testing new gapfilling fao data cleaning issue NP

globalprep/np/v2024/STEP1a_np_ornamentals_prep.Rmd

@@ -117,7 +117,7 @@ files_old <- list.files(dir_fao_data_old, pattern = glob2rx('*.csv'), full.names
 
 # ===== loop ================
 for (f in files) {
-  # f <- files[1] # un-comment and update to test individual files
+  f <- files[2] # un-comment and update to test individual files # 1 = quant, 2 = usd
   cat(sprintf('\n\n\n====\nfile: %s\n', basename(f)))
   
   #d <- read.csv(f, check.names = FALSE, strip.white = TRUE, stringsAsFactors = FALSE) # stringsAsFactors=T

globalprep/np/v2024/STEP1c_np_fishfeed_prep.html

@@ -9,7 +9,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Compiled on Mon Aug 19 17:18:37 2024 by ramji" />
+<meta name="author" content="Compiled on Tue Aug 27 16:14:14 2024 by ramji" />
 
 
 <title>OHI 2024: Natural Products, Preparing catch and B/Bmsy data for forage fish species</title>
@@ -1647,7 +1647,7 @@
 
 <h1 class="title toc-ignore">OHI 2024: Natural Products, Preparing catch
 and B/Bmsy data for forage fish species</h1>
-<h4 class="author"><em>Compiled on Mon Aug 19 17:18:37 2024 by
+<h4 class="author"><em>Compiled on Tue Aug 27 16:14:14 2024 by
 ramji</em></h4>
 
 </div>
@@ -1837,7 +1837,7 @@ <h2>Create a master list of forage species</h2>
 <div id="read-in-v2022-catch-data" class="section level2">
 <h2>Read in (v2022) catch data</h2>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="co"># This was not updated in v2023 or 2024 so we call out to the v2022 year on Mazu</span></span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>file <span class="ot">&lt;-</span> <span class="fu">file.path</span>(dir_M,<span class="st">&#39;git-annex/globalprep/fis/v2022/int/stock_catch_by_rgn_taxa.csv&#39;</span>)</span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>file <span class="ot">&lt;-</span> <span class="fu">file.path</span>(dir_M, <span class="st">&#39;git-annex/globalprep/fis/v2022/int/stock_catch_by_rgn_taxa.csv&#39;</span>)</span>
 <span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a></span>
 <span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="co"># read in Sea Around Us catch data</span></span>
 <span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a>catch_raw <span class="ot">&lt;-</span> readr<span class="sc">::</span><span class="fu">read_csv</span>(file) </span>

globalprep/np/v2024/STEP2_np_weighting_prep.Rmd

@@ -13,6 +13,7 @@ output:
   pdf_document:
     toc: true
 editor_options: 
+  chunk_output_type: inline
   markdown: 
     wrap: 72
 ---
@@ -194,7 +195,7 @@ rgns_eez <- rgns_eez %>%
 products <- data.frame(product = c("seaweeds", "ornamentals", "fish_oil"))
 
 # Create full rgn x product x years dataframe
-region_product_test <- rgns_eez %>% 
+region_product <- rgns_eez %>% 
   dplyr::select(rgn_id) %>%  # select rgn_id from rgns_eez
   cross_join(products) %>% # cross join with products (match every row in x with every row in y)
   cross_join(years_df) # cross join with years

