Merge pull request #111 from PIFSCstockassessments/fix-109-r4ss-depen…

…dency

gh::gh NA_character token; r4ss 1.49.3 dependency

DESCRIPTION

@@ -20,11 +20,12 @@ Depends:
     R (>= 3.5)
 Imports:
     dplyr,
+    gh,
     gplots,
     lifecycle,
     magrittr,
     mvtnorm,
-    r4ss (>= 1.46.1),
+    r4ss (== 1.49.3),
     randtests,
     reshape2,
     rlang
@@ -34,9 +35,9 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 Remotes: 
-    r4ss/r4ss@main
+    r4ss/r4ss@v1.49.3
 Encoding: UTF-8
 LazyData: True
 LazyDataCompression: gzip
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -19,7 +19,9 @@ export(SSretroComps)
 export(SSrmse)
 export(SSrunstest)
 export(SSsettingsBratioF)
+export(get_ss3_exe)
 export(ssruns_sig3)
+import(gh)
 importFrom(gplots,ci2d)
 importFrom(grDevices,adjustcolor)
 importFrom(grDevices,dev.new)

R/SSdeltaMVLN_old.R

@@ -3,7 +3,7 @@
 #' A function to generate kobe pdfs from a Multivariate Log-Normal Distribution including plotting option. This version is used for older versions of Stock Synthesis. For newer versions (v3.24 and newer), use SSdeltaMVLN().
 #'
 #'
-#' @param ss3rep from r4ss::SSgetoutput()$replist1
+#' @param ss3rep from r4ss::SSgetoutput()[["replist1"]]
 #' @param status covarying stock status quantaties to extract from Hessian
 #' @param quants additional stock quantaties to extract from Hessian
 #' @param Fref  Choice of reference point for stock SSB/XFref=c("MSY","Ftrg"),only if F_report_basis: 0 or 3

R/SSkobe.R

@@ -2,7 +2,7 @@
 #'
 #' Generates a Kobe plot or phase plot illustrating the stock status uncertainty over SSB/SSBmsy and F/Fmsy
 #'
-#' @param kb output from SSdeltaMVLN()$kb
+#' @param kb output from SSdeltaMVLN()[["kb"]]
 #' @param joint option FALSE shows individual runs
 #' @param year option to choose year for kobe, last year is default
 #' @param posterior visualization of posterior c("points","kernel")

R/SSplotEnsemble.R

@@ -236,8 +236,8 @@ SSplotEnsemble <- function(kb,
     n.quantiles <- length(quantiles)
     for (i in 1:n.quantiles) {
       exp[[i]] <- aggregate(y ~ year + run, kb, mean)
-      exp[[i]][["lower"]] <- aggregate(y ~ year + run, kb, quantile, quantiles[[i]][1])$y
-      exp[[i]][["upper"]] <- aggregate(y ~ year + run, kb, quantile, quantiles[[i]][2])$y
+      exp[[i]][["lower"]] <- aggregate(y ~ year + run, kb, quantile, quantiles[[i]][1])[["y"]]
+      exp[[i]][["upper"]] <- aggregate(y ~ year + run, kb, quantile, quantiles[[i]][2])[["y"]]
     }
 
 
@@ -444,7 +444,7 @@ ensemble_plot_index <- function(summaryoutput,
   # legendloc <- "topleft"
   # }
   # if (is.numeric(legendloc)) {
-  # Usr <- par()$usr
+  # Usr <- par()[["usr"]]
   # legendloc <- list(
   #   x = Usr[1] + legendloc[1] * (Usr[2] - Usr[1]),
   #   y = Usr[3] + legendloc[2] * (Usr[4] - Usr[3])

