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Welcome to the Rceattle wiki!

Rceattle is the TMB based implementation of the CEATTLE model developed by Holsman et al. (2016). Rceattle expands upon the original CEATTLE model by allowing more flexible data inputs and expanding parameterization. Specific updates to the Holsman et al. (2016) model are also described in the header of each CPP file and options for parameterization are described in the meta_data.xlsx file included on the first sheet of the data when written to excel.

Branches are briefly described as follows.

Single-sex models:

• ceattle_classic: The original Holsman et al. (2016) model implemented in TMB/R. Uses ceattle_v01_02.cpp
• ceattle_classic_reorganized: The original Holsman et al. (2016) model implemented in TMB/R but allowing more flexible data inputs via excel files. Also includes multiple additional suitability parameterizations to be estimated. Uses ceattle_v01_04.cpp
• time_varying_q_and_sel: The Holsman et al. (2016) model implemented in TMB/R with flexible data inputs via excel files. Includes time-varying selectivity and time-varying catchability. Analytical catchability/survey variance are also available and Kinzey and Punt (2009) parameterizations are also available. Also includes multiple additional suitability parameterizations to be estimated. Uses ceattle_v01_04.cpp

Two-sex models:

• time_varying_q_sel_2sex2: As above, but allows two-sex population models and comp data can either be jointly estimated or separately estimated for sexes. However, Kinzey and Punt (2009) parameterizations do not work. Uses ceattle_v01_06.cpp
• master: As above. This is the most up to date and currently supported branch.