globalprep/np/v2024/int/orn_tonnes.csv

@@ -4,24 +4,24 @@ rgn_id,product,tonnes,year
 3,ornamentals,0,2024
 4,ornamentals,0,2024
 5,ornamentals,3.2,2024
-6,ornamentals,4.61741404504902,2024
+6,ornamentals,0,2024
 7,ornamentals,0,2024
-8,ornamentals,2.7360748716512653,2024
-9,ornamentals,0.34197464973123815,2024
+8,ornamentals,1.7550055243212195,2024
+9,ornamentals,0,2024
 10,ornamentals,0,2024
-11,ornamentals,0.25875420970785895,2024
+11,ornamentals,0,2024
 12,ornamentals,0,2024
 13,ornamentals,0,2024
-14,ornamentals,42.1975,2024
-15,ornamentals,5591.2315,2024
-16,ornamentals,137.79129430005045,2024
-17,ornamentals,6.22,2024
-18,ornamentals,127.614,2024
+14,ornamentals,24.1,2024
+15,ornamentals,0,2024
+16,ornamentals,0,2024
+17,ornamentals,0.24586557855756866,2024
+18,ornamentals,39.45,2024
 19,ornamentals,0,2024
-20,ornamentals,0.18075530291330194,2024
+20,ornamentals,0.12430547813415416,2024
 21,ornamentals,0,2024
 24,ornamentals,0,2024
-25,ornamentals,653.0095,2024
+25,ornamentals,4.25,2024
 26,ornamentals,0,2024
 28,ornamentals,0,2024
 29,ornamentals,0,2024
@@ -32,49 +32,49 @@ rgn_id,product,tonnes,year
 34,ornamentals,0,2024
 35,ornamentals,0,2024
 36,ornamentals,0,2024
-37,ornamentals,5.049,2024
+37,ornamentals,3.8,2024
 38,ornamentals,0,2024
-39,ornamentals,302.6565,2024
-40,ornamentals,234.814,2024
+39,ornamentals,0,2024
+40,ornamentals,0,2024
 41,ornamentals,0.05,2024
-42,ornamentals,0.3715,2024
-43,ornamentals,174.40200000000002,2024
+42,ornamentals,0.15,2024
+43,ornamentals,20.25,2024
 44,ornamentals,0,2024
 45,ornamentals,0,2024
 46,ornamentals,0,2024
-47,ornamentals,0.1,2024
+47,ornamentals,0,2024
 48,ornamentals,0,2024
 49,ornamentals,0,2024
 50,ornamentals,0,2024
 51,ornamentals,0,2024
-52,ornamentals,2.43,2024
-53,ornamentals,44.138,2024
-54,ornamentals,8.0655,2024
+52,ornamentals,0,2024
+53,ornamentals,7.1,2024
+54,ornamentals,0,2024
 55,ornamentals,0,2024
 56,ornamentals,0,2024
 57,ornamentals,0,2024
 58,ornamentals,0,2024
-59,ornamentals,5.7090000000000005,2024
+59,ornamentals,2.4,2024
 60,ornamentals,0,2024
 61,ornamentals,0,2024
 62,ornamentals,0,2024
 63,ornamentals,0,2024
 64,ornamentals,0,2024
 65,ornamentals,0,2024
 66,ornamentals,0,2024
-67,ornamentals,601.88,2024
+67,ornamentals,0,2024
 68,ornamentals,0,2024
 69,ornamentals,0,2024
 70,ornamentals,0,2024
-71,ornamentals,172.868,2024
+71,ornamentals,0,2024
 72,ornamentals,0,2024
 73,ornamentals,0,2024
 74,ornamentals,0,2024
 75,ornamentals,0,2024
-76,ornamentals,1.6805,2024
-77,ornamentals,0.49918586123419434,2024
-78,ornamentals,1.343,2024
-79,ornamentals,2.207010771305258,2024
+76,ornamentals,0.65,2024
+77,ornamentals,0,2024
+78,ornamentals,0.2,2024
+79,ornamentals,0.26657143336115147,2024
 80,ornamentals,0,2024
 81,ornamentals,0,2024
 82,ornamentals,0,2024
@@ -94,20 +94,20 @@ rgn_id,product,tonnes,year
 98,ornamentals,0,2024
 99,ornamentals,0,2024
 100,ornamentals,0,2024
-101,ornamentals,0.025,2024
-102,ornamentals,10.86,2024
+101,ornamentals,0,2024
+102,ornamentals,5.7,2024
 103,ornamentals,0,2024
 104,ornamentals,0,2024
 105,ornamentals,0,2024
-106,ornamentals,23.285,2024
+106,ornamentals,0.35,2024
 107,ornamentals,0,2024
 108,ornamentals,0,2024
 110,ornamentals,0,2024
 111,ornamentals,0,2024
-112,ornamentals,3.7815,2024
+112,ornamentals,1.9,2024
 113,ornamentals,0,2024
-114,ornamentals,9.451162409145935,2024
-115,ornamentals,1.9234546726071866,2024
+114,ornamentals,0,2024
+115,ornamentals,0,2024
 116,ornamentals,0,2024
 117,ornamentals,0,2024
 118,ornamentals,0,2024
@@ -118,94 +118,94 @@ rgn_id,product,tonnes,year
 123,ornamentals,0,2024
 124,ornamentals,0,2024
 125,ornamentals,0,2024
-126,ornamentals,6.0765,2024
+126,ornamentals,0,2024
 127,ornamentals,0,2024
