diff --git a/R/MizerSim-class.R b/R/MizerSim-class.R index 354ed8691..5a505fae3 100644 --- a/R/MizerSim-class.R +++ b/R/MizerSim-class.R @@ -292,9 +292,9 @@ finalNResource <- function(sim) { #' idx <- idxFinalT(sim) #' idx #' # This coincides with -#' length(times(sim)) +#' length(getTimes(sim)) #' # and corresponds to the final time -#' times(sim)[idx] +#' getTimes(sim)[idx] #' # We can use this index to extract the result at the final time #' identical(N(sim)[idx, , ], finalN(sim)) #' identical(NResource(sim)[idx, ], finalNResource(sim)) diff --git a/docs/404.html b/docs/404.html index df2746551..300311f41 100644 --- a/docs/404.html +++ b/docs/404.html @@ -37,6 +37,12 @@ + + + + + + @@ -71,7 +77,7 @@ mizer - 2.0.1 + 2.0.2 @@ -89,8 +95,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -108,6 +158,12 @@
    • + + @@ -142,13 +198,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/articles/a_multispecies_model_of_the_north_sea.html b/docs/articles/a_multispecies_model_of_the_north_sea.html index 4dec11d32..24b816be4 100644 --- a/docs/articles/a_multispecies_model_of_the_north_sea.html +++ b/docs/articles/a_multispecies_model_of_the_north_sea.html @@ -11,7 +11,9 @@ - + + + @@ -329,14 +381,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/community_model.html b/docs/articles/community_model.html index 995f1850a..3f1bfb971 100644 --- a/docs/articles/community_model.html +++ b/docs/articles/community_model.html @@ -11,7 +11,9 @@ - + + + @@ -235,14 +287,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/developer_FAQ.html b/docs/articles/developer_FAQ.html index dbc6ae4f6..4e049794c 100644 --- a/docs/articles/developer_FAQ.html +++ b/docs/articles/developer_FAQ.html @@ -11,7 +11,9 @@ - + + + @@ -150,14 +202,27 @@

    Developer FAQ

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/developer_vignette.html b/docs/articles/developer_vignette.html index 83032e070..49d19fc25 100644 --- a/docs/articles/developer_vignette.html +++ b/docs/articles/developer_vignette.html @@ -11,7 +11,9 @@ - + + + @@ -268,14 +320,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/editing_website.html b/docs/articles/editing_website.html index f66cad1ef..36b7e8b37 100644 --- a/docs/articles/editing_website.html +++ b/docs/articles/editing_website.html @@ -11,7 +11,9 @@ - + + + @@ -182,14 +234,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/exploring_the_simulation_results.html b/docs/articles/exploring_the_simulation_results.html index 5bc4564f5..9bc004956 100644 --- a/docs/articles/exploring_the_simulation_results.html +++ b/docs/articles/exploring_the_simulation_results.html @@ -11,7 +11,9 @@ - + + + @@ -254,14 +306,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png b/docs/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png index f5e23392e..59ec7b91f 100644 Binary files a/docs/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png and b/docs/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index f0205755b..e5ccea309 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -37,6 +37,12 @@ + + + + + + @@ -71,7 +77,7 @@ mizer - 2.0.1 + 2.0.2 @@ -89,8 +95,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -108,6 +158,12 @@
    • + + @@ -172,13 +228,30 @@

    Developer Guide

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/articles/mizer.html b/docs/articles/mizer.html index 4850428be..e7b6a7a2a 100644 --- a/docs/articles/mizer.html +++ b/docs/articles/mizer.html @@ -11,7 +11,9 @@ - + + + @@ -270,14 +322,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/model_description.html b/docs/articles/model_description.html index 7eecc3841..530a58fdf 100644 --- a/docs/articles/model_description.html +++ b/docs/articles/model_description.html @@ -11,7 +11,9 @@ - + + + @@ -150,7 +202,7 @@

    The rate at which a predator of species \(i\) and weight \(w\) encounters food (mass per time) is determined by summing over all prey species and the resource spectrum and integrating over all prey sizes \(w_p\), weighted by the selectivity factors: \[\begin{equation} \label{eq:1} E_{i}(w) = \gamma_i(w) \int \left(\sum_{j} \theta_{ij} N_j(w_p) + - \theta_{iR} N_R(w_p) + \right) + \theta_{iR} N_R(w_p) \right) \phi_i(w,w_p) w_p \, dw_p. \end{equation}\] This is calculated by getEncounter(). The overall prefactor \(\gamma_i(w)\) sets the predation power of the predator. It could be interpreted as a search volume. It is set by setSearchVolume(). By default it is assumed to scale allometrically as \(\gamma_i(w) = \gamma_i\, w^q.\)

    The \(\theta\) matrix sets the interaction strength between predators and the various prey species and resource. It is changed with setInteraction().

    @@ -291,14 +343,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/multispecies_model.html b/docs/articles/multispecies_model.html index 3fa36ca12..1fbb7a4ad 100644 --- a/docs/articles/multispecies_model.html +++ b/docs/articles/multispecies_model.html @@ -11,7 +11,9 @@ - + + + @@ -399,14 +451,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/plotting.html b/docs/articles/plotting.html index a5cb22b2b..67b178be6 100644 --- a/docs/articles/plotting.html +++ b/docs/articles/plotting.html @@ -11,7 +11,9 @@ - + + + @@ -78,7 +130,7 @@ -
    +

    Using ggplot2 and plotly with mizer

    @@ -131,8 +183,8 @@ 

    pp <- plot_ly(biomass_frame) %>%
     add_lines(x = ~time, y = ~value, color = ~sp)
 pp
    -
    -

    We have specified that the time is plotted along the x axis, the value along the y axis and that the different species are represented by the colours of the lines. Note the American spelling “color” required by plotly.

