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View Code? Open in Web Editor NEWThis project forked from abennici/stockmonitoringtool
This project forked from abennici/stockmonitoringtool
(Dev) “Select all or a range of years covered by in the uploaded data set to be included in the analysis.”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Adjust length data : bin size will not adjust
What is the reasoning for adjusting the bin size here? It does not adjust, and it does not update when the other bin size field is changed. I recommend removing this box. The same is true for the ‘select years’ field.
(Dev) Retitled the Data Considerations tab “Data Loading and Formatting Considerations”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Population size - add more info to the info box about how to set this - is 100 a standard value?
(Dev) Add to t_a info page : “Values between 0 and 1. ”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Probability of mutation; Probability of crossover; Degree of elitism - explain in the info boxes how these are related to the ElefanGA algorithm and the impact they have on the results
(Dev) add a subtitle like: ‘Data settings’ or ‘Data exploration’
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) More information required to explain ‘K’. How would the user set the parameter range?
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Dev) Add this advice to the MA info popup : “The combination of bin size and MA critically affects the separation of peaks (i.e. potential cohorts) in the dataset and thus the estimation of growth parameters by ELEFAN. A good MA value leads to visually distinct peaks in particular among small length classes.”
(Expert) Also add the rule of thumb regarding the width of the smallest cohort in bins = MA.
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Dev) “The check does not produce and results (figures or tables),”
(Dev) “'Run Assessment' performs the main assessment and should yield plenty of figures and tables in the result ”
(Dev) Add to Amplitude C’s info box: “Values between 0 and 1. ”
Change step to 0.01. The same should be done for the upper limit (line 70).
(Dev) Seasonal model info box could point the user to the Supporting Tools: Seasonal VBGF page
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert/Dev) Download report does not work : Internal Server Error
(Dev) In code, add ignore.case=T for ‘midLengths’ column name when uploading data
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
Variable addl.sqrt
not used for plots returnResults[['plot1']]
and returnResults[['plot1']]
. Use addl.sqrt = addl.sqrt
.
Is there a recommended length of time/resolution of a length-data set or based on the life history of the species? 1 year if monthly, 1 month if daily? Is there a minimum amount of time that the length data should be distributed over (e.g. 1 year)?
You note that aggregation over several years will decrease run time - are there any other reasons to aggregate? Please expand the explanation/advise about how to aggregate.
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
Change upper limit of K to 10. Same is true for upper search space limit (line 69).
Parameters a and b (line 174) used in VPA and YPR should be user input.
(Dev) “A column indicating the length classes of measured individuals (first column of dataset with the column name : midLength).”
(Dev) “The number of caught individuals caught per length class (rows) and per sampling date (columns).”
(Dev) “An example dataset in this format can be downloaded from here~~ ~~.”
(Dev) "The separator for the .csv file should be a comma ‘,’."
italics indicate new text
strikethrough indicates text to delete
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
Default value for lower limit should be data dependent, e.g. 80% of maximum length in the data set. Same is true for default value of upper limit (line 68), e.g. 120% of maximum length.
synLFQ7
is a data object in the TropFishR package. Another name would avoid confusion.
(Expert) Prediction range - please explain the role of this box in the workflow and give advice for users to adjust for their purposes.
a <- validateElefanInputFile(csvFile)$contents
checkDelim<-validateElefanInputFile(csvFile)$checkDelim
check_dec<-validateElefanInputFile(csvFile)$check_dec
check_name<-validateElefanInputFile(csvFile)$check_name
could be simplified to
tmp <- validateElefanInputFile(csvFile)
a <- tmp$contents
checkDelim <- tmp$checkDelim
check_dec <- tmp$check_dec
check_name <- tmp$check_name
reducing the number of function calls and thus reducing the computation time. Link to lines:
(Expert) “More information” in Supporting Tools are missing? Did you delete/hide the additional information text?
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) I find it difficult to navigate between the assessment results info popup and the figures (you cannot simultaneously view the figure and read the caption). It would be simpler to include the full captions directly in the figure and table captions next to the figures and tables.
(Expert) Figure 1 - explain what the blue and red mean in A and B. How these colours can guide the user
(Expert) Table 1. Explain how the user should interpret the phi and Rn
(Dev) L-W info popup should give a link to fishbase (even though not dynamically linked due to R version requirements).
(Dev) For time anchor, it would be good to point the user to the Supporting Tools: VBGF page
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
Hide and/or deactivate parameters of the seasonalised VBGF if it is not being used (if clause dependent on "ELEFAN_GA_seasonalised
"). Do the same for upper bounds of these parameters (lines 73-74).
(Expert/Dev) Is it possible to change the location of the popup comments/error message/progress bar box from the bottom right to the center of the page?
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Info buttons need information for most of the fields in this tab
Set bin size default value to 1, and range to 0.1 and 100. Bin sizes smaller than 1cm might be meaningful for short-lived species.
(Expert) Only 3 methods available in the drop-down - these are the only ones available in TropFishR?
(Expert) Merge the ‘Considerations’ tabs information with the captions and information popups. Users should be able to access all advice on how to parameterise/set values at the popups, e.g.
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Dev) Natural mortality info button should link/refer to the Supporting Tools Natural Mortality tool.
MA
variable not used in this function and thus in the plots returnResults[['plot1']]
and returnResults[['plot2']]
. Use MA = MA
.
(Expert) Maturity - please ensure when including info for this section that you give advice on where Lm50 and Lm75 can be found/how to inform these parameters.
(Dev) Add this advice to the bin size info button : “The combination of bin size and MA critically affects the separation of peaks (i.e. potential cohorts) in the dataset and thus the estimation of growth parameters by ELEFAN. A good bin size value reduces noise in the data by aggregation. ”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Search space for growth parameters: either as a short description under the subtitle here or in the Methods Considerations, indicate that the values input here are a range of values over which the Elefan function will search and determine which combinations lead to the best result.
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
Preliminary results have shown that fishing mortality and selectivity (assuming logistic curve) are more robust than F-at-length estimation from VPA. Further simulations are needed, but so far consider using catch curve to define this vector.
Edit the Length-based workflow information page. Remove extraneous information and outline the broad workflow, following the ‘Considerations’ information, i.e.,
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
If upload data for ELEFAN only contains information about month, year or month and year, causes error.
(Expert) Review this T_s edit from : “At the time of the year when the fraction, (t_{s}) , has elapsed, the growth rate is the highest.” to “The time of the year when growth rate is highest, represented by the fraction of the calendar year, e.g. 0.25 is april 1st.”
Set bin size default value to 1, and range to 0.1 and 100. Bin sizes smaller than 1cm might be meaningful for short-lived species.
AE question: how does this work with the bin size issues we had previously?
(Expert) Are these assumptions covered in the “Methods Considerations” tab? If not, and they are valid and useful, please consider adding them:
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
(Expert) Review and (Dev) add this text. Either include this in the Information page, or possibly add another ‘Considerations’ tab, e.g. “Workflow Considerations” :
“To set up this length-based workflow in the Stock Monitoring Tool :
Note that error messages may display in the center of the page, in a box on the bottom-right, and in place of any figures where an error has occurred.”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
The purpose of this line of code is not clear. It implies that in a data set spanning multiple years, this line of code uses the second to last year is used for the estimation of total mortality. It its important that this variable becomes an input to be set by the user.
(Dev) “Subsequent Consecutive steps of length-based stock assessment routine workflow:”
(Dev) “~~Empirical formulae: ~~Estimation of the natural mortality rate (M).”
*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer
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