From a4187aea1b77365016b0d92f75342fa1d02de971 Mon Sep 17 00:00:00 2001 From: CarloBroderick Date: Fri, 8 Sep 2023 15:10:00 -0700 Subject: [PATCH 1/2] updated citations for layers --- .../np/v2023/STEP1c_np_fishfeed_prep.Rmd | 12 +++++-- .../np/v2023/STEP2_np_weighting_prep.Rmd | 18 +++++++--- .../v2023/targetedharvest_dataprep.Rmd | 35 +++++++++---------- 3 files changed, 38 insertions(+), 27 deletions(-) diff --git a/globalprep/np/v2023/STEP1c_np_fishfeed_prep.Rmd b/globalprep/np/v2023/STEP1c_np_fishfeed_prep.Rmd index 73615651..a0160db2 100644 --- a/globalprep/np/v2023/STEP1c_np_fishfeed_prep.Rmd +++ b/globalprep/np/v2023/STEP1c_np_fishfeed_prep.Rmd @@ -30,6 +30,8 @@ This script takes the SAUP 2023 catch data, a list of fish oil/fish meal (FOFM) # Data Source +## Sea Around us + **Reference**: Pauly D., Zeller D., Palomares M.L.D. (Editors), 2020. Sea Around Us Concepts, Design and Data (seaaroundus.org). **Downloaded**: September 27, 2022 @@ -42,6 +44,8 @@ This script takes the SAUP 2023 catch data, a list of fish oil/fish meal (FOFM) **Additional Information**: [Methods](http://www.seaaroundus.org/sea-around-us-methods-index/) +## Avoiding the ecological limits of forage fish + **Reference**: Froehlich, H.E., Jacobsen, N.S., Essington, T.E., Clavelle, T., and Halpern, B.S. (2018). Avoiding the ecological limits of forage fish for fed aquaculture. Nature Sustainability 1, 298. **Downloaded**: July 7, 2020. Obtained from Melanie Frazier (NCEAS). @@ -52,15 +56,17 @@ This script takes the SAUP 2023 catch data, a list of fish oil/fish meal (FOFM) **Format**: CSV format -**Reference**: [RAM Legacy Stock Assessment Database](http://ramlegacy.org) v4.495 +## RAM Legacy Data + +**Reference**: [RAM Legacy Stock Assessment Database](http://ramlegacy.org) v4.61, 05/10/2023 -**Downloaded**: 06/03/2021 +**Downloaded**: 07/6/2023 **Description**: B/Bmsy value by stock and year (other data, which we do not use, are also available in the database) **Native data resolution**: stock (fish stock, species and region specific) -**Time range**: 1950 - 2024 +**Time range**: 1800 - 2022 **Format**: CSV format diff --git a/globalprep/np/v2023/STEP2_np_weighting_prep.Rmd b/globalprep/np/v2023/STEP2_np_weighting_prep.Rmd index a4c0aa93..8a6a24ab 100644 --- a/globalprep/np/v2023/STEP2_np_weighting_prep.Rmd +++ b/globalprep/np/v2023/STEP2_np_weighting_prep.Rmd @@ -33,6 +33,8 @@ in ohi global. # Data Source +## FAO + **Reference**:\ App release date: July 2021 FAO raw commodities quantity 1976_2021 FAO @@ -49,6 +51,8 @@ details). **Time range**: 1976-2021 +## Sea Around Us Concepts + **Reference**: Pauly D., Zeller D., Palomares M.L.D. (Editors), 2020. Sea Around Us Concepts, Design and Data (seaaroundus.org). @@ -65,6 +69,8 @@ taxonomic information. **Additional Information**: [Methods](http://www.seaaroundus.org/sea-around-us-methods-index/) +## Avoiding the ecological limits of forage fish for fed aquaculture + **Reference**: Froehlich, H.E., Jacobsen, N.S., Essington, T.E., Clavelle, T., and Halpern, B.S. (2018). Avoiding the ecological limits of forage fish for fed aquaculture. Nature Sustainability 1, 298. @@ -77,10 +83,12 @@ of forage fish for fed aquaculture. Nature Sustainability 1, 298. **Format**: CSV format +## RAM + **Reference**: [RAM Legacy Stock Assessment -Database](http://ramlegacy.org) v4.491 +Database](http://ramlegacy.org) v4.61, 05/10/2023 -**Downloaded**: 06/03/2021 +**Downloaded**: 07/6/2023 **Description**: B/Bmsy value by stock and year (other data, which we do not use, are also available in the database) @@ -88,15 +96,15 @@ not use, are also available in the database) **Native