sborstein/dietr

Diet Estimated Trophic Levels in R: Estimates fractional trophic level from diet and food item data records in R.

dietr

Diet Estimated Trophic Levels in R: Estimates fractional trophic level from diet and food item data records in R.

dietr's Issues

FoodTroph make user specified iterations possible

It may be useful for users to set the number of iterations to run the routine. Historically, this has been 100 iterations in TrophLab, but we could provide flexibility for users to do more if they want. It would be easy to set this variable and leave the default to 100, which is in TrophLab.

rfishbase 4.0 Compatability

rfishbase just released a new version that significantly changes how they handle data. They try to maintain backwards compatability, but moving to their new data retrieval method should be done and will be included in either dieter 1.1.3 or 1.1.4.

Update Prey Values While Calculating Trophic Levels To Account For Species Who Feed On Species Already Calculated

From reviews of the manuscript. Example, you have a system with a planktivore, omnivore, and piscivore. The omnivore and piscivore are dependent on the planktivore and the piscivore feeds on both. It would calculate the trophic level of the planktivore, incorporate that in the prey trophic level values, then calculate the omnivore, incorporate that into the prey trophic level, and the calculate the piscivore.

This would require some form of a database for updating values and users supplying an order in which trophic level calculations are to be calculated. It also may become difficult for taxa which are cannibalistic as one would not know the trophic level of the same species ahead of time.

Make it Hierarchical

Add hierarchical trophic level calculations. This would allow for easy calculations of individuals->Populations->Species->Family etc. and report all information at all levels.

Prepare for Publication and CRAN submission

Prepare for CRAN and pick a journal to submit to.

Add MFI to CompositeIndices Function

Add Zander 1982 calculation to it. Easy enough to do, just need to code it.

Compound Indices Calculator

Could be nice to have function that calculates Index of Preponderance and Index of Relative Importance. These indices have issues, but are commonly used. These are simple math and easy to implement. Important will be providing checks for proper inputs. Also, it would be cool to do multiple ones at once.

GII for Compound Indices

Add GII from Assis 1996
GIIj = (%FOj + %Nj +%VOLj)(√n)−1, where GIIj = index value for the j-th
prey category and n = the number of relative measures of prey quantities used in the analysis.

Add in Electivity Indices

This should be easy to code. I need to think about the best way users can supply data for ease of use. Could also be done hierarchically so users could calculate it for a specific population all the way to species level? Could calculate the mean from all pops, etc.

Should implement at least Jacob's, Ivlev's, and Chesson's. Could also create plots for highlighting these.

Super customization of prey tables for users to input

Think about flexibility of base functions so users can easily input their own customized prey items and trophic levels.

rfishbase update writes a tmp table causing checks to fail

This is the same issue as the one posted on the rfishbase team by me from March. This is outside of my control to fix as it is specifically an issue with rfishbase. I will contact them to fix it. The package will work, but fail R CMD Check.

Add in Foraging Ratio

This should be easy to code. I need to think about the best way users can supply data for ease of use. Could also be done hierarchically so users could calculate it for a specific population all the way to species level? This may make sense, but could be problematic theoretically as it would probably be a mean.

Add Windell Significance to Compound Indices

“significance” of each food category, calculated as:
S = √(% occurrence)(%composition)

From:
Windell, J.T. 1971. Food analysis and rate of digestion. Pp. 215–226, In W.E. Ricker (Ed.).
Methods for Assessment of Fish Production in Fresh Waters. IBP Handbook No. 3,
Blackwell Scientific, Oxford, UK. 365 pp.

SeaLife Base Diet and Food Item Support

Check that this is possible.

Alternative Prey Values To Include in Package That May Be Useful for Users

Fairly self explanatory. Right now we include FishBase prey values and plan to implement the values for sharks from Cortes, 1999, but there may be additional one users may want to include.

FishBase Update Breaks Convert Function for FishBase Diet Data

The current version doesn't actually return the raw diet data, therefore, it fails to work. I will notify the rfishbase team and post the issue.

Add more features to PlotElectivity

• Allow users to name plots with a list of plot names if more than one index is to be plotted
• Better handling of bars for lots of prey items
• Better handling of legend position

Function for Index of Fullness

Could be useful. Is simple. Probably should be a separate function from electivity indices and compound indices.

Limit prey to only unique combinations

This should:

1. Speed up the functions slightly in general.
2. Limit possible issues when merging prey with their respective trophic levels.

Possibly look into some of the unique combination functions in mgcv.

Memory Allocation Issue with ConvertFishbaseDiet

This appears to be due to a new FishBase update, but it is giving a memory allocation issue as it reads in the data. This may be due to how FishBase handles the diet data. I will be looking at alternative ways to read in the data, but also may contact the FishBase team for help. Note, this appears to be the only function effected at this time and is causing build fails.