jabbamodel/JABBA

example code block error

Opened this issue · 0 comments

efletcherPIFSC commented

jbplot_Crisk

Example roxygen code block for jbplot_Crisk is missing a reference to fit2. This will cause an error if JABBA is checked with its examples. Error checks could be bypassed via \dontrun, however it looks like jbplot_Crisk documentation was designed to have working example code.

JABBA/R/jbplot_fwcrisk.R

Lines 61 to 76 in 425f1cd

#' @examples
#' data(iccat)
#' bet = iccat$bet
#' # Fit Fox and Schaefer
#' jb1 <- build_jabba(catch=bet$catch,cpue=bet$cpue,se=bet$se,scenario = "Fox",model.type="Fox")
#' fit1 = fit_jabba(jb1,quickmcmc=TRUE,verbose=TRUE)
#' # Compare
#' jbplot_ensemble(fit1)
#' # Do forecast
#' prjc = fw_jabba(list(fit1,fit2),quant="Catch",type="abs",imp.values = seq(60,100,1)*1000)
#' jbplot_Crisk(prjc,subplots=1)
#' jbplot_Crisk(prjc,subplots=2)
#' jbplot_Crisk(prjc,subplots=3) # MSST as (1-0.5)*Bmsy with bfrac =0.5
#' jbplot_Crisk(prjc,subplots=3, bfrac=0.2,bref="b0") # Blim = 0.2 B0
#' jbplot_Crisk(prjc,subplots=3, bfrac=0.2,bref="b0",ylabs=expression(B/B[lim])) # Blim = 0.2 B0

Looking further into the example code, fit2 may be extraneous; Removing the variable fixes the error without issue.

jbplot_ensemble

Another example code error was found at jbplot_ensemble. Here is the error log:

 Running examples in 'JABBA-Ex.R' failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: jbplot_ensemble
  > ### Title: jbplot_ensemble()
  > ### Aliases: jbplot_ensemble
  > 
  > ### ** Examples
  > 
  > data(iccat)
  > bet <- iccat$bet 
  > 
  > # Fit Fox and Schaefer
  > jb1 <- build_jabba(catch=bet$catch, 
  +                    cpue=bet$cpue,
  +                    se=bet$se,
  +                    scenario = "Fox",
  +                    model.type="Fox")
  
  ><> Prepare JABBA input data <><
  
  
  
  ><> Assume Catch with error CV = 0.1 <><
  
  
  
  ><> Model type:Fox <><
  
  
  ><> Shape m =1.001
  
  
  ><> K prior mean =1079485.2368and CV =1(log.sd = 0.832554611157698)
  
  
  ><> r prior mean =0.2and CV =0.532940350027788(log.sd = 0.5)
  
  
  ><> Psi (B1/K) prior mean =0.9and CV =0.25withlnormdestribution
  
  
  
  
  ><> ALWAYS ENSURE to adjust default settings to your specific stock <><
  
  
  > jb2 <- build_jabba(catch=bet$catch,
  +                    cpue=bet$cpue,
  +                    se=bet$se,
  +                    scenario = "Schaefer",
  +                    model.type="Schaefer")
  
  ><> Prepare JABBA input data <><
  
  
  
  ><> Assume Catch with error CV = 0.1 <><
  
  
  
  ><> Model type:Schaefer <><
  
  
  ><> Shape m =2
  
  
  ><> K prior mean =1079485.2368and CV =1(log.sd = 0.832554611157698)
  
  
  ><> r prior mean =0.2and CV =0.532940350027788(log.sd = 0.5)
  
  
  ><> Psi (B1/K) prior mean =0.9and CV =0.25withlnormdestribution
  
  
  ><> ALWAYS ENSURE to adjust default settings to your specific stock <><
  
  
  > fit1 <- fit_jabba(jb1,
  +                   quickmcmc=TRUE,
  +                   verbose=TRUE)
  Compiling model graph
     Resolving undeclared variables
     Allocating nodes
  Graph information:
     Observed stochastic nodes: 199
     Unobserved stochastic nodes: 358
     Total graph size: 4305
  
  Initializing model
  
  
  ><> Produce results output of Fox model for jabba Fox <><
  
  
  
  ><> Scenario Fox_Fox completed in 0 min and 33 sec <><
  
  > fit2 <- fit_jabba(jb2,
  +                   quickmcmc=TRUE,
  +                   verbose=TRUE)
  Compiling model graph
     Resolving undeclared variables
     Allocating nodes
  Graph information:
     Observed stochastic nodes: 199
     Unobserved stochastic nodes: 358
     Total graph size: 4305
  
  Initializing model
  
  
  ><> Produce results output of Schaefer model for jabba Schaefer <><
  
  
  
  ><> Scenario Schaefer_Schaefer completed in 0 min and 33 sec <><
  
  > # Compare
  > jbplot_ensemble(list(fit1,fit2))
  Error in kb[kb$type == "prj", ] : incorrect number of dimensions
  Calls: jbplot_ensemble -> pmin
  Execution halted

In the example code block, a list with fit1 and fit2 passes trough jbplot_ensemble as kb. Error occurs where it attempts to look for columns or find data frames subset kb$type == "prj". fit1 and fit2 does not have this column in which throws the error.

JABBA/R/jbplot_ensemble.R

Lines 158 to 160 in 425f1cd

# Constraint on F/Fmsy
kb$harvest[kb$type=="prj"] = pmin(kb[kb$type=="prj",]$harvest,fmax)
kb$H[kb$type=="prj"]= pmin(fmax*median(kb[kb$type=="prj",]$H/kb[kb$type=="prj",]$harvest),kb[kb$type=="prj",]$H)

To resolve this issue Separate list and data frame centric functionality.