R/SSplotHCxval.R

@@ -247,7 +247,7 @@ SSplotHCxval <- function(retroSummary,
     # legendloc <- "topleft"
     # }
     # if (is.numeric(legendloc)) {
-    # Usr <- par()$usr
+    # Usr <- par()[["usr"]]
     # legendloc <- list(
     #   x = Usr[1] + legendloc[1] * (Usr[2] - Usr[1]),
     #   y = Usr[3] + legendloc[2] * (Usr[4] - Usr[3])
@@ -613,7 +613,7 @@ SSplotHCxval <- function(retroSummary,
           filenameprefix = filenameprefix
         )
         par(par)
-        get_mase <- plot_hcxval(indexfleets)$MASE
+        get_mase <- plot_hcxval(indexfleets)[["MASE"]]
         dev.off()
         MASE <- rbind(MASE, get_mase)
       } # End of Fleet Loop
@@ -626,7 +626,7 @@ SSplotHCxval <- function(retroSummary,
       if (fi %in% legendindex) legend <- TRUE
       indexfleets <- unique(hcruns[["indices"]][["Fleet"]])[fi]
       if (!add) (par)
-      get_mase <- plot_hcxval(indexfleets)$MASE
+      get_mase <- plot_hcxval(indexfleets)[["MASE"]]
       MASE <- rbind(MASE, get_mase)
     } # End of Fleet Loop
   }

R/SSplotModelcomp.R

@@ -231,7 +231,7 @@ SSplotModelcomp <- function(summaryoutput,
     # legendloc <- "topleft"
     # }
     # if (is.numeric(legendloc)) {
-    # Usr <- par()$usr
+    # Usr <- par()[["usr"]]
     # legendloc <- list(
     #   x = Usr[1] + legendloc[1] * (Usr[2] - Usr[1]),
     #   y = Usr[3] + legendloc[2] * (Usr[4] - Usr[3])
@@ -510,7 +510,7 @@ SSplotModelcomp <- function(summaryoutput,
     # legendloc <- "topleft"
     # }
     # if (is.numeric(legendloc)) {
-    # Usr <- par()$usr
+    # Usr <- par()[["usr"]]
     # legendloc <- list(
     #   x = Usr[1] + legendloc[1] * (Usr[2] - Usr[1]),
     #   y = Usr[3] + legendloc[2] * (Usr[4] - Usr[3])

R/SSplotRetro.R

@@ -187,7 +187,7 @@ SSplotRetro <- function(summaryoutput,
     # legendloc <- "topleft"
     # }
     # if (is.numeric(legendloc)) {
-    # Usr <- par()$usr
+    # Usr <- par()[["usr"]]
     # legendloc <- list(
     #   x = Usr[1] + legendloc[1] * (Usr[2] - Usr[1]),
     #   y = Usr[3] + legendloc[2] * (Usr[4] - Usr[3])

R/SSplotRunstest.R

@@ -198,7 +198,7 @@ SSplotRunstest <- function(ss3rep,
   }
 
   if (subplots == "len" | subplots == "age" | subplots == "size") {
-    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)$runs_dat
+    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)[["runs_dat"]]
     comps[["residuals"]] <- ifelse(is.na(comps[["Obs"]]), NA, log(comps[["Obs"]]) - log(comps[["Exp"]]))
     if (is.null(comps[["Fleet_name"]])) { # Deal with Version control
       comps[["Fleet_name"]] <- comps[["Name"]]
@@ -207,7 +207,7 @@ SSplotRunstest <- function(ss3rep,
   }
 
   if (subplots == "con") {
-    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)$runs_dat
+    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)[["runs_dat"]]
     cond[["residuals"]] <- ifelse(is.na(cond[["Obs"]]), NA, log(cond[["Obs"]]) - log(cond[["Exp"]]))
     if (is.null(cond[["Fleet_name"]])) { # Deal with Version control
       cond[["Fleet_name"]] <- cond[["Name"]]
@@ -444,7 +444,7 @@ SSrunstest <- function(ss3rep,
   }
 
   if (subplots == "len" | subplots == "age") {
-    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)$runs_dat
+    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)[["runs_dat"]]
     comps[["residuals"]] <- ifelse(is.na(comps[["Obs"]]), NA, log(comps[["Obs"]]) - log(comps[["Exp"]]))
     if (is.null(comps[["Fleet_name"]])) { # Deal with Version control
       comps[["Fleet_name"]] <- comps[["Name"]]
@@ -453,7 +453,7 @@ SSrunstest <- function(ss3rep,
   }
 
   if (subplots == "con") {
-    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)$runs_dat
+    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)[["runs_dat"]]
     cond[["residuals"]] <- ifelse(is.na(cond[["Obs"]]), NA, log(cond[["Obs"]]) - log(cond[["Exp"]]))
     if (is.null(cond[["Fleet_name"]])) { # Deal with Version control
       cond[["Fleet_name"]] <- cond[["Name"]]

