Forced catch fix

.Rbuildignore

@@ -1,7 +1,8 @@
-
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.github$
-^_pkgdown\.yml$
-^docs$
-^pkgdown$
+
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^data-raw$

.gitignore

@@ -4,7 +4,6 @@
 *.png
 *.jpg
 *.tif
-data
 outputs
 code
 *.xlsx

DESCRIPTION

@@ -30,3 +30,5 @@ VignetteBuilder: knitr
 RoxygenNote: 7.1.1
 URL: https://github.com/NOAA-EDAB/Rpath
 BugReports: https://github.com/NOAA-EDAB/Rpath/issues
+Depends: 
+    R (>= 2.10)

R/data.R

@@ -0,0 +1,44 @@
+#' Eastern Bering Sea 1990s Ecopath model (53 biological groups and 1 fleet). 
+#'
+#' Rpath inputs (unbalanaced model).
+#'
+#' @format An Rpath unbalanced model object that contains:
+#' \describe{
+#'   \item{model}{A data.table containing Ecopath unbalanced ecosystem parameters (base parameters and fisheries).}
+#'   \item{diet}{A data.table containing the Ecopath model's diet matrix.}
+#'   \item{stanzas}{Parameters for multistanza groups.}
+#'   \item{pedigree}{A data.table containing the data quality (pedigree) for the Ecopath model.}   
+#'   ...
+#' }
+#' @source Whitehouse and Aydin 2020.  Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath. https://doi.org/10.1016/j.ecolmodel.2020.109074  
+"Ecosense.EBS"
+
+#' Gulf of Alaska (west/central) 1990s Ecopath model (49 biological groups and 1 fleet). 
+#'
+#' Rpath inputs (unbalanaced model).
+#'
+#' @format An Rpath unbalanced model object that contains:
+#' \describe{
+#'   \item{model}{A data.table containing Ecopath unbalanced ecosystem parameters (base parameters and fisheries).}
+#'   \item{diet}{A data.table containing the Ecopath model's diet matrix.}
+#'   \item{stanzas}{Parameters for multistanza groups.}
+#'   \item{pedigree}{A data.table containing the data quality (pedigree) for the Ecopath model.}   
+#'   ...
+#' }
+#' @source Whitehouse and Aydin 2020.  Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath. https://doi.org/10.1016/j.ecolmodel.2020.109074  
+"Ecosense.GOA"
+
+#' Eastern Chukchi Sea Ecopath model (52 biological groups and 1 fleet). 
+#'
+#' Rpath inputs (unbalanaced model).
+#'
+#' @format An Rpath unbalanced model object that contains:
+#' \describe{
+#'   \item{model}{A data.table containing Ecopath unbalanced ecosystem parameters (base parameters and fisheries).}
+#'   \item{diet}{A data.table containing the Ecopath model's diet matrix.}
+#'   \item{stanzas}{Parameters for multistanza groups.}
+#'   \item{pedigree}{A data.table containing the data quality (pedigree) for the Ecopath model.}   
+#'   ...
+#' }
+#' @source Whitehouse and Aydin 2020.  Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath. https://doi.org/10.1016/j.ecolmodel.2020.109074  
+"Ecosense.ECS"

R/param.R

@@ -376,9 +376,9 @@ check.rpath.params <- function(Rpath.params){
   }
 
 if(w == 0){
-  cat('Rpath parameter file is functional.\n')
+  cat('Rpath parameter file is functional. \n')
 } else {
-    cat('Rpath parameter file needs attention!\n')
+    cat('Rpath parameter file needs attention! \n')
   }  
 }
 

