de-linked a few non-links

README.md

@@ -195,7 +195,7 @@ The key word arguments available to the user for the ```add_body``` method are d
 
 Once all desired bodies have been added to the Swiftest simulation, the simulation parameters can be accessed and changed using the ```get_parameter``` and ```set_parameter``` methods. The key word arguments available to the user for the ```get_parameter``` and ```set_parameter``` are the same as those described in [simulation_kwargs](README_tables/simulation_kwargs.md).
 
-After all desired parameters have been set, the parameters can be saved to the **<span>param.in</span>** using the ```write_param``` method. The key word arguments available to the user for the ```write_param``` method are described in [write_param_kwargs](README_tables/write_param_kwargs.md).
+After all desired parameters have been set, the parameters can be saved to the **param<span>.in</span>** using the ```write_param``` method. The key word arguments available to the user for the ```write_param``` method are described in [write_param_kwargs](README_tables/write_param_kwargs.md).
 
 The state of the system can be saved to the initial conditions NetCDF file, **<span>init_cond.nc</span>**, using the ```save``` method. The key word arguments available to the user for the ```save``` method are described in [save_kwargs](README_tables/save_kwargs.md).
 
@@ -296,8 +296,8 @@ The number and type of output files generated by Swiftest depends on the input p
 - **<span>data.nc</span>** - Always generated, the output file containing the information for every body in the system, recorded every ```ISTEP_OUT``` timesteps and written every ```DUMP_CADENCE```. This file can be analyzed using the Swiftest Python package (```sim.data```).
 - **collisions.log** - The log containing the record of each fragmentation event, including the collisional regime, and the number of the fragments created, only if ```FRAGMENTATION``` is ```YES```, Swiftest SyMBA only.
 - **swiftest.log** - A log containing a brief update on the status of the run. Only generated if Swiftest is run through the Python package or through a shell script. If Swiftest is run directly through the terminal, these updates are output directly to the terminal.
-- **collisions.nc** - The details of each collision that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.collisions```).
-- **encounters.nc** - The details of each close encounter that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.encounters```).
+- **collisions<span>.nc</span>** - The details of each collision that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.collisions```).
+- **encounters<span>.nc</span>** - The details of each close encounter that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.encounters```).
 - **init_cond.nc** - The initial conditions used to run the simulation. This file can be analyzed using the Swiftest Python package (```sim.init_cond```).
 - **encounter_check_plpl_timer.log** - The log containing the encounter check timer for each massive body/massive body encounter,  only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```.
 - **encounter_check_pltp_time.log** - The log containing the encounter check timer for each massive body/test particle encounter, only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```.