Skip to content

Added full dependencies to TMB, spict and stockassessment #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
iagomosqueira wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Added full dependencies to TMB, spict and stockassessment #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 5 additions & 6 deletions FLfse/DESCRIPTION
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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)
Expand Down
13 changes: 13 additions & 0 deletions FLfse/R/FLfse.R
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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"))
Expand Down