data-raw/Ecosense_EBS_base.csv

@@ -0,0 +1,55 @@
+Group,Type,Biomass,PB,QB,EE,ProdCons,BioAcc,Unassim,DetInput,PelDetFate,BenthDetFate,F_Fishery,D_Fishery
+Toothed whales,0,0.03503154,0.06911141,17.39968,,,0,0.2,,0.4,0.6,2.52E-05,0.000006747
+Gray whales,0,0.0326672,0.063365,8.87285,,,0,0.2,,0.4,0.6,0,0
+Other baleen,0,0.5007642,0.02832879,6.642456,,,0,0.2,,0.4,0.6,0.000000183,1.91E-05
+Bowhead whales,0,0.007173534,0.01005034,8.679965,,,0,0.2,,0.4,0.6,0,0
+Other pinnipeds,0,0.04919672,0.09292668,33.97923,,,0,0.2,,0.4,0.6,0.000100598,5.62E-06
+Walrus/bearded seal,0,0.1142484,0.051293,15.37061,,,0,0.2,,0.4,0.6,3.09E-05,5.96E-06
+Wintering seals,0,0.03029022,0.068998,19.19651,,,0,0.2,,0.4,0.6,0.000031609,3.15E-07
+Procellarids,0,0.000920162,0.07456178,73,,,0,0.2,,0.4,0.6,2.20E-09,0.000003567
+Alcids piscivorous,0,0.008617982,0.1623509,72.05511,,,0,0.2,,0.4,0.6,2.08E-08,3.34E-05
+Larids,0,0.000767614,0.08903116,104.9432,,,0,0.2,,0.4,0.6,1.90E-09,2.98E-06
+Alcids planktivorous,0,0.001754495,0.1694877,110,,,0,0.2,,0.4,0.6,4.20E-09,6.80E-06
+Other seabirds,0,0.000101753,0.06846981,76.18891,,,0,0.2,,0.4,0.6,2.00E-10,3.94E-07
+Cormorants,0,0.000149799,0.1587271,73,,,0,0.2,,0.4,0.6,4.00E-10,5.81E-07
+Sharks,0,0.0532473,0.1,3,,,0,0.2,,0.4,0.6,1.55E-05,0.000695172
+Walleye pollock,0,22.97889,0.8208976,4.193416,,,0,0.2,,0.392,0.608,0.4041824,2.104923
+Pacific cod,0,2.650923,0.5080103,2.739351,,,0,0.2,,0.392,0.608,0.2240711,0.1983278
+Pelagic forage fish,0,7.644652,0.7672387,3.732284,,,0,0.2,,0.392,0.608,0.02158515,0.007684128
+Lg.-mouth flatfish,0,1.58756,0.1937844,1.213555,,,0,0.2,,0.392,0.608,0.01807182,0.04641179
+Sm.-mouth flatfish,0,11.31311,0.2096047,1.325415,,,0,0.2,,0.392,0.608,0.1925451,0.2227745
+Skates,0,0.7733867,0.2,2,,,0,0.2,,0.392,0.608,0.004292543,0.02400982
+Other demersals,0,1.382284,0.2117719,2.526838,,,0,0.2,,0.392,0.608,0.01536881,0.01027679
+Eelpouts,0,2.371533,0.4,2,,,0,0.2,,0.392,0.608,0,0
+Lg.-mouth sculpins,0,0.5403231,0.4,2,,,0,0.2,,0.392,0.608,0.000573506,0.009394558