R/SSretroComps.R

@@ -30,7 +30,7 @@ SSretroComps <- function(retroModels) {
       rep.temp <- retroModels[[paste(replist[i])]]
       rep.temp[["lendbase"]] <- rbind(rep.temp[["ghostlendbase"]], rep.temp[["lendbase"]][, 1:ncol(rep.temp[["ghostlendbase"]])])
       rep.temp[["lendbase"]] <- data.frame(rep.temp[["lendbase"]], imodel = i)
-      lencomps <- rbind(lencomps, data.frame(SScompsTA1.8(rep.temp, type = "len", plotit = F)$runs_dat, imodel = i))
+      lencomps <- rbind(lencomps, data.frame(SScompsTA1.8(rep.temp, type = "len", plotit = F)[["runs_dat"]], imodel = i))
     }
     lencomps <- lencomps[order(lencomps[["imodel"]], lencomps[["Fleet"]], lencomps[["Time"]]), ]
 
@@ -42,7 +42,7 @@ SSretroComps <- function(retroModels) {
     for (i in 1:length(replist)) {
       rep.temp <- retroModels[[paste(replist[i])]]
       rep.temp[["agedbase"]] <- rbind(rep.temp[["ghostagedbase"]], rep.temp[["agedbase"]][, 1:ncol(rep.temp[["ghostagedbase"]])])
-      agecomps <- rbind(agecomps, data.frame(SScompsTA1.8(rep.temp, type = "age", plotit = F)$runs_dat, imodel = i))
+      agecomps <- rbind(agecomps, data.frame(SScompsTA1.8(rep.temp, type = "age", plotit = F)[["runs_dat"]], imodel = i))
     }
     agecomps <- agecomps[order(agecomps[["imodel"]], agecomps[["Fleet"]], agecomps[["Time"]]), ]
     hccomps[["age"]] <- agecomps
@@ -53,7 +53,7 @@ SSretroComps <- function(retroModels) {
     for (i in 1:length(replist)) {
       rep.temp <- retroModels[[paste(replist[i])]]
       rep.temp[["condbase"]] <- rbind(rep.temp[["ghostcondbase"]], rep.temp[["condbase"]][, 1:ncol(rep.temp[["ghostcondbase"]])])
-      concomps <- rbind(concomps, data.frame(SScompsTA1.8(rep.temp, type = "con", plotit = F)$runs_dat, imodel = i))
+      concomps <- rbind(concomps, data.frame(SScompsTA1.8(rep.temp, type = "con", plotit = F)[["runs_dat"]], imodel = i))
     }
     concomps <- concomps[order(concomps[["imodel"]], concomps[["Fleet"]], concomps[["Time"]]), ]
     hccomps[["con"]] <- concomps

R/SSrmse.R

@@ -36,7 +36,7 @@ SSrmse <- function(ss3rep, quants = c("cpue", "len", "age", "con"), seas = NULL,
   }
 
   if (quants == "len" | quants == "age" | quants == "size") {
-    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = quants, plotit = FALSE)$runs_dat
+    comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = quants, plotit = FALSE)[["runs_dat"]]
     comps[["residuals"]] <- ifelse(is.na(comps[["Obs"]]), NA, log(comps[["Obs"]]) - log(comps[["Exp"]]))
     if (is.null(comps[["Fleet_name"]])) { # Deal with Version control
       comps[["Fleet_name"]] <- comps[["Name"]]
@@ -45,7 +45,7 @@ SSrmse <- function(ss3rep, quants = c("cpue", "len", "age", "con"), seas = NULL,
   }
 
   if (quants == "con") {
-    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = quants, plotit = FALSE)$runs_dat
+    cond <- SScompsTA1.8(ss3rep, fleet = NULL, type = quants, plotit = FALSE)[["runs_dat"]]
     cond[["residuals"]] <- ifelse(is.na(cond[["Obs"]]), NA, log(cond[["Obs"]]) - log(cond[["Exp"]]))
     if (is.null(cond[["Fleet_name"]])) { # Deal with Version control
       cond[["Fleet_name"]] <- cond[["Name"]]