adds results folders

pyindex/allagg_annual_500_lennosst_ALLsplit_biascorrect/packageDescription.txt

@@ -0,0 +1,83 @@
+Package: VAST
+Type: Package
+Title: Vector-Autoregressive Spatio-Temporal (VAST) Model
+Version: 3.10.0
+Date: 2022-03-18
+Authors@R: c(person(given = "James", family = "Thorson", role = c("aut", "cre"), email = "James.Thorson@noaa.gov",
+             comment = c(ORCID = "0000-0001-7415-1010")), person(given="Cole", family="Monnahan", role="ctb",
+             email="Cole.Monnahan@noaa.gov") )
+Description: VAST is an R package for conducting spatio-temporal analysis of data from multiple categories (species,
+             sizes, etc.), and includes both spatial and spatio-temporal variation in density for each category, with
+             either factor-analysis or autoregressive correlations among categories, with derived calculation of
+             abundance indices, center-of-gravity, and area-occupied.
+Imports: abind, effects, INLA, stats, ThorsonUtilities, utils, remotes, devtools
+Depends: TMB (>= 1.8.0), FishStatsUtils, R (>= 3.5.0)
+Suggests: testthat, knitr, rmarkdown, pscl, tweedie, mgcv, lme4
+Remotes: james-thorson-NOAA/FishStatsUtils@dev, james-thorson/utilities
+Additional_repositories: https://inla.r-inla-download.org/R/stable
+License: file LICENSE
+Encoding: UTF-8
+RoxygenNote: 7.2.0
+ByteCompile: true
+URL: http://github.com/James-Thorson-NOAA/VAST
+BugReports: http://github.com/James-Thorson-NOAA/VAST/issues
+VignetteBuilder: knitr
+RemoteType: github
+RemoteHost: api.github.com
+RemoteRepo: VAST
+RemoteUsername: james-thorson
+RemoteRef: dev
+RemoteSha: 8268ba4d7f2d8a00cc53be1307c88ec23b7716c2
+GithubRepo: VAST
+GithubUsername: james-thorson
+GithubRef: dev
+GithubSHA1: 8268ba4d7f2d8a00cc53be1307c88ec23b7716c2
+NeedsCompilation: no
+Packaged: 2022-08-29 15:10:43 UTC; sarah.gaichas
+Author: James Thorson [aut, cre] (<https://orcid.org/0000-0001-7415-1010>), Cole Monnahan [ctb]
+Maintainer: James Thorson <James.Thorson@noaa.gov>
+Built: R 4.2.1; ; 2022-08-29 15:10:44 UTC; unix
+
+-- File: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/VAST/Meta/package.rds 
+Package: FishStatsUtils
+Type: Package
+Title: Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox
+Version: 2.12.0
+Date: 2022-03-18
+Authors@R: c(person(given = "James", family = "Thorson", role = c("aut", "cre"), email = "James.Thorson@noaa.gov",
+             comment = c(ORCID = "0000-0001-7415-1010")) )
+Description: FishStatsUtils contains utilities (shared code and data) used by multiple packages (VAST,
+             SpatialDeltaGLMM, MIST, Spatial_FA, SpatialDFA, surplus_production, EOFR) that are designed for
+             spatio-temporal analysis of ecological data.