+Other sculpins,0,1.136692,0.4,2,,,0,0.2,,0.392,0.608,0,0
+Misc. shallow fish,0,1.167694,0.4,2,,,0,0.2,,0.392,0.608,1.13E-05,3.58E-05
+Octopods,0,0.192476,0.8,3.65,,,0,0.2,,0.392,0.608,7.99E-05,0.000228618
+Squids,0,0.9269976,3.2,10.67,,,0,0.2,,0.392,0.608,0.000454888,0.000875192
+Salmon returning,0,0.1637697,1.65,11.6,,,0,0.2,,0.392,0.608,0.1691487,0.00067146
+Salmon outgoing,0,0.0141972,1.28,13.56,,,0,0.2,,0.392,0.608,0,0
+Other crabs,0,3.244238,0.9338375,3.872315,,,0,0.2,,0.1,0.9,0.06657811,0.003027228
+Snow crab,0,2.178832,1.295101,3.117084,,,0,0.2,,0.1,0.9,0.3006897,0.006839902
+Shrimps,0,19.44489,0.5756463,2.40941,,,0,0.2,,0.1,0.9,2.25E-07,0.000001989
+Sea stars,0,2.471359,1.21,6.05,,,0,0.2,,0.1,0.9,3.87E-05,0.006488753
+Brittle stars,0,2.950093,1.21,6.05,,,0,0.2,,0.1,0.9,0,0
+Urchins dollars cucumbers,0,1.167418,0.61,3.05,,,0,0.2,,0.1,0.9,3.48E-07,6.56E-05
+Snails,0,0.8071689,1.81,9.049999,,,0,0.2,,0.1,0.9,1.88E-07,1.80E-05
+Misc. crustacean,0,8.88581,7.4,37,,,0,0.2,,0.1,0.9,0,0
+Benthic amphipods,0,12.79612,7.4,37,,,0,0.2,,0.1,0.9,0,0
+Anemones,0,0.1095207,1,5,,,0,0.4,,0.1,0.9,4.31E-07,0.000384743
+Corals and sea pens,0,0.02658792,0.06929576,0.3464788,,,0,0.4,,0.1,0.9,3.25E-07,0.000025347
+Worms etc.,0,3.905683,2.155615,10.77807,,,0,0.4,,0.1,0.9,0,0
+Benthic urochordate,0,0.3544967,3.58,17.9,,,0,0.4,,0.1,0.9,6.09E-06,0.001505825
+Sponge,0,0.05448509,1,5,,,0,0.4,,0.1,0.9,1.91E-06,0.00064731
+Bivalves,0,61.87307,1.3,6.5,,,0,0.4,,0.1,0.9,2.33E-08,1.11E-07
+Polychaetes,0,21.68738,2.97,14.85,,,0,0.4,,0.1,0.9,0,0
+Scyphozoid Jellies,0,0.3379304,0.88,3,,,0,0.2,,0.4,0.6,0.003364776,0.01527125
+Other zooplankton,0,22.7485,5.253331,15.00952,,,0,0.2,,0.4,0.6,0,0
+Copepods,0,26.85738,6,27.74,,,0,0.2,,0.4,0.6,0,0
+Pelagic microbes,0,45,36.5,104.2857,,,0,0.25,,0.4,0.6,0,0
+Benthic microbes,0,22.06101,36.5,104.2857,,,0,0.25,,0.1,0.9,0,0
+Primary production,1,48.60443,99.40636,,,,0,0,,0.4004332,0.5995669,0,0
+Pelagic detritus,2,,0.5,,,,0,0,0,0,0,0,0
+Benthic detritus,2,,0.5,,,,0,0,0,0,0,0,0
+Fishery/Subsistence,3,,,,,,,,,0.2278577,0.7721423,,

