Atlantis-Ecosystem-Model · andybeet · May 21, 2026 · May 15, 2026 · May 16, 2026 · May 16, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,9 +6,9 @@
 NEWS\.Rmd
 ^data-raw$
 ^appveyor\.yml$
-^cran-comments\.md$
 ^revdep$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
 ^\.github$
+air.toml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,47 +1,42 @@
 Package: atlantistools
 Type: Package
 Title: Process and Visualise Output from Atlantis Models
-Version: 0.5.1
+Version: 1.0.0
 Authors@R: 
   c(person("Alexander", "Keth", email = "alexander.keth@uni-hamburg.de", role = c("aut")),
-    person("Andy", "Beet", email = "andrew.beet@noaa.gov", role = c("cre")))
+    person("Andy", "Beet", email = "andrew.beet@noaa.gov", role = c("cre","aut"),
+           comment = c(ORCID = "0000-0001-8270-7090")))
 Description: Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (<http://atlantis.cmar.csiro.au>). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) <DOI:10.18637/jss.v059.i10>. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.
-URL: https://github.com/Atlantis-Ecosystem-Model/atlantistools
+URL: https://github.com/Atlantis-Ecosystem-Model/atlantistools, https://andybeet.github.io/atlantistools/
 BugReports: https://github.com/Atlantis-Ecosystem-Model/atlantistools/issues
 Depends:
-    R (>= 4.0)
+    R (>= 4.1)
 License: GPL-3
 LazyData: true
 Encoding: UTF-8
 RoxygenNote: 7.3.3
 Suggests:
   knitr,
-  rfishbase,
   rmarkdown,
-  testthat,
-  vdiffr
+  testthat
 Imports:
   circlize,
   curl,
-  devtools,
   dplyr,
   ggplot2,
   graphics,
   grDevices,
   grid,
   gridExtra,
   lazyeval,
-  magrittr,
   proj4,
   purrr,
   RColorBrewer,
   RNetCDF,
   rlang,
   rvest,
   scales,
-  stringi,
   stringr,
   tibble,
-  tidyr,
-  xml2
+  tidyr
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(agg_data)
 export(agg_perc)
 export(calculate_biomass_spatial)
@@ -29,16 +28,10 @@ export(get_boundary)
 export(get_cohorts_acronyms)
 export(get_colpal)
 export(get_conv_mgnbiot)
-export(get_diet_fishbase)
 export(get_fish_acronyms)
 export(get_fished_acronyms)
 export(get_groups)
-export(get_growth_fishbase)
-export(get_ids_fishbase)
-export(get_maturity_fishbase)
 export(get_nonage_acronyms)
-export(get_ref_biotic)
-export(get_ref_fishbase)
 export(get_turnedon_acronyms)
 export(group_data)
 export(load_box)
@@ -66,7 +59,6 @@ export(plot_bar)
 export(plot_boxes)
 export(plot_consumed_biomass)
 export(plot_diet)
-export(plot_diet_bec_dev)
 export(plot_line)
 export(plot_rec)
 export(plot_sc_init)
@@ -80,9 +72,7 @@ export(prm_to_df_ages)
 export(ref_to_bibkey)
 export(sc_init)
 export(scan_prm)
-export(scan_reference_fishbase)
 export(str_split_twice)
 export(theme_atlantis)
 export(write_diet)
-importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+# atlantistools 1.0.0
+
+## Major changes
+
+* Replaced `magrittr` with native pipe and dependence on `R version 4.1` (PR #74)
+* Removed `version_flag` argument from several functions (PR #64)
+* Removed all content (code and documentation) relating to a development model (`bec-dev`) (PR #65)
+* Removed all functions relating to `rfishbase` and `biotic` (PR #63)
+
+## Patch fixes
+
+* Removed unused dependencies, `stringi`, `vdiffr` (PR #61, PR #74)
+
+
 # atlantistools 0.5.1
 
 ## Patch fixes

diff --git a/R/calculate-consumed-biomass.R b/R/calculate-consumed-biomass.R
@@ -54,7 +54,7 @@
 #'                select_groups = groups_rest, select_variable = "Grazing",
 #'                prm_run = prm_run, bboxes = bboxes)
 #' df_dm <- load_dietcheck(dietcheck = file.path(d, "outputSETASDietCheck.txt"),
-#'                         fgs = fgs, prm_run = prm_run, version_flag = 2, convert_names = TRUE)
+#'                         fgs = fgs, prm_run = prm_run, convert_names = TRUE)
 #' vol <- load_nc_physics(nc = nc_gen, select_physics = "volume",
 #'                        prm_run = prm_run, bboxes = bboxes, aggregate_layers = FALSE)
 #'
@@ -96,7 +96,7 @@ calculate_consumed_biomass <- function(eat, grazing, dm, vol, bio_conv) {
       atoutput = atoutput * bio_conv
     ) |>
     # Step2: Combine with diet contribution. We need a full join to make sure no data is lost!
-    dplyr::full_join(dm, by = c("species" = "pred", "time", "agecl")) %>%
+    dplyr::full_join(dm, by = c("species" = "pred", "time", "agecl")) |>
     # Restrict timesteps to netcdf data! Last timestep is weird in Dietcheck.txt.
     dplyr::filter(time %in% ts_eat) |>
     dplyr::rename(pred = species)

