.3.0
[61] DBI_1.1.0 R6_2.5.0 lubridate_1.7.9
[64] knitr_1.33 utf8_1.1.4 rprojroot_2.0.2
[67] stringi_1.5.3 parallel_4.0.3 Rcpp_1.0.5
[70] vctrs_0.3.8 dbplyr_1.4.4 tidyselect_1.1.0
[73] xfun_0.25