data resolution**: stock (fish stock, species and region specific) -**Time range**: 1950 - 2024 +**Time range**: 1800 - 2022 **Format**: CSV format **Additional Information**: We use the finalized b/bmsy layer from OHI-global for this data prep. We do not actually read in the raw RAM -data here. We only use up to year == 2018. +data here. -- DOI: 10.5281/zenodo.2542919 +## FAO **Reference**:\ diff --git a/globalprep/prs_targetedharvest/v2023/targetedharvest_dataprep.Rmd b/globalprep/prs_targetedharvest/v2023/targetedharvest_dataprep.Rmd index e932ba2c..21af6eab 100644 --- a/globalprep/prs_targetedharvest/v2023/targetedharvest_dataprep.Rmd +++ b/globalprep/prs_targetedharvest/v2023/targetedharvest_dataprep.Rmd @@ -22,33 +22,33 @@ editor_options: # Summary -This analysis converts FAO capture production data into the OHI 2022 targeted harvest pressure data. +This analysis converts FAO capture production data into the OHI 2022 targeted harvest pressure data. # Updates from previous assessment -2023 - One more year of data, 2021 -Small fixes to how N data is handled in fao_fxn.R -Delete unused/not relevant code +2023 - One more year of data, 2021 Small fixes to how N data is handled in fao_fxn.R Delete unused/not relevant code -*** +------------------------------------------------------------------------ -# Data Source +# Data Source - http://www.fao.org/fishery/statistics/software/fishstatj/en#downlApp - Release date: March 2021 -FAO Global Capture Production Quantity 1950_2019 -Information: http://www.fao.org/fishery/statistics/global-capture-production/en +``` +http://www.fao.org/fishery/statistics/software/fishstatj/en#downlApp + Release date: March 2021 +``` -**Reference**: United Nations, 2021. FAO Fisheries & Aquaculture - Fishery Statistical Collections - Global Capture Production [WWW Document]. URL http://www.fao.org/fishery/statistics/global-capture-production/en (accessed 4.29.21). +FAO Global Capture Production Quantity 1950_2019\ +Information: +**Reference**: United Nations, 2021. FAO Fisheries & Aquaculture - Fishery Statistical Collections - Global Capture Production [WWW Document]. URL (accessed 4.29.21). -**Downloaded**: April 25, 2022 +**Downloaded**: June 1, 2023 -**Description**: Quantity (tonnes) of fisheries capture for each county, species, year. +**Description**: Quantity (tonnes) of fisheries capture for each county, species, year. **Time range**: 1950-2020 -*** +------------------------------------------------------------------------ # Methods @@ -126,7 +126,7 @@ fao_clean <- fao_clean %>% ## Identify the target species -This analysis only includes target species. The warning messages need to be checked and, if necessary, changes should be made to the raw/species2group.csv +This analysis only includes target species. The warning messages need to be checked and, if necessary, changes should be made to the raw/species2group.csv ```{r, eval=FALSE} @@ -218,9 +218,6 @@ sum <- sum %>% dplyr::mutate(country = as.character(country)) %>% dplyr::mutate(country = ifelse(stringr::str_detect(country, "C.*te d'Ivoire"), "Ivory Coast", country)) -sum <- sum %>% - ohicore::split_regions() - ### Function to convert to OHI region ID m_sum_rgn <- name_2_rgn(df_in = sum, fld_name='country', @@ -355,4 +352,4 @@ compare_plot <- ggplot(data = old, aes(x = pressure_score_2020, y = pressure_sco plot(compare_plot) ggplotly(compare_plot) -``` \ No newline at end of file +``` From 43f2818a96d7883789c1e259186741bb27e24ec7 Mon Sep 17 00:00:00 2001 From: eeerika Date: Mon, 11 Sep 2023 09:37:24 -0700 Subject: [PATCH 2/2] wrapup edits for all but TR --- globalprep/fis/readme.md | 4 +- ...TEP1_download_saup_match_fao_data_fix.html | 961 +++++----- .../fis/v2023/STEP2a_saup_catch_prep.html | 1575 ++++++++--------- .../fis/v2023/STEP3_calculate_bbmsy.html | 383 ++-- .../fis/v2023/STEP4a_RAM_data_prep.html | 1145 ++++++------ globalprep/fis/v2023/STEP4b_fao_ohi_rgns.html | 1117 ++++++------ .../fis/v2023/STEP5_RAM_CMSY_combine.html | 535 +++--- globalprep/fis/v2023/readme.md | 14 +- globalprep/fp/README.md | 4 +- globalprep/fp/v2023/FP_script.Rmd | 20 +- globalprep/fp/v2023/FP_script.html | 604 +++++++ globalprep/prs_alien/README.md | 4 +- globalprep/prs_alien/v2023/README.md | 2 +- .../prs_alien/v2023/prs_alien_data_prep.html | 1035 ++++++----- .../v2023/prs_coral_harvest.Rmd | 2 +- .../v2023/prs_coral_harvest.html | 4 +- globalprep/prs_coral_harvest/v2023/readme.md | 4 +- globalprep/prs_slr/readme.md | 4 +- globalprep/prs_slr/v2023/readme.md | 2 +- .../prs_slr/v2023/slr_layer_prep_v2.Rmd | 4 +- .../prs_slr/v2023/slr_layer_prep_v2.html | 1080 ++++++----- globalprep/prs_uv/README.md | 4 +- globalprep/prs_uv/v2023/readme.md | 2 +- globalprep/prs_uv/v2023/uv_dataprep.html | 1435 ++++++++------- 24 files changed, 5184 insertions(+), 4760 deletions(-) create mode 100644 globalprep/fp/v2023/FP_script.html diff --git a/globalprep/fis/readme.md b/globalprep/fis/readme.md index 4fdccc9d..5b79cd70 100644 --- a/globalprep/fis/readme.md +++ b/globalprep/fis/readme.md @@ -4,10 +4,10 @@ This folder describes the methods used to prepare data for the Fisheries subgoal More information about this goal is available [here](http://ohi-science.org/goals/#food-provision). -The folders in this file include the metadata, R scripts, and data for each assessement year (i.e., the year the assessment was conducted). The most current year represents the best available data and methods, and previous years are maintained for archival purposes. +The folders in this file include the metadata, R scripts, and data for each assessment year (i.e., the year the assessment was conducted). The most current year represents the best available data and methods, and previous years are maintained for archival purposes. Our [data managment SOP](https://rawgit.com/OHI-Science/ohiprep/master/src/dataOrganization_SOP.html) describes how we manage OHI global data, including a description of the file structure. -Please see our [citation policy](http://ohi-science.org/citation-policy/) if you use OHI data or methods. +Please see our [citation policy](https://oceanhealthindex.org/global-scores/data-download/) if you use OHI data or methods. Thank you! diff --git a/globalprep/fis/v2023/STEP1_download_saup_match_fao_data_fix.html b/globalprep/fis/v2023/STEP1_download_saup_match_fao_data_fix.html index 3f6f2529..08c871df 100644 --- a/globalprep/fis/v2023/STEP1_download_saup_match_fao_data_fix.html +++ b/globalprep/fis/v2023/STEP1_download_saup_match_fao_data_fix.html @@ -9,7 +9,7 @@ - + OHI 2023: Download SAUP production data and match FAO regions @@ -31,7 +31,7 @@ !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return t.concat.apply([],e)},u=t.push,i=t.indexOf,n={},o=n.toString,v=n.hasOwnProperty,a=v.toString,l=a.call(Object),y={},m=function(e){return"function"==typeof e&&"number"!=typeof 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background-color: rgba(0, 0, 0, 0.04);} +pre:not([class]) { background-color: white } - +h1.title {font-size: 38px;} +h2 {font-size: 30px;} +h3 {font-size: 24px;} +h4 {font-size: 18px;} +h5 {font-size: 16px;} +h6 {font-size: 12px;} +code {color: inherit; background-color: rgba(0, 0, 0, 0.04);} +pre:not([class]) { background-color: white } + + + + + + + + +