data-raw/Ecosense_EBS_diet.csv

@@ -0,0 +1,55 @@
+DIETS,Toothed whales,Gray whales,Other baleen,Bowhead whales,Other pinnipeds,Walrus/bearded seal,Wintering seals,Procellarids,Alcids piscivorous,Larids,Alcids planktivorous,Other seabirds,Cormorants,Sharks,Walleye pollock,Pacific cod,Pelagic forage fish,Lg.-mouth flatfish,Sm.-mouth flatfish,Skates,Other demersals,Eelpouts,Lg.-mouth sculpins,Other sculpins,Misc. shallow fish,Octopods,Squids,Salmon returning,Salmon outgoing,Other crabs,Snow crab,Shrimps,Sea stars,Brittle stars,Urchins dollars cucumbers,Snails,Misc. crustacean,Benthic amphipods,Anemones,Corals and sea pens,Worms etc.,Benthic urochordate,Sponge,Bivalves,Polychaetes,Scyphozoid Jellies,Other zooplankton,Copepods,Pelagic microbes,Benthic microbes,Primary production
+Toothed whales,6.47E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Gray whales,0.000133081,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other baleen,0.002040034,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Bowhead whales,2.92E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other pinnipeds,0.000205117,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Walrus/bearded seal,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Wintering seals,,,,,,0.001017812,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Procellarids,,,,,,,,6.33E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Alcids piscivorous,,,,,,,,0.00059265,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Larids,,,,,,,,5.28E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Alcids planktivorous,,,,,,,,0.000120655,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other seabirds,,,,,,,,7.00E-06,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Cormorants,,,,,,,,1.03E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Sharks,0.000239291,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Walleye pollock,0.1698044,,0.08070278,,0.2811362,,0.4888999,0.1655044,0.2614391,0.2021952,0.002550183,0.1678919,0.02434087,0.2,0.08240532,0.2243627,,0.5571692,0.03047612,0.4114217,0.004290166,0.00395613,0.1298186,,,,,,,,,,,,,,,,,,,,,,,0.001,,,,,
+Pacific cod,0.01947363,,,,0.01366742,,0.0049334,0.007216445,0.1888303,0.008816263,0.000111195,0.007320547,0.001061329,,0.000594541,0.00446721,,0.006268422,3.22E-05,0.006085007,,,0.000913099,0.04028247,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Pelagic forage fish,0.2487804,,0.1201802,,0.2320068,,0.1287617,0.3508018,0.3939846,0.6618846,0.05411142,0.3104237,0.931414,,0.005597626,0.03139776,,0.0777799,0.04213176,0.0297038,0.004689368,0.01307451,0.08628711,,,,0.15,,,,,,,,,,,,,,,,,,,0.008,,,,,
+Lg.-mouth flatfish,0.001034033,,,,5.86E-06,,,,,,,,,0.2,0.000824726,0.001458564,,0.002081271,6.93E-05,0.02431003,1.60E-06,,0.000360408,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Sm.-mouth flatfish,0.006842509,,,,0.08088505,,0.0394672,,,,,,,,0.000164344,0.02012908,,0.02068678,0.000488947,0.09006111,0.000020214,7.38E-06,0.03985396,0.009723351,0.007394266,,,,,,,,,,,,,,,,,,,,,,,,,,
