Column inventories
Jens Daniel Müller
30 July, 2021
Last updated: 2021-07-30
Checks: 7 0
Knit directory: emlr_obs_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 964b616 | jens-daniel-mueller | 2021-07-30 | Build site. |
| html | 0a09f3e | jens-daniel-mueller | 2021-07-30 | Build site. |
| html | 3a48c91 | jens-daniel-mueller | 2021-07-27 | Build site. |
| html | b32149b | jens-daniel-mueller | 2021-07-27 | Build site. |
| Rmd | e71970f | jens-daniel-mueller | 2021-07-27 | rebuildt with budget analysis |
| html | 3402949 | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | fe80715 | jens-daniel-mueller | 2021-07-26 | added ensemble analysis |
| html | d0441c4 | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | d298b24 | jens-daniel-mueller | 2021-07-26 | added ensemble analysis |
| html | 7a1b358 | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | 51e22f6 | jens-daniel-mueller | 2021-07-26 | cleaned code and output |
| html | 860126c | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | 123c854 | jens-daniel-mueller | 2021-07-26 | cleaned code and output |
| html | 432df8a | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | 310fd35 | jens-daniel-mueller | 2021-07-26 | cleaned code and output |
| html | 93a27dd | jens-daniel-mueller | 2021-07-26 | Build site. |
| Rmd | f000466 | jens-daniel-mueller | 2021-07-26 | rebuildt with latest results |
| html | 7493389 | jens-daniel-mueller | 2021-07-05 | Build site. |
| html | 8b2e4d3 | jens-daniel-mueller | 2021-06-22 | Build site. |
| html | 8756c6f | jens-daniel-mueller | 2021-06-02 | Build site. |
| Rmd | 9881e98 | jens-daniel-mueller | 2021-06-02 | include GLODAP beta 2021 based results |
| html | 4d8b4e7 | jens-daniel-mueller | 2021-06-02 | Build site. |
| Rmd | 05184e5 | jens-daniel-mueller | 2021-06-02 | include GLODAP beta 2021 based results |
| html | 878aef7 | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 2c347cd | jens-daniel-mueller | 2021-05-28 | plotted C* rmse, MLR target, vif max |
| html | 92cae2e | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 87a8c49 | jens-daniel-mueller | 2021-05-28 | plotted Canyon B max |
| html | 998f4a6 | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 3c6f0f4 | jens-daniel-mueller | 2021-05-28 | including cases 109-116 |
| html | a28ce5c | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 2f6d0c0 | jens-daniel-mueller | 2021-05-28 | including cases 109-116 |
| html | 3454b72 | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 1b46b2a | jens-daniel-mueller | 2021-05-28 | including cases 109-116 |
| html | db22706 | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 9bb2f7a | jens-daniel-mueller | 2021-05-28 | plot global budgets |
| html | 87481da | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | 154a8fc | jens-daniel-mueller | 2021-05-28 | plot global budgets |
| html | bd4af9d | jens-daniel-mueller | 2021-05-28 | Build site. |
| Rmd | cdd2cc8 | jens-daniel-mueller | 2021-05-28 | plot global budgets |
| html | ee5b15d | jens-daniel-mueller | 2021-05-27 | Build site. |
| Rmd | 83f3e37 | jens-daniel-mueller | 2021-05-27 | plot bias maps |
| html | e8bd251 | jens-daniel-mueller | 2021-05-27 | Build site. |
| Rmd | f642ef2 | jens-daniel-mueller | 2021-05-27 | plot bias maps |
| html | ea0153f | jens-daniel-mueller | 2021-05-27 | Build site. |
| Rmd | 8b38db1 | jens-daniel-mueller | 2021-05-27 | plot bias maps |