+ohi logo
OHI Science | Citation policy +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + +
+

1 Summary

+

This script combines the fisheries catch data with the mariculture +production data to create the weights for how much of each score will +affect the entire food provision score.

+
+
+

2 Updates from previous +assessment

+
    +
  • Mariculture data was updated since last scenario year but fisheries +wasn’t
    • +
  • Updated scenario year input/some file paths to be more +programmatic
    • +
  • Updated labeling of the graphs
    • +
+
+
+

3 Methods

+
## load libraries
+library(dplyr)
+library(tidyr)
+library(here)
+
+scen_year <- 2023 # change to latest year
+prev_scen_year <- scen_year - 1
+
+setwd(here::here("globalprep","fp", paste0("v", scen_year)))
+
+## Load FAO-specific user-defined functions
+source('http://ohi-science.org/ohiprep_v2021/workflow/R/common.R')
+
+
+

4 Import Output Data: +Mariculture data

+

Mariculture production in tonnes.

+
mar <- read.csv(file.path("..", "..", "mar", paste0("v", scen_year), "output", "MAR_FP_data.csv")) # see metadata in its prep
+

Fisheries data.

+
fis <- read.csv(file.path("..", "..", "fis", paste0("v", scen_year), "output", "FP_fis_catch.csv")) %>%
+  dplyr::select(rgn_id, year, fis_t = fis_catch) # see metadata in its prep
+
+
+

5 Wrangle

+
+

5.1 Tidy MAR data

+
mar_tidy <- mar %>%
+  group_by(rgn_id, year) %>%
+  summarize(mar_t = sum(value, na.rm=TRUE)) %>%
+  dplyr::select(rgn_id, year, mar_t) %>%
+  ungroup()
+
+# this one is turning to NA in FP
+filter(mar_tidy, rgn_id == 95) # ok, this makes sense
+
+
+

5.2 Tidy FIS data

+
fis_tidy <- fis %>%
+  mutate(fis_t = ifelse(fis_t == 0, NA, fis_t)) %>%  # 11 NA values is correct (there were 0 in v2023)
+  group_by(rgn_id) %>%
+  arrange(year) %>%
+  fill(fis_t) %>% 
+  ungroup()
+
+
+

5.3 Combine MAR and +FIS

+

Adjust years so they are equivalent.