+Skates,0.003475559,,,,,,,,,,,,,,,5.18E-07,,1.45E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other demersals,0.005536608,,,,0.01134714,,,0.000564447,0.000998577,0.000999001,0.001003092,0.000032534,0.00084674,0.2,4.84E-07,0.001655552,,0.001043523,,,0.000351201,,5.16E-06,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Eelpouts,0.141124,,,,0.008174762,,0.05969413,,,,,,,,0.000426192,0.03098069,,0.04269749,0.001878417,0.08047485,3.13E-06,0.01845699,0.03330814,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Lg.-mouth sculpins,,,,,,,,,,,,,,,7.54E-06,0.001176434,,0.0002093,1.93E-05,0.000021452,0.000121231,,0.001836508,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other sculpins,0.05504273,,,,0.01009857,,0.07893439,,,,,,,,0.000323667,0.01049386,,0.01287026,0.001030404,0.02096508,0.000147024,0.01351007,0.02105363,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Misc. shallow fish,0.03660734,,0.01555704,,0.02213815,,0.09866799,,,,,,,0.02,8.52E-05,0.003238108,,0.004294502,0.000809832,0.007287188,5.99E-06,0.000986537,0.01898878,0.04985736,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Octopods,0.005624069,,,,0.02070426,0.01017812,0.009866798,,,,,,,0.02,2.62E-05,0.005013016,,0.000651224,7.19E-05,,0.000360057,,0.01435832,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Squids,0.2922446,,0.002097894,,0.2519298,,0.00049334,0.4435776,0.03470331,0.006531665,0.00074037,0.503465,,0.2,0.001616147,0.00071992,,0.07333685,0.00012839,2.53E-05,0.2840489,,6.85E-05,,,,,0.2,,,,,,,,,,,,,,,,,,0.001,,,,,
+Salmon returning,0.01169868,,0.005824628,,0.008696572,,,,,,,,,0.05,,0.001279095,,,,0.02247792,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Salmon outgoing,7.14E-08,,3.56E-08,,0.008696572,,,,,,,7.53E-08,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other crabs,,0.002564021,,0.001170194,0.01055097,0.006252694,0.009866799,,,,,,0.000783198,0.0025,0.001008549,0.1117827,,0.01110253,0.01499601,0.05703641,0.001302062,0.008096965,0.06165776,0.05453778,0.000531343,0.15,,,,0.005500491,0.06013035,,0.01,,,,,,,,,,,,,,,,,,
+Snow crab,,0.001909877,,0.000871649,0.000698742,0.003925424,,,,,,,0.00121494,,1.81E-05,0.05749471,,0.004300768,0.004455289,0.0300742,,0.09333689,0.03866288,,,0.05,,,,,,,0.005,,,,,,,,,,,,,,,,,,
+Shrimps,,0.01358641,,0.006200707,0.02408229,0.02035623,0.0542674,,,,,,0.0086428,0.005,0.03297897,0.1420867,0,0.05616299,0.08154,0.07128841,0.2867417,0.01367033,0.1972778,0.5433436,0.225388,,,,,,,,0.01,,,,,,,,,,,,,,,,,,
+Sea stars,,0.001959092,,0.000894111,,,,,,,,,,,2.83E-05,0.00012312,,1.04E-08,3.16E-06,0.00055577,4.92E-06,,5.38E-05,,,,,,,0.000382242,0.000603733,,,,,,,,,,,,,,,,,,,,
+Brittle stars,,0.002253839,,0.00102863,,,,,,,,,,,3.63E-05,0.000185201,,6.63E-05,0.05973076,5.11E-05,2.43E-06,0.1822525,0.000102108,0.000181826,,,,,,0.01228855,0.07161608,,0.03,,,,,,,,,,,,,,,,,,
+Urchins dollars cucumbers,,0.000840129,,0.000383427,0.01513655,,,,,,,,,,1.25E-07,0.000107477,,5.44E-06,0.02279872,8.06E-08,,,2.12E-05,,,,,,,0.01201729,0.007422531,,,,,,,,,,,,,,,,,,,,
+Snails,,0.000502282,,0.000229237,2.21E-05,0.0610687,,,,,,,,0.0025,0.000179459,0.004685467,,0.000333693,0.007431038,0.000301499,0.000000029,,0.001372771,,,0.4,,,,0.01685826,0.04829947,,0.005,,,,,,,,,,,,,,,,,,
