Getting ready for release

DESCRIPTION

@@ -18,7 +18,7 @@ Authors@R: c(person("Gustav", "Delius", email="[email protected]",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="[email protected]",
                     role=c("ctb", "cph")))
-Version: 2.0.1.9002
+Version: 2.0.2
 License: GPL-3
 Imports:
     assertthat,

NAMESPACE

@@ -134,9 +134,11 @@ export(project)
 export(project_simple)
 export(removeComponent)
 export(resource_constant)
+export(resource_encounter)
 export(resource_params)
 export(resource_semichemostat)
 export(retune_erepro)
+export(semichemostat)
 export(setColours)
 export(setComponent)
 export(setExtMort)
@@ -161,6 +163,7 @@ export(sigmoid_length)
 export(sigmoid_weight)
 export(species_params)
 export(steady)
+export(test_dyn)
 export(truncated_lognormal_pred_kernel)
 export(upgradeParams)
 export(upgradeSim)

NEWS.md

@@ -1,15 +1,15 @@
-# mizer 2.0.1.9002
+# mizer 2.0.2
 
 ## Bug fixes
 
-* Time passed to rate functions is now the actual time, not the time elapsed
-  since start of simulation.
+* Time passed to rate functions is now the actual simulation time, not the time 
+  elapsed since start of simulation.
 * `upgradeParams()` works also on params objects that were created with a
   development version of mizer.
 * When upgrading an older params object, `upgradeParams()` does a better job at 
   guessing the value for `w_pp_cutoff`.
 * `getFeedingLevel()`, `getPredMort()`, `setInitialValues()` and `steady()` now
-  works also when model has extra components.
+  work also when model has extra components.
 * The critical feeding level lines are now mentioned in the legend of
   `plotFeedinglevel()` when called with `include_critical = TRUE`, see #162.
 * Avoid annoying warnings from dplyr package when `species_params` is a tibble.
@@ -36,7 +36,8 @@
   time steps. This might be useful to extension writers.
 * The `...` argument to `project()` is passed on to the dynamics and rate
   functions.
-* `steady()` runs faster using `project_simple()`.
+* `steady()` runs faster by using `project_simple()`.
+* Documentation on mizer website now has a search bar.
 
 
 # mizer 2.0.1
@@ -57,7 +58,7 @@ renaming
 * `r_resource` -> `resource_rate`
 * `K_resource` -> `resource_capacity`
 
-## New functionality
+## Minor enhancements
 
 * New functions `other_params()<-` and `other_params()` for setting and 
   getting other parameters, for example to be used in user-defined rate

R/extension.R

@@ -274,20 +274,31 @@ finalNOther <- function(sim) {
     n_other
 }
 
-#' Dummy functions used during testing only
+#' Dummy function used during testing only
 #' 
 #' @param params A MizerParams object
 #' @param ... Other parameters
+#' @export
 test_dyn <- function(params, ...) {
     111
 }
+#' Dummy function used during testing only
+#' 
+#' @inheritParams resource_constant
+#' @inheritParams constant_other
+#' @param ... Unused
+#' @export
 semichemostat <- function(params, n_other, rates, dt, component, ...) {
     c <- params@other_params[[component]]
     interaction <- params@species_params$interaction_resource
     mort <- as.vector(interaction  %*% rates$pred_rate)
     tmp <- c$rate * c$capacity / (c$rate + mort)
     return(tmp - (tmp - n_other[[component]]) * exp(-(c$rate + mort) * dt))
 }
+#' Dummy function used during testing only
+#' 
+#' @inheritParams resource_constant
+#' @export
 resource_encounter <- function(params, n, n_pp, n_other, ...) {
     mizerEncounter(params, n = n, n_pp = n_other$resource, ...)
 }

R/steady.R

@@ -188,6 +188,11 @@ retune_erepro <- function(params, species = species_params(params)$species) {
 
