### Install DYM package from tar.gz (Windows) Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/dym/README.txt Install the DYM package from a tar.gz file using R CMD INSTALL in the Windows command prompt. Ensure Rtools is installed to enable installation from tar.gz files. ```bash R CMD INSTALL dym_0.0.tar.gz ``` -------------------------------- ### Install seamaps from tar.gz (Windows) Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/seamaps/README.txt Install the seamaps package from a tar.gz file using R CMD INSTALL in the Windows command prompt. Ensure Rtools is installed. ```bash R CMD INSTALL seamaps_0.0.tar.gz ``` -------------------------------- ### Run SEAPODYM Usage Instructions Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute this command to display the usage instructions and running options for the SEAPODYM model after installing precompiled binaries. ```bash ~/seapodym/bin/ seapodym -h ``` -------------------------------- ### Install SEAMOVE R Package Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/seamove/README.md Two methods for installing the SEAMOVE R package are provided: using Rtools from a tar.gz file or using the devtools package to install directly from GitHub. ```bash CMD build seamove ``` ```bash R CMD INSTALL seamove_0.0.tar.gz ``` ```R library(devtools) devtools::install_github("[path]/seapodym/rtools/seamove") ``` -------------------------------- ### Install seamaps from GitHub using devtools Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/seamaps/README.txt Install the seamaps package directly from a GitHub repository using the R devtools package. This method does not require building the package first. ```r library(devtools) devtools::install_github("[path]/seapodym/rtools/seamaps") ``` -------------------------------- ### Install libxml2-dev Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Command to install the libxml2 development package, which is required for reading and writing application parameters in XML files. ```bash sudo apt-get install libxml2-dev ``` -------------------------------- ### Install DYM package with devtools (R) Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/dym/README.txt Install the DYM package directly from a GitHub repository using the R devtools package. This method does not require building the package first. ```r library(devtools) devtools::install_github("PacificCommunity/seapodym-codebase/rtools/dym") ``` -------------------------------- ### Multifan-CL Movement Matrix Format Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/seamove/README.md Example of the output file format for movement matrices in Multifan-CL, showing the structure for the first and the 48th age classes. ```text # movement matrices # Movement period 1 age class 1 0.838916915 0.0656896789 4.21166e-05 0.0815094382 0.1457539343 0.6141360933 0.0768163309 0.040903316 0.0005730184 0.3075730943 0.9112193905 0.0142863863 0.0147561323 0.0126011335 0.011922162 0.8633008595 ... # Movement period 4 age class 48 0.4060219046 0.1762980184 0.0365511329 0.009762555 0.4817955074 0.5495944799 0.2966057932 0.0494251044 0.0774210711 0.2225508171 0.5968152217 0.0592941163 0.0347615169 0.0515566846 0.0700278521 0.8815182243 ``` -------------------------------- ### Set ADMB_HOME Environment Variable Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Declare the ADMB_HOME environment variable in your .bashrc file to point to the ADMB installation directory. ```bash export ADMB_HOME=/your-path-to-admb-folder/ ``` -------------------------------- ### Prepare and Run SEAPODYM Skipjack Model Optimization Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Prepare for optimization by copying and modifying the skipjack configuration file to generate pseudo-observations. Then, run the optimization using seapodym_densities. ```bash cd ~/seapodym/example-configs/skipjack/ cp skipjack_F0.xml initparfile.xml seapodym -s initparfile.xml cp output/output_F0/skj_totbm.dym output/output_F0/skj_density_input.dym seapodym_densities initparfile.xml ``` -------------------------------- ### Run SEAPODYM Habitats Usage Instructions Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute this command to display the running options for the SEAPODYM habitats sub-model after compilation. ```bash ~/seapodym/bin/ seapodym_habitats -h ``` -------------------------------- ### Run SEAPODYM Habitat Model in Simulation Mode Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute the habitat model in simulation mode using the '-s' option. The simulation log can be compared with the sim.out file. ```bash cd ~/seapodym/examples-configs/habitat seapodym_habitats -s habitat.xml ``` -------------------------------- ### Compile All SEAPODYM Model Applications Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Run this batch file to compile all SEAPODYM model applications at once. This should be executed from the folder containing the Makefiles. ```bash . all.bat ``` -------------------------------- ### Run SEAPODYM Habitat Model in Optimization Mode Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute the habitat model in optimization mode by omitting the '-s' option. This mode estimates habitat parameters by fitting the model to a priori known habitat fields. Optimization requires significantly more CPU and RAM. ```bash cd ~/seapodym/examples-configs/habitat seapodym_habitats habitat.xml ``` -------------------------------- ### Build DYM package (Linux) Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/dym/README.txt Build the DYM package from the command line on Linux systems. This command should be run outside the downloaded package directory. ```bash CMD build dym ``` -------------------------------- ### Compile SEAPODYM Application Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Compile the main SEAPODYM application from the source code. This command should be run from the directory containing the src directory and Makefiles. ```bash make ``` -------------------------------- ### Run SEAPODYM Habitats Sub-model Compilation Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Compile the sub-model for species habitats using the specified Makefile. ```bash make -f Makefile.hab ``` -------------------------------- ### Run SEAPODYM Skipjack Model in Simulation Mode Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute the skipjack tuna model in simulation mode. Ensure forcing files are downloaded and the SEAPODYM_HOME path is correctly set in the configuration file. ```bash cd example-configs/skipjack/ seapodym -s skipjack_F0.xml ``` -------------------------------- ### Create Symbolic Link for AUTODIF Library Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Create a symbolic link for the optimized AUTODIF library in the ADMB lib folder. Replace 'libadmbo-x86_64-linux-g++11.a' with the actual library file name. ```bash cd ~/admb/lib ln -s libadmbo-x86_64-linux-g++11.a libadmbo.a ``` -------------------------------- ### Run Albacore Tuna Model Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Execute the pre-configured albacore tuna population dynamics model. Ensure the forcing files are in place and the SEAPODYM_HOME environment variable is correctly set in the configuration file. ```bash [~]$ cd example-configs/albacore/ ``` ```bash [~/seapodym/example-configs/albacore/]$ seapodym -s albacore_F0.xml ``` -------------------------------- ### Run SEAMOVE Main Function Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/rtools/seamove/README.md This function processes SEAPODYM flux data to extract, convert units, and plot movement probabilities for Multifan-CL. It aggregates age classes and handles specified age ranges. ```R dir.in <- paste0(ALB.DIR,"/output/") dir.out<-paste0(ALB.DIR,"/output-mfcl/") sea2mfcl.movement(dir.in,dir.out,1979:2010,age.in=5:148,age.plus=FALSE,aggregate.age=3,nbr.in=4) ``` -------------------------------- ### Clone SEAPODYM Source Code Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Download the SEAPODYM source code from the GitHub repository using git clone. ```bash git clone https://github.com/PacificCommunity/seapodym-codebase.git ``` -------------------------------- ### Set LD_LIBRARY_PATH for Shared Libraries Source: https://github.com/pacificcommunity/seapodym-codebase/blob/master/README.md Add this line to your .bashrc file if you intend to use shared (dynamic) libraries for ADMB. ```bash export LD_LIBRARY_PATH=$ADMB_HOME/lib:$LD_LIBRARY_PATH ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. 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