+Imports: abind, alphahull, corpcor, corrplot, DHARMa, ecodist, fastcluster, INLA, plotrix, RANN, raster, reshape2,
+             rgdal, rnaturalearth, rnaturalearthdata, seriation, shape, sp, stats, TMB (>= 1.8.0), TMBhelper (>=
+             1.4.0), utils, viridisLite, spacetime, gstat
+Depends: R (>= 3.5.0), units
+Enhances: tidyr
+Suggests: testthat
+Remotes: kaskr/TMB_contrib_R/TMBhelper
+Additional_repositories: https://inla.r-inla-download.org/R/stable
+License: GPL-3
+LazyData: yes
+BuildVignettes: yes
+Encoding: UTF-8
+RoxygenNote: 7.1.2
+URL: http://github.com/james-thorson-NOAA/FishStatsUtils
+BugReports: http://github.com/james-thorson-NOAA/FishStatsUtils/issues
+RemoteType: github
+RemoteHost: api.github.com
+RemoteRepo: FishStatsUtils
+RemoteUsername: james-thorson
+RemoteRef: dev
+RemoteSha: c25de1767dba25375e35025108bf5ca3f51d5c90
+GithubRepo: FishStatsUtils
+GithubUsername: james-thorson
+GithubRef: dev
+GithubSHA1: c25de1767dba25375e35025108bf5ca3f51d5c90
+NeedsCompilation: no
+Packaged: 2022-08-31 18:24:14 UTC; sarah.gaichas
+Author: James Thorson [aut, cre] (<https://orcid.org/0000-0001-7415-1010>)
+Maintainer: James Thorson <James.Thorson@noaa.gov>
+Built: R 4.2.1; ; 2022-08-31 18:24:21 UTC; unix
+
+-- File: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/FishStatsUtils/Meta/package.rds 

pyindex/allagg_annual_500_lennosst_ALLsplit_biascorrect/parameter_estimates.txt

@@ -0,0 +1,242 @@
+$par
+  ln_H_input   ln_H_input     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft 
+ -0.09926780   0.57828493  -2.90405351  -2.72358536  -2.82203160  -2.92596835  -2.52879718  -2.83994148  -3.04491782  -2.74807118 
+    beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft 
+ -2.80182766  -2.91404593  -2.85087065  -3.01433927  -2.96569168  -2.92213651  -2.87832448  -3.03140713  -3.24083060  -3.42507751 
+    beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft 
+ -3.40595263  -3.45296500  -3.49809469  -3.48137254  -3.11664859  -3.24104515  -3.11191330  -3.12363899  -3.24468220  -2.99092121 
+    beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft     beta1_ft    lambda1_k 
+ -3.38157695  -3.46917866  -3.38464021  -3.31330801  -3.44105325  -3.46461301  -3.42950073  -3.03535466  -3.30441464   0.41445990 
+   lambda1_k    lambda1_k   L_omega1_z L_epsilon1_z    logkappa1     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft 
+  0.01483591   0.04363493   0.56260182   0.36727907  -3.87152545   0.69004135   0.54975307   0.64489404   0.35975243   0.04702710 
+    beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft 
+  0.47555709   0.33017946   0.49202655   0.59610573   0.35074756   0.32940705   0.60807993   0.53048328   0.47532079   0.82344342 
+    beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft 
+  1.01386829   1.10744096   1.10995489   1.07389406   1.18651251   1.15524624   0.96180138   0.91507947   0.98010797   0.83062567 
+    beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft     beta2_ft 
+  0.92136672   1.11044898   1.04210122   1.14193346   0.98389558   1.15432157   1.03207060   0.99272368   1.00145122   1.20252276 
+    beta2_ft     beta2_ft    lambda2_k    lambda2_k    lambda2_k   L_omega2_z L_epsilon2_z    logkappa2    logSigmaM 
+  0.59325417   0.96513901  -0.25511798   0.04047366  -0.01513390   0.42111513   0.63302783  -3.11469495   0.16707952 
+
+$objective
+[1] 49723.06
+attr(,"logarithm")
+[1] TRUE
+
+$iterations
+[1] 22
+
+$evaluations
+function gradient 
+      54       22 
+
+$time_for_MLE
+Time difference of 27.80621 mins
+
+$max_gradient
+[1] 1.406148e-06
+
+$Convergence_check
