FIMS
v0.11.0
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intro to fims
introducing the fisheries integrated modeling system (fims)
introducing FIMS input data
FIMS Growth with VonBertalanffySchnute
introducing the fims logging system
fims user setup guide
simple projections using fims
running diagnostics on a FIMS model
developer
adding a new c++ module
fims path - maturity
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intro to c++
intro to rcpp
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re sparsity
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config.h
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// RTMB configuration to include by TMB.h
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// Prevent Rcpp from masking valid uses of Rf_error
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#undef RCPP_NO_MASK_RF_ERROR
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#define RCPP_NO_MASK_RF_ERROR
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#include "
../rcpp/rcpp_include.hpp
"
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// Any failed internal assertion sends Rcpp::exception
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#define TMB_ABORT Rcpp::stop("TMB unexpected")
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// Catch *all* std exceptions (not just bad_alloc)
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#define TMB_CATCH catch(std::exception& excpt)
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// Do not include TMB's thread-safe workarounds
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#ifdef _OPENMP
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#define TMB_HAVE_THREAD_SAFE_R
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#endif
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// Use TMBad
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#define TMBAD_FRAMEWORK
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// Use 64 bit integers to ensure sizeof(ad)=16 (128 bit)
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#define TMBAD_INDEX_TYPE uint64_t
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// Enable out-of-bounds checking
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#define TMB_SAFEBOUNDS
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// TMB FIXME: Some occurrences of ASSERT and ASSERT2
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#undef ASSERT
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#define ASSERT(x) TMBAD_ASSERT(x)
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#undef ASSERT2
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#define ASSERT2(x, msg) TMBAD_ASSERT2(x, msg)
rcpp_include.hpp
The single place FIMS includes Rcpp. Include this header instead of <Rcpp.h> so that every translatio...
inst
include
interface
TMB
config.h
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