diff --git a/R/calculate-spatial-overlap.R b/R/calculate-spatial-overlap.R
@@ -146,7 +146,7 @@ schoener <- function(predgrp, ageclass, biomass, avail) {
     df_avail,
     df_pred,
     by = c("pred" = "species", "pred_stanza" = "species_stanza")
-  ) %>%
+  ) |>
     dplyr::inner_join(
       biomass_clean,
       by = c(

diff --git a/R/change-prm.R b/R/change-prm.R
@@ -32,8 +32,7 @@ change_prm <- function(
   roc,
   parameter,
   relative = TRUE,
-  save_to_disc = TRUE,
-  version_flag = 2
+  save_to_disc = TRUE
 ) {
   if (length(parameter) != 1) {
     stop("Please suply only one parameter per function call.")
@@ -64,15 +63,10 @@ change_prm <- function(
       new_value <- roc
     }
 
-    # Update value. Some pesky expectations have to be added here.
-    if (
-      is.element(parameter, c("mum", "C", "mQ", "mL", "jmL", "jmQ")) &
-        version_flag == 1
-    ) {
-      prm_biol[pos] <- paste(paste0(flag, "_T15"), new_value, sep = "\t")
-    } else {
-      prm_biol[pos] <- paste(flag, new_value, sep = "\t")
-    }
+    # Update value.
+
+    prm_biol[pos] <- paste(flag, new_value, sep = "\t")
+
     return(prm_biol)
   }
 

diff --git a/R/check-growth.R b/R/check-growth.R
@@ -28,15 +28,6 @@ check_growth <- function(data, yearly = FALSE) {
     df
   }
 
-  # Divide output with initial value!
-  # ref <- data[data$time == min(data$time), ]
-  # ref$time <- NULL
-  # names(ref)[names(ref) == "atoutput"] <- "atoutput_ref"
-  # result <- data %>%
-  #   dplyr::left_join(ref) %>%
-  #   dplyr::mutate(atoutput = atoutput / atoutput_ref)
-  # result$atoutput[result$atoutput_ref == 0] <- 0
-  # outcomment in case lm procedure is used! This is a bit messy.
   result <- data
 
   # Split dataframe into species and age specific subdataframes!

diff --git a/R/combine-ages.R b/R/combine-ages.R
@@ -43,10 +43,10 @@ combine_ages <- function(data, grp_col, agemat, value_col = "atoutput") {
   data_stanza$stanza <- ifelse(data_stanza$agecl < data_stanza$age_mat, 1, 2)
   data_stanza$stanza[is.na(data_stanza$stanza)] <- 1 # Not sure if this is correct!
 
-  result <- data_stanza %>%
+  result <- data_stanza |>
     agg_data(
       col = value_col,
-      groups = names(.)[!names(.) %in% c(value_col, "agecl")],
+      groups = setdiff(colnames(data_stanza), c(value_col, "agecl")),
       out = value_col,
       fun = sum
     )

diff --git a/R/combine-groups.R b/R/combine-groups.R
@@ -29,8 +29,8 @@ combine_groups <- function(
   # Arrange by group_col and group by groups to select the 1:combinthethresh
   # group in group_col for each grouping combination.
   if (length(groups) > 0) {
-    comb_grps <- comb_grps %>%
-      as.data.frame() %>%
+    comb_grps <- comb_grps |>
+      as.data.frame() |>
       group_data(groups = groups)
   }
   imp_species <- comb_grps |>
@@ -47,7 +47,7 @@ combine_groups <- function(
     # Only combine groups if necessary!
     low_contrib[, group_col] <- "Rest"
 
-    new_data <- dplyr::inner_join(data, imp_species) %>%
+    new_data <- dplyr::inner_join(data, imp_species) |>
       rbind(low_contrib)
 
     # This should never happen...

diff --git a/R/data.R b/R/data.R
@@ -227,29 +227,6 @@
 "ref_bio_sp"
 