+[1] "There is no evidence that the model is not converged"
+
+$number_of_coefficients
+ Total  Fixed Random 
+ 42117     89  42028 
+
+$AIC
+[1] 99624.11
+attr(,"logarithm")
+[1] TRUE
+
+$diagnostics
+          Param starting_value     Lower         MLE     Upper final_gradient
+1    ln_H_input    -0.09925301 -5.000000 -0.09926780  5.000000   7.869755e-11
+2    ln_H_input     0.57830079 -5.000000  0.57828493  5.000000  -1.875582e-08
+3      beta1_ft    -2.90402412      -Inf -2.90405351       Inf  -5.288364e-09
+4      beta1_ft    -2.72359267      -Inf -2.72358536       Inf   7.154191e-09
+5      beta1_ft    -2.82201296      -Inf -2.82203160       Inf  -3.010054e-09
+6      beta1_ft    -2.92595855      -Inf -2.92596835       Inf  -1.337916e-10
+7      beta1_ft    -2.52879013      -Inf -2.52879718       Inf   1.662261e-09
+8      beta1_ft    -2.83992039      -Inf -2.83994148       Inf  -2.817308e-09
+9      beta1_ft    -3.04489695      -Inf -3.04491782       Inf  -4.401337e-09
+10     beta1_ft    -2.74804058      -Inf -2.74807118       Inf  -8.340611e-09
+11     beta1_ft    -2.80182129      -Inf -2.80182766       Inf   1.780557e-09
+12     beta1_ft    -2.91401416      -Inf -2.91404593       Inf  -6.926141e-09
+13     beta1_ft    -2.85085661      -Inf -2.85087065       Inf  -1.753548e-09
+14     beta1_ft    -3.01431847      -Inf -3.01433927       Inf  -3.935968e-09
+15     beta1_ft    -2.96567317      -Inf -2.96569168       Inf  -2.310148e-09
+16     beta1_ft    -2.92214339      -Inf -2.92213651       Inf   9.333618e-09
+17     beta1_ft    -2.87832745      -Inf -2.87832448       Inf   7.618250e-09
+18     beta1_ft    -3.03134382      -Inf -3.03140713       Inf  -1.771516e-08
+19     beta1_ft    -3.24084965      -Inf -3.24083060       Inf   1.600247e-08
+20     beta1_ft    -3.42506132      -Inf -3.42507751       Inf  -1.233981e-09
+21     beta1_ft    -3.40593326      -Inf -3.40595263       Inf  -3.108598e-09
+22     beta1_ft    -3.45298686      -Inf -3.45296500       Inf   1.713203e-08
+23     beta1_ft    -3.49807958      -Inf -3.49809469       Inf  -9.666463e-10
+24     beta1_ft    -3.48134540      -Inf -3.48137254       Inf  -5.146328e-09
+25     beta1_ft    -3.11662552      -Inf -3.11664859       Inf  -5.031115e-09
+26     beta1_ft    -3.24104211      -Inf -3.24104515       Inf   3.385116e-09
+27     beta1_ft    -3.11190676      -Inf -3.11191330       Inf   2.742001e-09
+28     beta1_ft    -3.12361091      -Inf -3.12363899       Inf  -8.984786e-09
+29     beta1_ft    -3.24469641      -Inf -3.24468220       Inf   1.308234e-08
+30     beta1_ft    -2.99093218      -Inf -2.99092121       Inf   1.214921e-08
+31     beta1_ft    -3.38157416      -Inf -3.38157695       Inf   3.123182e-09
+32     beta1_ft    -3.46918713      -Inf -3.46917866       Inf   9.198092e-09
+33     beta1_ft    -3.38462353      -Inf -3.38464021       Inf  -2.300259e-09
+34     beta1_ft    -3.31327055      -Inf -3.31330801       Inf  -1.061366e-08
+35     beta1_ft    -3.44101913      -Inf -3.44105325       Inf  -6.674662e-09
+36     beta1_ft    -3.46455916      -Inf -3.46461301       Inf  -9.752952e-09
+37     beta1_ft    -3.42949303      -Inf -3.42950073       Inf   1.440293e-09
+38     beta1_ft    -3.03534854      -Inf -3.03535466       Inf   7.411601e-10
+39     beta1_ft    -3.30439846      -Inf -3.30441464       Inf  -2.181708e-09
+40    lambda1_k     0.41446011      -Inf  0.41445990       Inf  -2.283184e-08
+41    lambda1_k     0.01483593      -Inf  0.01483591       Inf   8.640163e-07
+42    lambda1_k     0.04363484      -Inf  0.04363493       Inf  -4.314575e-07
+43   L_omega1_z     0.56260091      -Inf  0.56260182       Inf  -7.989955e-08
