Mismatch with getSummaryTable() return type

[markpayneatwork]

According to the documentation, getSummaryTable() should return a dataframe. However, it returns a list:

> assessmentKey <- findAssessmentKey("cod-2224", year = 2016)
GETing ... http://sg.ices.dk/StandardGraphsWebServices.asmx/getListStocks?year=2016
> sumtab <- getSummaryTable(assessmentKey)
GETing ... http://sg.ices.dk/StandardGraphsWebServices.asmx/getSummaryTable?assessmentKey=7999
> class(sumtab)
[1] "list"
> 

Unsure if this is a bug in the documentation or the code...

[colinpmillar]

Thanks Mark! Yes a documentation problem. It returns a list of data.frames - one for each stock key provided.

so for ecxampe:

assessmentKeys <- findAssessmentKey("cod", year = 2019, full = TRUE)
assessmentKeys <- unique(assessmentKeys) # having to do this indicates a bug though...
sumtab <- getSummaryTable(assessmentKeys$AssessmentKey)
str(sumtab, 1)
# List of 16
#  $ :'data.frame':       44 obs. of  24 variables:
#  $ :'data.frame':       67 obs. of  24 variables:
#  $ :'data.frame':       47 obs. of  24 variables:
#  $ :'data.frame':       74 obs. of  24 variables:
#  $ :'data.frame':       35 obs. of  24 variables:
#  $ :'data.frame':       23 obs. of  24 variables:
#  $ :'data.frame':       35 obs. of  24 variables:
#  $ :'data.frame':       74 obs. of  24 variables:
#  $ :'data.frame':       57 obs. of  24 variables:
#  $ :'data.frame':       57 obs. of  24 variables:
#  $ :'data.frame':       67 obs. of  24 variables:
#  $ :'data.frame':       61 obs. of  24 variables:
#  $ :'data.frame':       55 obs. of  24 variables:
#  $ :'data.frame':       39 obs. of  24 variables:
#  $ :'data.frame':       51 obs. of  24 variables:
#  $ :'data.frame':       49 obs. of  24 variables:
head(
  sumtab[[
    which(
      assessmentKeys$StockKeyLabel == "cod.21.1" & 
      assessmentKeys$Purpose == "Advice"
    )
  ]]
)

#   Year recruitment high_recruitment low_recruitment low_SSB   SSB high_SSB catches landings
# 1 1976       14515            34209            6159    5177  7598    11151      NA     5174
# 2 1977       20885            46241            9433   10904 17996    29702      NA    13999
# 3 1978       44659           104978           18999   17970 32800    59868      NA    19679
# 4 1979       15111            35785            6381   27186 48796    87587      NA    35590
# 5 1980       43223           106786           17495   22570 37858    63502      NA    38571
# 6 1981       16230            35795            7359   17200 25104    36639      NA    39703
#   discards low_F     F high_F StockPublishNote Purpose Fage fishstock recruitment_age
# 1       NA 0.394 0.591  0.888  Stock published  Advice  4-8  cod.21.1               1
# 2       NA 0.420 0.598  0.851  Stock published  Advice  4-8  cod.21.1               1
# 3       NA 0.392 0.537  0.736  Stock published  Advice  4-8  cod.21.1               1
# 4       NA 0.436 0.579  0.769  Stock published  Advice  4-8  cod.21.1               1
# 5       NA 0.501 0.655  0.855  Stock published  Advice  4-8  cod.21.1               1
# 6       NA 0.577 0.755  0.990  Stock published  Advice  4-8  cod.21.1               1
#   AssessmentYear  units stockSizeDescription stockSizeUnits fishingPressureDescription
# 1           2019 tonnes                  SSB         tonnes                          F
# 2           2019 tonnes                  SSB         tonnes                          F
# 3           2019 tonnes                  SSB         tonnes                          F
# 4           2019 tonnes                  SSB         tonnes                          F
# 5           2019 tonnes                  SSB         tonnes                          F
# 6           2019 tonnes                  SSB         tonnes                          F
#   fishingPressureUnits
# 1               Year-1
# 2               Year-1
# 3               Year-1
# 4               Year-1
# 5               Year-1
# 6               Year-1

Will update docs - thanks for this!

[markpayneatwork]

Ok great.

As a design comment, would it not be cleaner to have it returned as a dataframe with the first column being “stock” or similar? There seems to be a move in the R community (at least in the tidyverse anyway) away from lists towards tibbles / dataframes wherever possible?

[colinpmillar]

I think so - we can add an argument, simplifyToDataFrame or similar, which will return a data.frame. with the defaut as FALSE to maintain back compatability.

Will implement and close issue when I push the changes.