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Added full dependencies to TMB, spict and stockassessment #4

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Added full dependencies to TMB, spict and stockassessment #4

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11 changes: 5 additions & 6 deletions FLfse/DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,11 @@ Imports:
foreach,
stats,
utils,
FLCore (>= 2.6.5)
Depends:
Suggests:
spict (>= 1.2.1),
FLCore (>= 2.6.5),
stockassessment (>= 0.9.0),
TMB,
mgcv,
TMB
Depends:
Suggests:
doParallel
RoxygenNote: 7.1.1
RoxygenNote: 7.3.2
3 changes: 3 additions & 0 deletions FLfse/NAMESPACE
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Expand Up @@ -8,6 +8,9 @@ export(getpars)
import(FLCore)
import(foreach)
import(methods)
import(spict)
import(stockassessment)
importFrom(TMB,sdreport)
importFrom(stats,complete.cases)
importFrom(stats,plogis)
importFrom(stats,weighted.mean)
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13 changes: 13 additions & 0 deletions FLfse/R/FLfse.R
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Expand Up @@ -18,3 +18,16 @@ NULL
### import functions from stats
#' @importFrom stats complete.cases plogis weighted.mean
NULL

### import functions from TMB
#' @importFrom TMB sdreport
NULL

### import all functionality from spict
#' @import spict
NULL

### import all functionality from stockassessment
#' @import stockassessment
NULL

2 changes: 1 addition & 1 deletion FLfse/R/sam.R
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Expand Up @@ -1508,7 +1508,7 @@ setMethod(f = "SAM_uncertainty",
##Resample estimated values to get N, F and q

### calculate standard deviations of model parameters
. <- capture.output(sds <- TMB::sdreport(obj = fit$obj,
. <- capture.output(sds <- sdreport(obj = fit$obj,
par.fixed = fit$opt$par,
getJointPrecision = TRUE))
if (isTRUE(print_screen)) cat(paste0(., sep = "\n"))
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