+44 L_epsilon1_z     0.36727831      -Inf  0.36727907       Inf  -1.374760e-06
+45    logkappa1    -3.87153191 -6.390438 -3.87152545 -1.767562   4.548782e-07
+46     beta2_ft     0.69003213      -Inf  0.69004135       Inf   3.293081e-10
+47     beta2_ft     0.54976411      -Inf  0.54975307       Inf   1.084031e-09
+48     beta2_ft     0.64490242      -Inf  0.64489404       Inf  -4.824585e-10
+49     beta2_ft     0.35976345      -Inf  0.35975243       Inf  -3.580389e-10
+50     beta2_ft     0.04702445      -Inf  0.04702710       Inf   1.472447e-09
+51     beta2_ft     0.47550904      -Inf  0.47555709       Inf  -6.782500e-09
+52     beta2_ft     0.33019344      -Inf  0.33017946       Inf  -2.048093e-09
+53     beta2_ft     0.49202897      -Inf  0.49202655       Inf  -6.059722e-10
+54     beta2_ft     0.59611017      -Inf  0.59610573       Inf   1.105395e-09
+55     beta2_ft     0.35073426      -Inf  0.35074756       Inf   4.276774e-10
+56     beta2_ft     0.32941841      -Inf  0.32940705       Inf  -5.205578e-10
+57     beta2_ft     0.60808602      -Inf  0.60807993       Inf  -5.884306e-10
+58     beta2_ft     0.53047194      -Inf  0.53048328       Inf   1.025541e-09
+59     beta2_ft     0.47531753      -Inf  0.47532079       Inf   2.436536e-09
+60     beta2_ft     0.82343791      -Inf  0.82344342       Inf   2.067814e-09
+61     beta2_ft     1.01388547      -Inf  1.01386829       Inf  -5.789133e-09
+62     beta2_ft     1.10743248      -Inf  1.10744096       Inf   2.666052e-09
+63     beta2_ft     1.10993540      -Inf  1.10995489       Inf   8.036061e-10
+64     beta2_ft     1.07390197      -Inf  1.07389406       Inf  -5.314487e-10
+65     beta2_ft     1.18647938      -Inf  1.18651251       Inf  -2.122292e-09
+66     beta2_ft     1.15522730      -Inf  1.15524624       Inf   2.489386e-10
+67     beta2_ft     0.96178809      -Inf  0.96180138       Inf   6.490524e-10
+68     beta2_ft     0.91507782      -Inf  0.91507947       Inf   3.361968e-10
+69     beta2_ft     0.98010716      -Inf  0.98010797       Inf   1.201958e-09
+70     beta2_ft     0.83060816      -Inf  0.83062567       Inf   2.168079e-09
+71     beta2_ft     0.92139959      -Inf  0.92136672       Inf  -8.510781e-09
+72     beta2_ft     1.11045297      -Inf  1.11044898       Inf   1.857821e-09
+73     beta2_ft     1.04210115      -Inf  1.04210122       Inf   2.562263e-09
+74     beta2_ft     1.14195048      -Inf  1.14193346       Inf  -1.660302e-09
+75     beta2_ft     0.98389992      -Inf  0.98389558       Inf   1.313772e-09
+76     beta2_ft     1.15431679      -Inf  1.15432157       Inf   1.323960e-09
+77     beta2_ft     1.03207107      -Inf  1.03207060       Inf  -2.883986e-10
+78     beta2_ft     0.99273733      -Inf  0.99272368       Inf  -2.119675e-09
+79     beta2_ft     1.00141368      -Inf  1.00145122       Inf  -2.089088e-09
+80     beta2_ft     1.20252166      -Inf  1.20252276       Inf   9.524150e-10
+81     beta2_ft     0.59325664      -Inf  0.59325417       Inf   8.011458e-11
+82     beta2_ft     0.96514218      -Inf  0.96513901       Inf   4.596128e-10
+83    lambda2_k    -0.25511847      -Inf -0.25511798       Inf  -3.852529e-08
+84    lambda2_k     0.04047372      -Inf  0.04047366       Inf   1.406148e-06
+85    lambda2_k    -0.01513378      -Inf -0.01513390       Inf  -8.973439e-08
+86   L_omega2_z     0.42111613      -Inf  0.42111513       Inf  -2.257678e-10
+87 L_epsilon2_z     0.63302731      -Inf  0.63302783       Inf  -4.307986e-07
+88    logkappa2    -3.11469575 -6.390438 -3.11469495 -1.767562   1.832629e-07
+89    logSigmaM     0.16707974      -Inf  0.16707952 10.000000  -2.346772e-07
