multisca renamed to scax

flr · Dec 18, 2024 · a0e610c · a0e610c
1 parent 4336231
commit a0e610c
Show file tree

Hide file tree

Showing 9 changed files with 20 additions and 25 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -45,12 +45,12 @@ export(defaultVmod)
 export(defaultSRmod)
 export(a4aSCA)
 export(sca.sa)
+export(scax)
 export(sep.sa)
 #export(makePrediction)
 #export(os.32or64bit)
 #export(os.type)
 #export(plotIters)
-
 exportClasses(a4aFit)
 exportClasses(a4aFits)
 exportClasses(a4aFitResiduals)
@@ -66,7 +66,6 @@ exportClasses(SCAPars)
 exportClasses(a4aStkParams)
 exportClasses(submodel)
 exportClasses(submodels)
-
 exportMethods("distr<-")
 exportMethods("grInvMod<-")
 exportMethods("grMod<-")

diff --git a/NEWS b/NEWS
@@ -2,7 +2,7 @@
 
  NEW FEATURES
 - plot for residuals by age
-- multisca method to run several sca
+- scax method to run several sca
 - plot for multiple fits
 - new classes for plural fit objects
 

diff --git a/R/a4aFitMCMCs-class.R b/R/a4aFitMCMCs-class.R
@@ -99,7 +99,7 @@ setMethod("a4aFitMCMCs", signature(object="missing"),
 #'     )
 #' }
 #' myFits <-
-#'   FLa4a:::multisca(
+#'   scax(
 #'     FLStocks(ple4), list(FLIndices(ple4.index)),
 #'     fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC()
 #'   )

diff --git a/R/a4aFits-class.R b/R/a4aFits-class.R
@@ -100,7 +100,7 @@ setMethod("a4aFits", signature(object="missing"),
 #'     )
 #' }
 #' myFits <-
-#'   FLa4a:::multisca(
+#'   scax(
 #'     FLStocks(ple4), list(FLIndices(ple4.index)),
 #'     fmodel = fmods, qmodel=qmods, fit="MP"
 #'   )

diff --git a/R/fittingFunctions.R b/R/fittingFunctions.R
@@ -1489,9 +1489,9 @@ fitADMB <- function(fit, wkdir, df.data, stock, indices, full.df,
 }
 
 #' @title Run several stock assessments in a single run
-#' @name multisca
+#' @name scax
 #' @docType methods
-#' @rdname multisca
+#' @rdname scax
 #' @description Internal method to run several stock assessment fits with different stocks, indices and submodels
 #' @param stocks an \code{FLStocks} object containing catch and stock information
 #' @param indicess a list of \code{FLIndices} objects containing survey indices
@@ -1504,8 +1504,8 @@ fitADMB <- function(fit, wkdir, df.data, stock, indices, full.df,
 #' @param combination.all  bolean parameter (default is FALSE) to define if a full factorial across all stocks, indices, and submodel is run or just a sequence of runs.
 #' @param ... all other arguments to be passed to \code{sca}
 #' @return an \code{a4aFits} or \code{a4aFitSAs} or \code{a4aFitMCMCs} depending on the argument \code{fit}
-#' @aliases multisca
-# multisca <- function(stocks, indicess,
+#' @aliases scax
+# scax <- function(stocks, indicess,
 #	fmodel = missing,
 #	qmodel = missing,
 #	srmodel = missing,
@@ -1514,7 +1514,7 @@ fitADMB <- function(fit, wkdir, df.data, stock, indices, full.df,
 #	combination.all = FALSE,
 #	...)
 
-multisca <- function(stocks, indicess, fmodel = missing, qmodel = missing, srmodel = missing, n1model = missing, vmodel = missing, combination.all = FALSE, ...){
+scax <- function(stocks, indicess, fmodel = missing, qmodel = missing, srmodel = missing, n1model = missing, vmodel = missing, combination.all = FALSE, ...){
 
 	args <- list(...)
 

diff --git a/man/plot-mfits.Rd b/man/plot-mfits.Rd
diff --git a/man/plot-mmcfits.Rd b/man/plot-mmcfits.Rd
diff --git a/man/multisca.Rd → man/scax.Rd b/man/multisca.Rd → man/scax.Rd
diff --git a/tests/multisca.R → tests/scax.R b/tests/multisca.R → tests/scax.R
@@ -22,7 +22,7 @@ idxss <- list(FLIndices(ple4.index))
 # MP 
 #--------------------------------------------------------------------
 
-fits <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MP")
+fits <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MP")
 
 is(fits, "a4aFits")
 is(fits[[1]], "a4aFit")
@@ -32,7 +32,7 @@ is(fits[[1]], "a4aFit")
 # SA 
 #--------------------------------------------------------------------
 
-fitsa <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="assessment")
+fitsa <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="assessment")
 
 is(fitsa, "a4aFitSAs")
 is(fitsa[[1]], "a4aFitSA")
@@ -41,7 +41,7 @@ is(fitsa[[1]], "a4aFitSA")
 # MCMC 
 #--------------------------------------------------------------------
 
-fitsm <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC())
+fitsm <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC())
 
 is(fitsm, "a4aFitMCMCs")
 is(fitsm[[1]], "a4aFitMCMC")
@@ -74,10 +74,6 @@ stks.mc <- stks + fitsm
 length(stks.mc) == length(fitsm)
 identical(stks.mc[[2]], stks[[1]] + fitsm[[2]])
 
-
-
-
-
 #====================================================================
 # run fits sca multiple stocks and indices
 #====================================================================
@@ -89,7 +85,7 @@ idxss[1:j] <- idxss[1]
 # MP 
 #--------------------------------------------------------------------
 
-fits <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MP")
+fits <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MP")
 
 is(fits, "a4aFits")
 is(fits[[1]], "a4aFit")
@@ -99,7 +95,7 @@ is(fits[[1]], "a4aFit")
 # SA 
 #--------------------------------------------------------------------
 
-fitsa <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="assessment")
+fitsa <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="assessment")
 
 is(fitsa, "a4aFitSAs")
 is(fitsa[[1]], "a4aFitSA")
@@ -108,7 +104,7 @@ is(fitsa[[1]], "a4aFitSA")
 # MCMC 
 #--------------------------------------------------------------------
 
-fitsm <- FLa4a:::multisca(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC())
+fitsm <- scax(stks, idxss, fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC())
 
 is(fitsm, "a4aFitMCMCs")
 is(fitsm[[1]], "a4aFitMCMC")