shcaba / natural-mortality-tool Goto Github PK

This is readily available for the Hamel model. How would this be done for the others?

These currently show as errors until there is an input.

• For the call to FishLife() , add mfrow = c(2,2). This makes it so the you can see the y-axis label and see what is being plotted against what in each of the figures:
  spp_info <- try(FishLife::Plot_taxa(FishLife::Search_species(Genus=genus, Species=species)$match_taxonomy, mfrow = c(2,2)))

• In output$Mtable2 <- renderTable(...) you no longer need:
  User_M<-input$User_M
  since User_M is now dealt with in output$MtableUser <- renderTable(...)

• "Approximate the density (spelled denisty) function" 'f' is created but not used:
  f <- approxfun(M.densum$x, M.densum$y, yleft=0, yright=0

• Having the weighting for User_M be just UserM and not, e.g. UserM_wt, was confusing.

• You no longer need the wrapper shinyServer() nor shinyUI() as of Shiny 0.10, see the help for each.

• You don't explicitly explain that if one wants an entire group to be down-weighted what is course of action. Is it possible to reduce each member by that value? Continuing your example, if one wants the entire Amax group to be down-weighted by 0.5 compared to the other methods, then would reducing each 0.25 by 0.5 work or not.

Great tool :-)

Fishlife currently crashes the plot if name is spelled wrong. Would like it to not do that.

This could be an alternative way of putting the M prior together.

For Chen and Watanabe and Lorenzen methods, could plot all age values on the plot, and report age specifics values (report already done for C-W). Mark differently the value for age at maturity, which is suggested for use if using only one M value.

This will aid transparency in reporting what people do/what decisions are made.

Some way to attach what values produced what M values.

This would come from adjusting bandwidth.

Add an input to allow the user to connect to FishLife and add its calculated M to the plot and output. Could also consider using other FishLife inputs into other life history values (longevity, Linf, K) applied in the empirical M values. FishLife values may also have a distribution.

Provide expert opinion on how to conduct weighting. Don't be afraid to give opinions on some methods.

For example, multiple longevity values. This would provide a sensitivity that could be included in the prior.

Provide plot of these curves using the point estimates for each method. Also can add the age max if inputted ( as suggested by JW) to help with the life history red face test.

See Thorson, Taylor et al for examples.