+Misc. crustacean,,0.006993907,,0.003191952,,,,0.004287296,0.009203487,0.003571809,0.00072099,3.73E-05,0.004449074,,0.007055759,0.002030444,,2.65E-05,0.02593507,0.000023285,4.31E-07,0.005357117,0.000792121,0.01442491,4.38E-05,,,,,0.001538223,0.01720634,,,,,,,,0.125,0.125,0.003506872,0.125,0.125,0.125,,,,,,,
+Benthic amphipods,,0.9,,0.004360963,,,,6.32E-05,,0.004879939,0.000985044,5.10E-05,0.006078489,,0.03478977,0.1104455,2.96E-06,0.001273519,0.09940312,0.008388263,0.001051775,0.3280452,0.05959997,0.1947338,0.09178961,,,,,0.005461351,0.04782058,0.3,,0.1,,,,,0.125,0.125,0.003506872,0.125,0.125,0.125,,,,,,,
+Anemones,,8.68E-05,,3.96E-05,,,,,,,,,,,,,,,,,,,,,,,,,,,0.001850753,,,,,,,,,,,,,,,,,,,,
+Corals and sea pens,,2.11E-05,,9.62E-06,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Worms etc.,,0.002718438,,0.001240668,,0.1832061,0.02614701,1.69E-05,,0.001301065,0.000262628,1.36E-05,,,0.001353052,0.02704704,,0.000266081,0.09399602,5.84E-05,7.86E-07,0.02537635,0.01925321,0.03702217,,,,,,0.2085163,0.03021216,,0.01,,,0.2,,,,,,,,,,,,,,,
+Benthic urochordate,,0.000281016,,0.000128253,,,,,,,,,,,1.68E-05,0.000549436,,3.16E-06,0.002288761,1.66E-06,0.000489444,,,,,,,,,0.000570783,,,,,,,,,,,,,,,,,,,,,
+Sponge,,4.32E-05,,1.97E-05,,,,,,,,,,,5.47E-05,4.36E-05,,9.00E-10,9.09E-05,7.98E-06,,,,,,,,,,0.00023874,0.002601985,,,,,,,,,,,,,,,,,,,,
+Bivalves,,0.04904792,,0.022385,2.21E-05,0.7139949,,0.00032442,,0.02504892,0.005056271,0.000261789,,,0.000490379,0.00165732,,0.000577568,0.08503099,2.78E-05,8.08E-06,0.05257819,0.000393605,,,0.4,,,,0.2533802,0.2524816,0.1,0.91,,,0.2,,,,,,,,,,,,,,,
+Polychaetes,,0.01719198,,0.007846256,,,,0.000113714,,0.008779998,0.001772293,9.18E-05,,,0.00366851,0.03710564,3.12E-05,0.000641417,0.3154908,0.002781462,0.000225772,0.2386699,0.10978,0.02550208,1.19E-05,,,,,0.263431,0.2847306,,0.02,,,0.2,,,,,,,,,,,,,,,
+Scyphozoid Jellies,,,,,,,,,,,,,,,2.91E-05,3.76E-06,,1.33E-06,0.001530271,1.47E-05,0.0001446,,7.51E-06,,0.06429844,,,,,,,,,,,,,,,,,,,,,,,,,,
+Other zooplankton,,,0.5746825,0.55,,,,0.01148704,0.04877095,0.03297732,0.4103911,0.004580894,0.008569111,,0.4335781,0.1106963,0.9033016,0.09674293,0.09784253,0.000493316,0.3819539,0.001346271,0.1561293,0.01137116,0.6102213,,0.65,0.6,0.5,,0.004736442,0.2,,,,,,,,,,,,,,0.74,0.008073313,,,,
+Copepods,,,0.200955,0.4,,,,0.01519615,0.06206967,0.04196949,0.5222954,0.00583,0.01259939,,0.3857745,0.001424687,0.09666412,0.000011405,0.00054752,,0.03367182,,2.77E-05,0.01865575,0.000321321,,0.2,0.2,0.5,,,,,,,,,,,,,,,,,0.15,0.25,,,,
+Pelagic microbes,,,,,,,,,,,,,,,1.93E-06,8.57E-06,,,0.000224104,,,0.00065419,,0.000363653,,,,,,,,,,,,,,,,,,,,,,0.05,0.15,0.5,,,
+Benthic microbes,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.5,0.5,0.15,0.15,0.4901808,0.15,0.15,0.15,0.5,,,,,,
+Primary production,,,,,,,,,,,,,,,,1.85E-05,,1.76E-07,5.60E-09,,,,,,,,,,,0.001516897,0.004452738,,,,0.25,0.2,,,,,,,,,,0.05,0.5919268,0.5,0.7,,
+Pelagic detritus,,,,,,,,,,0.00104472,,,,,,,,,,,,,,,,,,,,0.000994342,0.005903513,,,,,,,,,,,,,,,,,,0.3,,
+Benthic detritus,,,,,,,,,,,,,,0.1,0.006865464,0.0561312,,0.02938087,0.009528337,0.1360623,0.000363454,0.00062444,0.008015924,,,,,,,0.2173052,0.1599311,0.4,,0.9,0.75,0.2,0.5,0.5,0.6,0.6,0.5028055,0.6,0.6,0.6,0.5,,,,,1,
+Import,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