 
 #' Helper function to keep other components constant
+#' 
+#' @param params MizerParams object
+#' @param n_other Abundances of other components
+#' @param component Name of the component that is being updated
+#' @param ... Unused
 #' @export
 constant_other <- function(params, n_other, component, ...) {
     n_other[[component]]

R/summary_methods.R

@@ -46,7 +46,7 @@ NULL
 #' available biomass. Outside the range of sizes for a predator species the
 #' returned rate is zero.
 #'
-#' @param params A MizerParams object
+#' @inheritParams getEncounter
 #' @param proportion If TRUE (default) the function returns the diet as a
 #'   proportion of the total consumption rate. If FALSE it returns the 
 #'   consumption rate in grams.

cran-comments.md

@@ -4,5 +4,5 @@
 
   0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
-* win-builder (devel, release and oldrelease)
+* win-builder (release and oldrelease)
   No Notes, Warnings or Errors

inst/WORDLIST

@@ -1,92 +1,85 @@
 Acad
 Algolia
 allometrically
+backreaction
 Bertalanffy
 Beverton
 Beyer
 bycatch
 camelCase
+Canales
 catchabilities
 catchability
 Catchability
 cdot
-Cefas
-chemostatic
 cjfas
 Collingridge
+color
+colors
 com
 Conseil
 cran
 csv
 cutoff
 cutoffs
-cW
 Datta
 Deepfishman
 Deepwater
 DEFINEIT
 Defra
 demersal
-detritivores
-detritivorous
 devtools
+dialog
 discretisation
 discretises
-DK
-DP
 Docsearch
 doi
+DP
+dplyr
 dropdown
 dt
-DTU
 du
 dw
 EBFM
 eq
-Eq
-erepro
+eqn
 etc
 eu
 faf
-feces
 fft
 Foerster
 frac
-func
+getEncounter
 getERepro
-getFeedingLevel
 getGrowthCurves
-getM
 getMort
-getResourceMort
 getPredMort
+getResourceMort
+gganimate
 ggplot
 github
 Github
 GitHubPages
+harddrive
 Hinzen
 Holling
-ht
 iframe
 ij
 inf
 Inf
 infty
 int
-io
-ip
-IPSC
+iR
 ji
 jp
-knitr
 ks
 Lenfest
 LFI
-linecolour
 linetype
 linetypes
-macroflora
+Mariella
 Marifish
+McKendrick
 McKendrik
 md
 MERP
@@ -95,46 +88,37 @@ MESOPP
 metab
 minouw
 MINOUW
-mizer's
 mizerExamples
 mizerExperimental
 MizerParams
 MizerSim
-modeled
 modeling
 mort
 MSY
 muf
 mup
 mupp
 MvF
-MVF
 navbar
-nb
-ncolumns
-nrows
 Oceanologica
 offs
 org
-packageDescription
 parameterisations
 parameterise
 params
 Pedersen
 Piet
 pkgdown
 PLoS
-plotBiomass
 plotFeedingLevel
-plotFMort
 plotGrowthCurves
 plotly
-Plotly
 plotPredMort
 ppmr
 pred
 Proc
 proj
+propto
 R's
 R’s
 rdd
@@ -144,54 +128,46 @@ Rdoc
 reexports
 Ren
 repro
-res
 Ricker
 rmarkdown
 Rmarkdown
-Rmax
+RMarkdown
 Rmd
 roxygen
-Roxygen
-roxygenize
 Rp
+Rstudio
 RStudio
+RStudio's
 Sandeel
 Sci
 sel
 selectivities
 semichemostat
-setparams
+setParams
 Sheperd
 shinytest
 sigmoidal
-sim
 Sinica
 sIZE
+sizer
 sizespectrum
 sp
 spawners
-srr
-SRR
-SRRs
 SSB
 stackoverflow
-std
 subfunctions
 Szuwalski
 testthat
-th
+tibble
 tidyverse
-tol
 trophic
 Trophic
 tt
 u
 unfished
-Ursin
 vb
 vdiffr
 vol
-WMAT
 www
 Xue
 zooplanktivorous