Merging sense_beta (manual conflicts in DESCRIPTION)

.Rbuildignore

@@ -7,4 +7,4 @@
 ^pkgdown$
 ^data-raw$
 ^doc$
-^Meta$
+^Meta$

.github/workflows/secretScan.yml

@@ -10,4 +10,5 @@ jobs:
       with:
         fetch-depth: '2'
     - name: gitleaks-action
-      uses: gitleaks/gitleaks-action@v1.6.0
+      uses: gitleaks/gitleaks-action@v1.6.0
+

NAMESPACE

@@ -38,6 +38,8 @@ export(rsim.params)
 export(rsim.plot)
 export(rsim.run)
 export(rsim.scenario)
+export(rsim.sense)
+export(rsim.sense.path)
 export(rsim.stanzas)
 export(rsim.state)
 export(rsim.step)

NEWS.md

@@ -1,3 +1,9 @@
+# Rpath 0.0.1.3
+
+## Major Changes
+- Added bioenergetic code
+- adjust functions can now supply values by individual months rather than by years
+
 # Rpath 0.0.1.2
 
 ## Major Changes
@@ -72,4 +78,4 @@
 
 Did not keep good track of notes prior to version 0.0.0.9003 - My Bad
 
-The initial files were the code sent by Kerim to Sean on March 31, 2014 (ecopath_sim_r_v0_04_toSean_31_03_14.zip) Files have been renamed to drop the version number and take advantage of this VCS.
+The initial files were the code sent by Kerim to Sean on March 31, 2014 (ecopath_sim_r_v0_04_toSean_31_03_14.zip) Files have been renamed to drop the version number and take advantage of this VCS.

data-raw/Ecosense_EBS_base.csv

@@ -1,55 +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,,
+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,,