| html | cf3365a | jens-daniel-mueller | 2021-05-27 | Build site. |
| Rmd | 2eb7603 | jens-daniel-mueller | 2021-05-27 | plot bias maps |
| html | 57ddd1f | jens-daniel-mueller | 2021-05-27 | Build site. |
| Rmd | f403434 | jens-daniel-mueller | 2021-05-27 | sensitivity case comparison included |
1 Read files
# identify required version IDs
# Version_IDs <- list.files(
# path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
# pattern = "v_")[1:34]
Version_IDs_1 <- list.files(
path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
pattern = "v_10")[1:4]
Version_IDs_2 <- list.files(
path = "/nfs/kryo/work/jenmueller/emlr_cant/observations",
pattern = "v_20")[1:4]
Version_IDs <- c(Version_IDs_1, Version_IDs_2)
rm(Version_IDs_1, Version_IDs_2)
# 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_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 = ""))
dcant_inv <- bind_rows(dcant_inv,
dcant_inv_mod_truth)
dcant_inv <- dcant_inv %>%
mutate(Version_ID = i_Version_IDs)
dcant_inv_bias <- dcant_inv_bias %>%
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,
MLR_basins = params_local$MLR_basins,
tref1 = params_local$tref1,
tref2 = params_local$tref2,
gap_filling = params_local$gap_filling,
rarefication = params_local$rarefication,
rarefication_threshold = params_local$rarefication_threshold,
MLR_predictors = str_c(params_local$MLR_predictors, collapse = "+"),
vif_max = params_local$vif_max
)
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("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_101"
[1] "v_102"
[1] "v_103"
[1] "v_104"
[1] "v_201"
[1] "v_202"
[1] "v_203"
[1] "v_204"rm(dcant_inv, dcant_inv_bias, dcant_inv_mod_truth,
params_local, tref)
dcant_inv_all <- full_join(dcant_inv_all,
params_local_all)
dcant_inv_bias_all <- full_join(dcant_inv_bias_all,
params_local_all)dcant_inv_all <- dcant_inv_all %>%
filter(inv_depth == params_global$inventory_depth_standard)2 Individual cases
2.1 Absoulte values
dcant_inv_all %>%
filter(data_source %in% c("mod", "obs")) %>%
group_by(period) %>%
group_split() %>%
# head(1) %>%
map(
~ p_map_cant_inv(df = .x,
var = "dcant",
subtitle_text = paste("period:",
unique(.x$period))) +
facet_grid(MLR_basins ~ data_source)
)[[1]]
| Version | Author | Date |
|---|---|---|
| 432df8a | jens-daniel-mueller | 2021-07-26 |
[[2]]
| Version | Author | Date |
|---|---|---|
| 432df8a | jens-daniel-mueller | 2021-07-26 |
2.2 Biases
dcant_inv_bias_all %>%
p_map_cant_inv(var = "dcant_bias",
col = "bias",
subtitle_text = "data_source: mod - mod_truth") +
facet_grid(MLR_basins ~ period)
| Version | Author | Date |
|---|---|---|
| 432df8a | jens-daniel-mueller | 2021-07-26 |
3 Ensemble
dcant_inv_ensemble <- dcant_inv_all %>%
filter(data_source %in% c("mod", "obs")) %>%
group_by(lat, lon, data_source, period) %>%
summarise(dcant_mean = mean(dcant),
dcant_sd = sd(dcant),
dcant_range = max(dcant)- min(dcant)) %>%
ungroup()3.1 Mean
p_map_cant_inv(df = dcant_inv_ensemble,
var = "dcant_mean",
subtitle_text = paste("Ensemble means")) +
facet_grid(period ~ data_source)
3.2 Mean bias
dcant_inv_ensemble_bias <- full_join(
dcant_inv_ensemble %>%
filter(data_source == "mod") %>%
select(lat, lon, period, dcant_mean, dcant_sd),
dcant_inv_all %>%
filter(data_source == "mod_truth",
MLR_basins == "2") %>%
select(lat, lon, period, dcant)
)
dcant_inv_ensemble_bias <- dcant_inv_ensemble_bias %>%