data-raw/Ecosense_EBS_pedigree.csv

@@ -0,0 +1,54 @@
+Group,B,PB,QB,Diet,F_Fishery/Subsistence
+Toothed whales,0.8,0.6,0.6,0.8,0.3
+Gray whales,0.5,0.6,0.6,0.8,0
+Other baleen,0.8,0.6,0.6,0.8,0.3
+Bowhead whales,0.5,0.1,0.6,0.8,0
+Other pinnipeds,0.5,0.6,0.8,0.8,0.3
+Walrus/bearded seal,0.5,0.6,0.6,0.7,0.3
+Wintering seals,0.5,0.6,0.6,0.7,0.3
+Procellarids,0.8,0.6,0.6,0.8,0.5
+Alcids piscivorous,0.5,0.6,0.6,0.8,0.5
+Larids,0.5,0.6,0.6,0.8,0.5
+Alcids planktivorous,0.5,0.6,0.6,0.8,0.5
+Other seabirds,0.8,0.6,0.6,0.8,0.5
+Cormorants,0.5,0.6,0.6,0.8,0.5
+Sharks,0.5,0.7,0.7,0.8,0.7
+Walleye pollock,0.5,0.4,0.4,0.1,0.1
+Pacific cod,0.8,0.4,0.4,0.1,0.7
+Pelagic forage fish,0.8,0.7,0.7,0.8,0.5
+Lg.-mouth flatfish,0.8,0.6,0.8,0.3,0.7
+Sm.-mouth flatfish,0.8,0.6,0.8,0.7,0.3
+Skates,0.5,0.7,0.7,0.7,0.7
+Other demersals,0.8,0.7,0.8,0.8,0.8
+Eelpouts,0.8,0.7,0.7,0.8,0.7
+Lg.-mouth sculpins,0.1,0.7,0.7,0.3,0.8
+Other sculpins,0.8,0.7,0.7,0.3,0
+Misc. shallow fish,0.8,0.7,0.7,0.7,0.7
+Octopods,0.8,0.7,0.7,0.8,0.4
+Squids,0.8,0.7,0.7,0.8,0.4
+Salmon returning,0.8,0.5,0.8,0.7,0.3
+Salmon outgoing,0.8,0.6,0.6,0.8,0
+Other crabs,0.8,0.6,0.8,0.8,0.8
+Snow crab,0.1,0.6,0.8,0.7,0.3
+Shrimps,0.8,0.6,0.8,0.8,0.5
+Sea stars,0.5,0.6,0.7,0.8,0.8
+Brittle stars,0.8,0.6,0.7,0.8,0
+Urchins dollars cucumbers,0.8,0.6,0.7,0.8,0.5
+Snails,0.8,0.6,0.7,0.8,0.5
+Misc. crustacean,0.8,0.6,0.7,0.8,0
+Benthic amphipods,0.8,0.6,0.7,0.8,0
+Anemones,0.5,0.6,0.7,0.8,0.5
+Corals and sea pens,0.5,0.6,0.7,0.8,0.5
+Worms etc.,0.8,0.6,0.7,0.8,0
+Benthic urochordate,0.5,0.6,0.7,0.8,0.5
+Sponge,0.5,0.6,0.7,0.8,0.5
+Bivalves,0.8,0.6,0.7,0.8,0.5
+Polychaetes,0.8,0.6,0.7,0.8,0
+Scyphozoid Jellies,0.5,0.6,0.6,0.8,0.5
+Other zooplankton,0.8,0.7,0.8,0.8,0
+Copepods,0.8,0.7,0.8,0.8,0
+Pelagic microbes,0.8,0.7,0.7,0.8,0
+Benthic microbes,0.8,0.7,0.7,0.1,0
+Primary production,0.8,0.7,0,0.01,0
+Pelagic detritus,0.8,0,0,0,0
+Benthic detritus,0.8,0,0,0,0