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stockmonitoringtool's Issues

Selected years info popup text (Dev)

(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

Adjust length data fields (Expert)

(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.

Data Considerations : retitle (Dev)

(Dev) Retitled the Data Considerations tab “Data Loading and Formatting Considerations”

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

t_a info popup (Dev)

(Dev) Add to t_a info page : “Values between 0 and 1. ”

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

Elefan GA's algorithm info fields : text (Expert)

(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

Assessment Settings/Data subtitle (Dev)

(Dev) add a subtitle like: ‘Data settings’ or ‘Data exploration’

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

K info popup (Expert)

(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

MA info popup: text (Expert/Dev)

(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

Allow smaller step for t_a

StockMonitoringTool/ui/elefan/elefanGaUI.R

Line 55 in bad1210

numericInput(ns("ELEFAN_GA_lowPar_t_anchor"), p("Time point anchoring the growth curves in the year-length coordinate system, corresponds to the peak spawning month. The fraction of the year where yearly repeating growth curves cross length equal to zero; for example a value of 0.25 refers to April 1st of any year (", withMathJax("\\(t_{anchor}\\)"), ")"), 0, min = 0, max = 1, step=0.1)

Change step to 0.01. The same should be done for the upper limit (line 70).

Seasonal info popup: text (Dev)

(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

Data load: ignore.case=T (Dev)

(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

Data aggregation info popup (Expert)

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

Data Considerations tab: text edits (Dev)

(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

Make default lower bound data dependent

StockMonitoringTool/ui/elefan/elefanGaUI.R

Line 53 in bad1210

numericInput(ns("ELEFAN_GA_lowPar_Linf"), p("Asymptotic length/length infinity of the von Bertalanffy growth function (",withMathJax("\\(L_\\infty\\)"), "in cm):"), 119, min = 1, max = 1000, step=1),

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.

Prediction range (Expert)

(Expert) Prediction range - please explain the role of this box in the workflow and give advice for users to adjust for their purposes.

reduce function calls 

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:

StockMonitoringTool/assets/tropFishR/elefan_common.R

Line 54 in bad1210

a <- validateElefanInputFile(csvFile)$contents

Supporting Tools: More information (Expert)

(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

Results Consideration tab : text (Expert)

(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

L-W info popup: text (Dev)

(Dev) L-W info popup should give a link to fishbase (even though not dynamically linked due to R version requirements).

t_a: Supporting tools reference (Dev)

(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

Deactivate/hide soVBGF pars

StockMonitoringTool/ui/elefan/elefanGaUI.R

Line 58 in bad1210

numericInput(ns("ELEFAN_GA_lowPar_C"), p("Amplitude of growth oscillation (", withMathJax("\\(C\\)"), "): The higher the value of C the more pronounced are the seasonal oscillations. C = 0 implies that there is no seasonality in the growth rate; if C = 1, the growth rate becomes zero at the winter point."), 0, min = 0, max = 1, step=0.1),

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).

Info page content - error bars (Expert/Dev)

(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

Merge 'Considerations' tab information with popups (Expert)

(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.

  • Figure 1 considerations should be put in the Figure captions directly. Advice for the parameters that are currently in the figure considerations would also be good in the info popup for that parameter. E.g. MA and bin size recommendations.
  • Also note this for bin size : order of operations to be considered: the bin size should be set first and large enough to reduce the noise in the data and at the same time small enough to reduce information loss due to data aggregation

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

Maturity (Expert)

(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.

Bin size info popup (Dev)

(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

Elefan tab: subtitle (Expert)

(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

Information page content (Expert)

Edit the Length-based workflow information page. Remove extraneous information and outline the broad workflow, following the ‘Considerations’ information, i.e.,

  • (Expert) editing the Method Description to that outlined in the Methods Consideration tab , and
  • (Expert) the Data Considerations in the Info page to that outlined in the Data Considerations tab.
  • (Expert) Remove references to ELEFAN and ELEFAN SA except to say that they exist but that Elefan GA is recommended.
  • (Dev) Update reference list

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

T_s info popup: text (Expert)

(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.”

Bin size default and ranges

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.

StockMonitoringTool/ui/elefan/elefanGaUI.R

Line 33 in bad1210

numericInput(ns("ELEFAN_GA_binSize"), "Bin size : length interval over which the length frequency data are aggregated", 4, min = 1, max = 100, step=1),

AE question: how does this work with the bin size issues we had previously?

Method Considerations: assumptions (Expert)

(Expert) Are these assumptions covered in the “Methods Considerations” tab? If not, and they are valid and useful, please consider adding them:

  • Ensure that your length-frequency data is representative of the full population. (If this is not so, then estimates of fishing mortality will be biased.)
  • Ensure that all age groups were sampled.
  • Ensure that the sample was from a range of areas where different life histories might live. (e.g., if juveniles occupy nearshore habitat and adults are offshore)
  • Ensure that a variety of gears with different selectivities used to collect the samples so that the samples contain multiple age groups.

*NB: Issues can be fixed by (Expert) = Tobias, (Dev) = qualified shiny developer

"Workflow Considerations" tab? (Expert/Dev)

(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 :

  1. Upload a size frequency data set (see Data Considerations or the Elefan Sample dataset) [include links here]
  2. Adjust the Assessment Settings:
    a. Data Settings - adjust the aggregation, bin size and moving average (MA) of the dataset to optimise cohort recognition by the Elefan algorithm
    b. Elefan - set the search space of the Elefan algorithm to estimate growth parameters
    c. Stock status - set the parameters required to estimate mortality and perform YPR (and SPR; optional)
  3. Check and Run the Assessment
    a. Run a check on the parameterisations prior to running the full assessment
    b. Run the assessment. Watch for the progress bar in the lower right corner to help
    c. Download the report as a pdf
  4. Further information can be found in the popup information buttons at each field, and in the Data, Methods, and Results Considerations tabs.

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

Methods Considerations : text (Dev)

(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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