+
+$SD
+sdreport(.) result
+                Estimate  Std. Error
+ln_H_input   -0.09926780 0.107791194
+ln_H_input    0.57828493 0.126336574
+beta1_ft     -2.90405351 0.189698214
+beta1_ft     -2.72358536 0.189643348
+beta1_ft     -2.82203160 0.191951907
+beta1_ft     -2.92596835 0.196049927
+beta1_ft     -2.52879718 0.187542533
+beta1_ft     -2.83994148 0.189768616
+beta1_ft     -3.04491782 0.187693461
+beta1_ft     -2.74807118 0.184756782
+beta1_ft     -2.80182766 0.184426258
+beta1_ft     -2.91404593 0.186163733
+beta1_ft     -2.85087065 0.184261377
+beta1_ft     -3.01433927 0.187977743
+beta1_ft     -2.96569168 0.187951018
+beta1_ft     -2.92213651 0.185049785
+beta1_ft     -2.87832448 0.184330979
+beta1_ft     -3.03140713 0.186468520
+beta1_ft     -3.24083060 0.188596343
+beta1_ft     -3.42507751 0.189230011
+beta1_ft     -3.40595263 0.190958963
+beta1_ft     -3.45296500 0.191603471
+beta1_ft     -3.49809469 0.193308748
+beta1_ft     -3.48137254 0.190414994
+beta1_ft     -3.11664859 0.186669318
+beta1_ft     -3.24104515 0.188654337
+beta1_ft     -3.11191330 0.184549465
+beta1_ft     -3.12363899 0.185294579
+beta1_ft     -3.24468220 0.186397698
+beta1_ft     -2.99092121 0.184749462
+beta1_ft     -3.38157695 0.185478930
+beta1_ft     -3.46917866 0.188391653
+beta1_ft     -3.38464021 0.186915226
+beta1_ft     -3.31330801 0.185997660
+beta1_ft     -3.44105325 0.191120009
+beta1_ft     -3.46461301 0.191177425
+beta1_ft     -3.42950073 0.187559389
+beta1_ft     -3.03535466 0.227333726
+beta1_ft     -3.30441464 0.187093432
+lambda1_k     0.41445990 0.008785974
+lambda1_k     0.01483591 0.000760803
+lambda1_k     0.04363493 0.002117602
+L_omega1_z    0.56260182 0.052568919
+L_epsilon1_z  0.36727907 0.021367151
+logkappa1    -3.87152545 0.096052866
+beta2_ft      0.69004135 0.166131501
+beta2_ft      0.54975307 0.162973461
+beta2_ft      0.64489404 0.165786413
+beta2_ft      0.35975243 0.176185342
+beta2_ft      0.04702710 0.159996142
+beta2_ft      0.47555709 0.163429609
+beta2_ft      0.33017946 0.160694571
+beta2_ft      0.49202655 0.153060408
+beta2_ft      0.59610573 0.152977505
+beta2_ft      0.35074756 0.158131979
+beta2_ft      0.32940705 0.152201554
+beta2_ft      0.60807993 0.157923353
+beta2_ft      0.53048328 0.158095667
+beta2_ft      0.47532079 0.150975049
+beta2_ft      0.82344342 0.150675799
+beta2_ft      1.01386829 0.155290665
+beta2_ft      1.10744096 0.157898616
+beta2_ft      1.10995489 0.160273578
+beta2_ft      1.07389406 0.165537511
+beta2_ft      1.18651251 0.162372594
+beta2_ft      1.15524624 0.170899475
+beta2_ft      0.96180138 0.164486437
+beta2_ft      0.91507947 0.155148010
+beta2_ft      0.98010797 0.162745610
+beta2_ft      0.83062567 0.151704948
+beta2_ft      0.92136672 0.151766773
+beta2_ft      1.11044898 0.156650234
+beta2_ft      1.04210122 0.151239353
+beta2_ft      1.14193346 0.153887433
+beta2_ft      0.98389558 0.157931222
+beta2_ft      1.15432157 0.156492549
+beta2_ft      1.03207060 0.154208488
+beta2_ft      0.99272368 0.165947988
+beta2_ft      1.00145122 0.163895987
+beta2_ft      1.20252276 0.158254115
+beta2_ft      0.59325417 0.218878247
+beta2_ft      0.96513901 0.157296390
+lambda2_k    -0.25511798 0.012271796
+lambda2_k     0.04047366 0.001089763
+lambda2_k    -0.01513390 0.003055112
+L_omega2_z    0.42111513 0.032809287
+L_epsilon2_z  0.63302783 0.033813857
+logkappa2    -3.11469495 0.091236134
+logSigmaM     0.16707952 0.006814471
+Maximum gradient component: 1.406148e-06 
+
+$time_for_sdreport
+Time difference of 42.31323 mins
+
+$time_for_run
+Time difference of 7024.93 secs
+