 
-#' fishbase_data
-#'
-#' A table of all the the species found in Fihsbase, including taxonomic classification.
-#'
-#' @format A data frame with 33104 rows and 12 variables:
-#' \describe{
-#'   \item{\code{SpecCode}}{integer. Species code.}
-#'   \item{\code{Genus}}{character.}
-#'   \item{\code{Species}}{character.}
-#'   \item{\code{SpeciesRefNo}}{integer. Reference number.}
-#'   \item{\code{FBname}}{character. Fishbase name.}
-#'   \item{\code{SubFamily}}{character.}
-#'   \item{\code{FamCode}}{integer. Family Code.}
-#'   \item{\code{GenCode}}{integer. Genetic Code.}
-#'   \item{\code{SubGenCode}}{integer. Sub Genetic Code.}
-#'   \item{\code{Family}}{character.}
-#'   \item{\code{Order}}{character.}
-#'   \item{\code{Class}}{character.}
-#' }
-#' @source \url{http://www.fishbase.org/} rfishbase::fishbase
-"fishbase_data"
-
-
 #' Reference dataframe
 #'
 #' Year, author and title from 3 random publications

diff --git a/R/get-boundary.R b/R/get-boundary.R
@@ -5,7 +5,6 @@
 #'
 #' @family get functions
 #' @seealso \code{\link{load_box}}
-#' @author Kelli Faye Johnson
 #'
 #' @param boxinfo A \code{list} as returned from \code{\link{load_box}}.
 #'

diff --git a/R/load-box.R b/R/load-box.R
@@ -4,7 +4,6 @@
 #' for an Atlantis scenario.
 #'
 #' @family load functions
-#' @author Kelli Faye Johnson
 #'
 #' @param bgm Character string giving the connection to the atlantis bgm file.
 #' The filename ends in \code{.bgm}.

diff --git a/R/load-dietcheck.R b/R/load-dietcheck.R
@@ -14,15 +14,6 @@
 #'   time, pred, habitat, prey and atoutput (i.e., variable).
 #'
 #' @examples
-#' # Apply to bec-dev models.
-#' d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
-#' dietcheck <- file.path(d, "outputSETASDietCheck.txt")
-#' fgs <- file.path(d, "SETasGroups.csv")
-#' prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")
-#'
-#' diet <- load_dietcheck(dietcheck, fgs, prm_run, version_flag = 1)
-#' head(diet, n = 10)
-#'
 #' # Apply to trunk models.
 #' d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
 #' dietcheck <- file.path(d, "outputSETASDietCheck.txt")
@@ -32,14 +23,12 @@
 #' diet <- load_dietcheck(dietcheck, fgs, prm_run)
 #' head(diet, n = 10)
 
-#BJS 7/6/16 change to be compatible with trunk version; added version_flag
 load_dietcheck <- function(
   dietcheck,
   fgs,
   prm_run,
   convert_names = FALSE,
-  report = FALSE,
-  version_flag = 2
+  report = FALSE
 ) {
   # read in diet information
   diet <- utils::read.table(
@@ -50,20 +39,19 @@ load_dietcheck <- function(
   )
 
   #Check if multiple stocks are available per functional group for trunk branch!
-  if (version_flag == 2) {
-    if (all(diet$Stock) == 0) {
-      diet$Stock <- NULL
-    } else {
-      stop(
-        "Multiple stocks present. Dietcheck only works with 1 stock per funtional group."
-      )
-    }
 
-    diet$Cohort <- diet$Cohort + 1 # Cohorts start with 0 in DietCheck.txt!
+  if (all(diet$Stock) == 0) {
+    diet$Stock <- NULL
+  } else {
+    stop(
+      "Multiple stocks present. Dietcheck only works with 1 stock per funtional group."
+    )
   }
 
+  diet$Cohort <- diet$Cohort + 1 # Cohorts start with 0 in DietCheck.txt!
+
   # Column Updated was added to trunk code.
-  if (version_flag == 2 & "Updated" %in% names(diet)) {
+  if ("Updated" %in% names(diet)) {
     prey_col_start <- 5 #bjs remove magic number below
   } else {
     prey_col_start <- 4 #bjs remove magic number below
@@ -121,12 +109,10 @@ load_dietcheck <- function(
 
   names(diet_long)[names(diet_long) == "Predator"] <- "pred" #bjs predator -> colnames(diet)[2]
 
-  if (version_flag == 2) {
-    names(diet_long)[names(diet_long) == "Cohort"] <- "agecl" #bjs cohort -> colnames(diet)[3]
-    # Column Updated was added to trunk code.
-    if ("Updated" %in% names(diet_long)) {
-      diet_long <- diet_long[, names(diet_long) != "Updated"]
-    }
+  names(diet_long)[names(diet_long) == "Cohort"] <- "agecl" #bjs cohort -> colnames(diet)[3]
+  # Column Updated was added to trunk code.
+  if ("Updated" %in% names(diet_long)) {
+    diet_long <- diet_long[, names(diet_long) != "Updated"]
   }
 
   names(diet_long) <- tolower(names(diet_long))