+
adjust <- max(mar_tidy$year) - max(fis_tidy$year)
+
+mar_adjust <- mar_tidy %>%
+  mutate(year = year - adjust)
+
+tmp <- full_join(fis_tidy, mar_adjust, by = c('rgn_id', 'year')) # v2023: removed all = TRUE because was not a valid argument, did not see an equivalent
+
+## If NA, turn it into a 0 before weighting
+tmp_weights <- tmp %>%
+  mutate(fis_t = ifelse(is.na(fis_t), 0, fis_t)) %>%
+  mutate(mar_t = ifelse(is.na(mar_t), 0, mar_t)) %>%
+  mutate(w_fis = fis_t/(fis_t + mar_t)) %>%
+  mutate(w_fis = ifelse(mar_t == 0 & fis_t == 0, NA, w_fis)) %>%
+  filter(year >= 2005) %>%
+  dplyr::select(rgn_id, year, w_fis) 
+
+hist(tmp_weights$w_fis,
+     main = "Weights",
+     xlab = "Value")
+
+
+
+

6 Data check

+

Compare to previous year data

+
compare <- read.csv(paste0("../../fp/v", prev_scen_year, "/output/wildcaught_weight.csv")) %>%
+  rename(w_fis_old = w_fis) %>%
+  left_join(tmp_weights, by = c('rgn_id', 'year'))
+plot(compare$w_fis_old, compare$w_fis,
+     xlab = paste0("Old data (v", prev_scen_year, ")"),
+     ylab = paste0("New data (v", scen_year, ")"))
+abline(0, 1, col="red")
+
+
+

7 Save data

+
write.csv(tmp_weights, 'output/wildcaught_weight.csv', row.names=FALSE)
+
+## add gf file (no gapfilling)
+tmp_gf <- tmp_weights %>%
+  mutate(w_fis = 0) %>%
+  dplyr::select(rgn_id, year, gapfilled = w_fis)
+
+write.csv(tmp_gf, 'output/wildcaught_weight_gf.csv', row.names=FALSE)
+
+ + + + +
+ + + + + + + + + + + + + + + diff --git a/globalprep/prs_alien/README.md b/globalprep/prs_alien/README.md index f7ac1eae..9389cb7c 100644 --- a/globalprep/prs_alien/README.md +++ b/globalprep/prs_alien/README.md @@ -2,10 +2,10 @@ This folder describes the methods used to prepare data for the nonindigenous species data for the global OHI assessment. These data are used as a pressure. -The folders in this file include the metadata, R scripts, and data for each assessement year (i.e., the year the assessment was conducted). The most current year represents the best available data and methods, and previous years are maintained for archival purposes. +The folders in this file include the metadata, R scripts, and data for each assessment year (i.e., the year the assessment was conducted). The most current year represents the best available data and methods, and previous years are maintained for archival purposes. Our [data managment SOP](https://rawgit.com/OHI-Science/ohiprep/master/src/dataOrganization_SOP.html) describes how we manage OHI global data, including a description of the file structure. -Please see our [citation policy](http://ohi-science.org/citation-policy/) if you use OHI data or methods. +Please see our [citation policy](https://oceanhealthindex.org/global-scores/data-download/) if you use OHI data or methods. Thank you! diff --git a/globalprep/prs_alien/v2023/README.md b/globalprep/prs_alien/v2023/README.md index d3d33c7e..dd54cee6 100644 --- a/globalprep/prs_alien/v2023/README.md +++ b/globalprep/prs_alien/v2023/README.md @@ -10,5 +10,5 @@ Information about [calculating pressure](http://ohi-science.github.io/ohiprep_v2 ### Additional information -If using these data, please see our [citation policy](http://ohi-science.org/citation-policy/). +If using these data, please see our [citation policy](https://oceanhealthindex.org/global-scores/data-download/). diff --git a/globalprep/prs_alien/v2023/prs_alien_data_prep.html b/globalprep/prs_alien/v2023/prs_alien_data_prep.html index 9f42c1fd..25a90800 100644 --- a/globalprep/prs_alien/v2023/prs_alien_data_prep.html +++ b/globalprep/prs_alien/v2023/prs_alien_data_prep.html @@ -9,7 +9,7 @@ - + OHI 2023 - Pressure: Invasive Species @@ -31,7 +31,7 @@ !function(e,t){"use strict";"object"==typeof module&&"object"==typeof 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