 129,ornamentals,0,2024
-130,ornamentals,18.7115,2024
-131,ornamentals,114.038,2024
-132,ornamentals,67.6065,2024
+130,ornamentals,2.65,2024
+131,ornamentals,9.85,2024
+132,ornamentals,0,2024
 133,ornamentals,0,2024
 134,ornamentals,0,2024
-135,ornamentals,7.983337888470418,2024
+135,ornamentals,6.927561280082898,2024
 136,ornamentals,0,2024
-137,ornamentals,4.501,2024
-138,ornamentals,16.166,2024
+137,ornamentals,3.3,2024
+138,ornamentals,16.1,2024
 139,ornamentals,0,2024
 140,ornamentals,0,2024
 141,ornamentals,0,2024
 143,ornamentals,0,2024
 144,ornamentals,0,2024
 145,ornamentals,0,2024
 146,ornamentals,0,2024
-147,ornamentals,40.13,2024
+147,ornamentals,1.05,2024
 148,ornamentals,0,2024
 149,ornamentals,0,2024
 150,ornamentals,0,2024
 151,ornamentals,0,2024
 152,ornamentals,0,2024
-153,ornamentals,0.7623480747042777,2024
+153,ornamentals,0,2024
 154,ornamentals,0,2024
 155,ornamentals,0,2024
 156,ornamentals,0,2024
 157,ornamentals,0,2024
 158,ornamentals,0,2024
 159,ornamentals,0,2024
 161,ornamentals,0,2024
-162,ornamentals,0.2915,2024
-163,ornamentals,3.25125846040474e-4,2024
+162,ornamentals,0,2024
+163,ornamentals,0,2024
 164,ornamentals,0,2024
 166,ornamentals,0,2024
-167,ornamentals,4.712,2024
-168,ornamentals,1.554,2024
+167,ornamentals,4.05,2024
+168,ornamentals,0,2024
 169,ornamentals,0,2024
-171,ornamentals,2.823,2024
+171,ornamentals,1.8,2024
 172,ornamentals,0,2024
 173,ornamentals,0,2024
 174,ornamentals,0,2024
-175,ornamentals,3.7645,2024
-176,ornamentals,1.4565000000000001,2024
-177,ornamentals,931.5725,2024
-178,ornamentals,0.2485,2024
-179,ornamentals,42.598,2024
-180,ornamentals,101.3845,2024
-181,ornamentals,1.6335,2024
-182,ornamentals,5330.178,2024
-183,ornamentals,41.086,2024
-184,ornamentals,48.0705,2024
+175,ornamentals,3.75,2024
+176,ornamentals,1.1,2024
+177,ornamentals,0,2024
+178,ornamentals,0,2024
+179,ornamentals,28.2,2024
+180,ornamentals,5.6,2024
+181,ornamentals,1.2,2024
+182,ornamentals,0,2024
+183,ornamentals,18.9,2024
+184,ornamentals,21.3,2024
 185,ornamentals,0,2024
 186,ornamentals,0,2024
 187,ornamentals,0,2024
 188,ornamentals,0,2024
-189,ornamentals,21.5725,2024
+189,ornamentals,0,2024
 190,ornamentals,0,2024
-191,ornamentals,140.3075,2024
+191,ornamentals,8.3,2024
 192,ornamentals,0,2024
 193,ornamentals,0,2024
 194,ornamentals,0,2024
 195,ornamentals,0,2024
-196,ornamentals,3.1799999999999997,2024
+196,ornamentals,0,2024
 197,ornamentals,0,2024
 198,ornamentals,0,2024
-199,ornamentals,0.6085,2024
+199,ornamentals,0,2024
 200,ornamentals,0,2024
-202,ornamentals,144.15,2024
-203,ornamentals,62.979,2024
+202,ornamentals,9.086901564891923,2024
+203,ornamentals,22,2024
 204,ornamentals,0,2024
-205,ornamentals,55.094845472663856,2024
-206,ornamentals,0.4377968394194891,2024
-207,ornamentals,625.3974567651605,2024
-208,ornamentals,673.2823599598491,2024
-209,ornamentals,0.014000000000000002,2024
-210,ornamentals,2.6125000000000003,2024
-212,ornamentals,0.4002279063750713,2024
-214,ornamentals,54.116,2024
+205,ornamentals,0,2024
+206,ornamentals,0,2024
+207,ornamentals,0,2024
+208,ornamentals,0,2024
+209,ornamentals,0,2024
+210,ornamentals,1.8,2024
+212,ornamentals,0,2024
+214,ornamentals,13.1,2024
 215,ornamentals,0,2024
-216,ornamentals,613.645,2024
-218,ornamentals,0.2455,2024
+216,ornamentals,0,2024
+218,ornamentals,0.15,2024
 219,ornamentals,0,2024
 220,ornamentals,0,2024
 221,ornamentals,0,2024
-222,ornamentals,2.0615,2024
+222,ornamentals,1.9,2024
 223,ornamentals,0,2024
 224,ornamentals,0,2024
 227,ornamentals,0,2024
@@ -218,4 +218,4 @@ rgn_id,product,tonnes,year
 247,ornamentals,0,2024
 248,ornamentals,0,2024
 249,ornamentals,0,2024
-250,ornamentals,2.96,2024
+250,ornamentals,2.8,2024