Launch shiny gadget for tuning parameters

The shiny gadget has sliders for the model parameters and tabs with a variety of plots to visualise the steady-state

tuneParams(p, catch = NULL)

Arguments

p	MizerParams object to tune. If missing, the gadget tries to recover information from log files left over from aborted previous runs.
catch	Data frame holding binned observed catch data. The data can be binned either into length bins or weight bins. In the former case the data frame should have columns `length` and `dl` holding the start of the size bins in cm and the width of the size bins in cm respectively. In the latter case the data frame should have columns `weight` and `dw` holding the start of the size bins in grams and the width of the size bins in grams. The data frame also needs to have the columns `species` (the name of the species), `catch` (the number of individuals of a particular species caught in a size bin). This gadget is meant for tuning a model to steady state. It is not meant for tuning the dynamics of the model. That should be done in a second step using functions like `setRmax()` or `changePlankton()`. The function opens a shiny gadget, an interactive web page. This page has a side panel with controls for various model parameters and a main panel with tabs for various diagnostic plots. After you click the "Done" button in the side panel, the function will return the parameter object in the state at that time, with `Rmax` set to `Inf` and `erepro` set to the value it had after the last run to steady state. The gadget keeps a log of all steady states you create while working with the gadget. You can go back to the last steady state by hitting the "Undo" button. You can go back an arbitrary number of states and also go forward again. There is also a button to go right back to the initial steady state. When you leave the gadget by hitting the "Done" button, this log is cleared. If you stop the gadget from RStudio by hitting the "Stop" button, then the log is left behind. You can then restart the gadget by calling `tuneParams()` without a `params` argument and it will re-instate the states from the log. At any time the gadget allows the user to download the current params object as an .rds file via the "Download" button in the "File" section, or to upload a params object from an .rds file. There are currently several restrictions on what the gadget can do: The gadget currently assumes that each species is selected by only one gear. It allows the user to change the parameters for that gear. It also enforces the same effort for all gears. It sets all efforts to that for the first gear and then allows the user to change that single effort value.

MizerParams object to tune. If missing, the gadget tries to recover information from log files left over from aborted previous runs.

catch

Data frame holding binned observed catch data. The data can be binned either into length bins or weight bins. In the former case the data frame should have columns length and dl holding the start of the size bins in cm and the width of the size bins in cm respectively. In the latter case the data frame should have columns weight and dw holding the start of the size bins in grams and the width of the size bins in grams. The data frame also needs to have the columns species (the name of the species), catch (the number of individuals of a particular species caught in a size bin).

This gadget is meant for tuning a model to steady state. It is not meant for tuning the dynamics of the model. That should be done in a second step using functions like setRmax() or changePlankton().

The function opens a shiny gadget, an interactive web page. This page has a side panel with controls for various model parameters and a main panel with tabs for various diagnostic plots.

After you click the "Done" button in the side panel, the function will return the parameter object in the state at that time, with Rmax set to Inf and erepro set to the value it had after the last run to steady state.

The gadget keeps a log of all steady states you create while working with the gadget. You can go back to the last steady state by hitting the "Undo" button. You can go back an arbitrary number of states and also go forward again. There is also a button to go right back to the initial steady state. When you leave the gadget by hitting the "Done" button, this log is cleared. If you stop the gadget from RStudio by hitting the "Stop" button, then the log is left behind. You can then restart the gadget by calling tuneParams() without a params argument and it will re-instate the states from the log.

At any time the gadget allows the user to download the current params object as an .rds file via the "Download" button in the "File" section, or to upload a params object from an .rds file.

There are currently several restrictions on what the gadget can do:

The gadget currently assumes that each species is selected by only one gear. It allows the user to change the parameters for that gear. It also enforces the same effort for all gears. It sets all efforts to that for the first gear and then allows the user to change that single effort value.

Value

The tuned MizerParams object

Launch shiny gadget for tuning parameters

Arguments

Value

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