Setup Muscle Analysis for OpenSim — setup_muscle_analysis

This function configures and sets up a muscle analysis in OpenSim for a given model. The analysis will run using the specified parameters, with options to save results, and return the analysis tool object for further use.

Usage

setup_muscle_analysis_osim(
  model_file = "model_scaled.osim",
  replace_force_set = FALSE,
  force_set_file = "reserve_actuators.xml",
  results_directory = ".",
  start_time = 0,
  end_time = 3,
  solve_for_equilibrium_for_auxiliary_states = TRUE,
  coordinates_file = NULL,
  controls_file = NULL,
  states_file = NULL,
  in_degrees = TRUE,
  muscle_list = c("bflh_r", "bfsh_r", "semimem_r", "semiten_r"),
  moment_arm_coordinate_list = c("knee_angle_r", "hip_flexion_r"),
  compute_moments = TRUE,
  step_interval = 1,
  setup_filename = "setup_ma.xml",
  write_file = FALSE,
  return_object = TRUE
)

Arguments

model_file: A string specifying the path to the OpenSim model file. Default is "model_scaled.osim".
replace_force_set: A logical indicating whether to replace the force set. Default is FALSE.
force_set_file: A string specifying the path to the force set file (e.g., "reserve_actuators.xml").
results_directory: A string specifying the directory where results will be saved. Default is the current directory ("./").
start_time: A numeric value indicating the start time for the analysis. Default is 0.
end_time: A numeric value indicating the end time for the analysis. Default is 3.
solve_for_equilibrium_for_auxiliary_states: A logical indicating whether to solve for equilibrium for auxiliary states. Default is TRUE.
coordinates_file: A string specifying the path to the coordinates file. Default is NULL.
controls_file: A string specifying the path to the controls file. Default is NULL.
states_file: A string specifying the path to the states file. Default is NULL.
in_degrees: A logical indicating whether to use degrees for coordinate values. Default is TRUE.
muscle_list: A character vector specifying the list of muscles to include in the analysis. Default is `c("bflh_r", "bfsh_r", "semimem_r", "semiten_r")`.
moment_arm_coordinate_list: A character vector specifying the coordinates for moment arm calculation. Default is `c("knee_angle_r", "hip_flexion_r")`.
compute_moments: A logical indicating whether to compute muscle moment arms. Default is TRUE.
step_interval: A numeric value specifying the step interval for the analysis. Default is 1.
setup_filename: A string specifying the filename for the XML setup file. Default is "setup_ma.xml".
write_file: A logical indicating whether to write the analysis tool to an XML file. Default is FALSE.
return_object: A logical indicating whether to return the analysis tool object. Default is TRUE.

Value

If `return_object` is TRUE, returns the OpenSim `AnalyzeTool` object. If neither `write_file` nor `return_object` is TRUE, returns NULL invisibly.