mutate(dcant_mean_bias = dcant_mean - dcant)
dcant_inv_ensemble_bias %>%
p_map_cant_inv(var = "dcant_mean_bias",
col = "bias",
subtitle_text = "Ensemble mean - mod_truth") +
facet_grid(. ~ period)
| Version | Author | Date |
|---|---|---|
| 7a1b358 | jens-daniel-mueller | 2021-07-26 |
3.3 Standard deviation
p_map_cant_inv(
df = dcant_inv_ensemble,
var = "dcant_sd",
breaks = c(seq(0,4,0.4), Inf),
subtitle_text = paste("Ensemble SD")
) +
facet_grid(period ~ data_source)
3.4 SD vs bias
dcant_inv_ensemble_bias %>%
ggplot(aes(dcant_mean_bias, dcant_sd)) +
geom_bin2d() +
scale_fill_viridis_c() +
facet_grid(. ~ period)
| Version | Author | Date |
|---|---|---|
| d0441c4 | jens-daniel-mueller | 2021-07-26 |
dcant_inv_ensemble_bias %>%
select(dcant_mean, dcant_mean_bias, period) %>%
pivot_longer(dcant_mean:dcant_mean_bias,
names_to = "estimate",
values_to = "value") %>%
ggplot(aes(value, col=estimate, linetype = period)) +
scale_color_brewer(palette = "Set1") +
geom_density()
dcant_inv_ensemble %>%
ggplot(aes(dcant_sd)) +
geom_histogram() +
facet_grid(data_source ~ period) +
coord_cartesian(ylim = c(0,50))
3.5 Range
p_map_cant_inv(
df = dcant_inv_ensemble,
var = "dcant_range",
breaks = c(seq(0,8,0.8), Inf),
subtitle_text = paste("Ensemble range")
) +
facet_grid(period ~ data_source)
| Version | Author | Date |
|---|---|---|
| 860126c | jens-daniel-mueller | 2021-07-26 |
4 Cases vs ensemble
4.1 Offset from mean
dcant_inv_all <- full_join(dcant_inv_all,
dcant_inv_ensemble)
dcant_inv_all <- dcant_inv_all %>%
mutate(dcant_offset = dcant - dcant_mean)
dcant_inv_all %>%
filter(data_source %in% c("mod", "obs")) %>%
group_by(period) %>%
group_split() %>%
# head(1) %>%
map(
~ p_map_cant_inv(df = .x,
var = "dcant_offset",
col = "bias",
subtitle_text = paste("period:",
unique(.x$period))) +
facet_grid(MLR_basins ~ data_source)
)[[1]]
| Version | Author | Date |
|---|---|---|
| 7a1b358 | jens-daniel-mueller | 2021-07-26 |
[[2]]
| Version | Author | Date |
|---|---|---|
| 7a1b358 | jens-daniel-mueller | 2021-07-26 |
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
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] ggforce_0.3.3 metR_0.9.0 scico_1.2.0 patchwork_1.1.1
[5] collapse_1.5.0 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.5
[9] purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.0.4
[13] ggplot2_3.3.3 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 blob_1.2.1
[7] cellranger_1.1.0 yaml_2.2.1 pillar_1.4.7
[10] backports_1.1.10 lattice_0.20-41 glue_1.4.2
[13] RcppEigen_0.3.3.7.0 digest_0.6.27 RColorBrewer_1.1-2
[16] promises_1.1.1 polyclip_1.10-0 checkmate_2.0.0
[19] rvest_0.3.6 colorspace_1.4-1 htmltools_0.5.0
[22] httpuv_1.5.4 Matrix_1.2-18 pkgconfig_2.0.3
[25] broom_0.7.5 haven_2.3.1 scales_1.1.1
[28] tweenr_1.0.2 whisker_0.4 later_1.1.0.1
[31] git2r_0.27.1 generics_0.0.2 farver_2.0.3
[34] ellipsis_0.3.1 withr_2.3.0 cli_2.1.0
[37] magrittr_1.5 crayon_1.3.4 readxl_1.3.1
[40] evaluate_0.14 fs_1.5.0 fansi_0.4.1
[43] MASS_7.3-53 xml2_1.3.2 RcppArmadillo_0.10.1.2.0
[46] tools_4.0.3 data.table_1.13.2 hms_0.5.3
[49] lifecycle_1.0.0 munsell_0.5.0 reprex_0.3.0
[52] compiler_4.0.3 rlang_0.4.10 grid_4.0.3
[55] rstudioapi_0.11 labeling_0.4.2 rmarkdown_2.5
[58] gtable_0.3.0 DBI_1.1.0 R6_2.5.0
[61] lubridate_1.7.9 knitr_1.30 rprojroot_2.0.2
[64] stringi_1.5.3 parallel_4.0.3 Rcpp_1.0.5
[67] vctrs_0.3.5 dbplyr_1.4.4 tidyselect_1.1.0
[70] xfun_0.18