    +
    +

    We have specified that the time is plotted along the x axis, the value along the y axis and that the different species are represented by the colours of the lines. Note the American spelling “color” required by plotly.

    Alternatively we can do the same thing with ggplot():

    pg <- ggplot(biomass_frame) +
     geom_line(aes(x = time, y = value, colour = sp))
@@ -141,8 +193,8 @@ 
    
 
    Notice the different syntax for the ggplot2 and for plotly packages. The underlying ideas are similar: they are both implementations of the grammar of graphics. I recommend learning ggplot2 first, and switching to plotly only when it has clear advantages (in particular for animations, see below).
    
 
    The main advantage of plotly, namely the interactivity of the resulting figures, can be obtained also with the ggplot syntax by running the result of ggplot() through the function ggplotly():
    
 
-
    
-
    Below we will always for each plot first give the ggplot code and then the plotly code.
    
+
    
+
    Below we will always for each plot first give the ggplot code and then the plotly code.

    @@ -162,8 +214,8 @@

    title = "Biomass [g]" ) )

    -
    - +
    +

    @@ -201,8 +253,8 @@ 

    plot_ly(biomass_frame) %>%
     add_lines(x = ~time, y = ~value, color = ~sp,
               colors = getColours(params))
    -
    -

    Again note the American spelling “colors” required by plotly.

    +
    +

    Again note the American spelling “colors” required by plotly.

    @@ -244,8 +296,8 @@

    yaxis = list(type = "log", exponentformat = "power")) p

    -
    - In the above we used the pipe operator %>% which feeds the return value of one function into the first argument of the next function. +
    + In the above we used the pipe operator %>% which feeds the return value of one function into the first argument of the next function.

    @@ -295,8 +347,8 @@

    range = c(-4, 4)), yaxis = list(type = "log", exponentformat = "power", range = c(-14, 20)))

    -
    -

    Note how in plotly the range is specified by giving the logarithm to base 10 of the limits.

    +
    +

    Note how in plotly the range is specified by giving the logarithm to base 10 of the limits.

    @@ -311,8 +363,8 @@

    line = list(simplify = FALSE)) %>% layout(xaxis = list(type = "log", exponentformat = "power"), yaxis = list(type = "log", exponentformat = "power"))

    -
    -

    Note how this produces a smooth animation in spite of the fact that we saved the abundances only once a year. That interpolation is facilitated by the line = list(simplify = FALSE) argument.

    +
    +

    Note how this produces a smooth animation in spite of the fact that we saved the abundances only once a year. That interpolation is facilitated by the line = list(simplify = FALSE) argument.

    The ggplot package does not provide a similarly convenient way of creating animations. There is the gganimate package, but it is not nearly as convenient.

    @@ -366,20 +418,20 @@

    ylim(0,1.75e12)

    We can then create a widget that allows the user to toggle between the two plots by clicking on it,

    vdiffr::widget_toggle(p1, p2)
    -
    -

    or by sliding across it:

    +
    +

    or by sliding across it:

    vdiffr::widget_slide(p1, p2)
    -
    -

    plotly is less good at faceting, but it can put arbitrary plots side-by-side (or arrange them into a grid) with subplot()

    +
    +

    plotly is less good at faceting, but it can put arbitrary plots side-by-side (or arrange them into a grid) with subplot()

    subplot(p1, p2, shareX = TRUE, shareY = TRUE)
    -
    -

    Note how the shareY = TRUE argument to suplot() makes sure the two plots use the same scale on the y axis, and similarly for shareX = TRUE.

    +
    +

    Note how the shareY = TRUE argument to suplot() makes sure the two plots use the same scale on the y axis, and similarly for shareX = TRUE.

    Also in plotly we can now tie the effort variable to the line type.

    plot_ly(yield) %>%
     add_lines(x = ~time, y = ~value,
               color = ~sp, linetype = ~effort)
    -
    -

    Arguably, ggplot2 does a nicer job in this case.

    +
    +

    Arguably, ggplot2 does a nicer job in this case.

    @@ -398,14 +450,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/publications.html b/docs/articles/publications.html index 5f805856e..0906713d4 100644 --- a/docs/articles/publications.html +++ b/docs/articles/publications.html @@ -11,7 +11,9 @@ - + + + @@ -144,14 +196,27 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    - - - + + diff --git a/docs/articles/running_a_simulation.html b/docs/articles/running_a_simulation.html index c89b2eedc..8face1102 100644 --- a/docs/articles/running_a_simulation.html +++ b/docs/articles/running_a_simulation.html @@ -11,7 +11,9 @@ - + + + @@ -182,8 +234,8 @@

    The big difference between this multispecies model and the trait-based model can be seen in the range of predation mortality and feeding level values. With the trait-based model all the species had the same predation mortality and feeding level patterns. Here the species all have different patterns, driven by their differing life history characteristics and the heterogeneous interaction matrix.

    You can also see in the above figure that each species has different fishing selectivity (see the fishing mortality panel). Remember that the default setting for the fishing gears is a knife-edge gear where the knife-edge is positioned at the species w_mat parameter.

    -

    The effort through time can be inspected with effort() (we use the head() function to just show the first few lines).

    -
    head(effort(sim))
    +

    The effort through time can be inspected with getEffort() (we use the head() function to just show the first few lines).

    +
    head(getEffort(sim))
    ##     gear
 ## time Industrial Pelagic Beam Otter
 ##    0          1       1    1     1
@@ -197,7 +249,7 @@ 
    
 
    summary(sim)
    
 
    If we decrease t_save but keep t_max the same then we can see that the time dimension of the effort array changes accordingly. This will also be true of the simulation results returned by N() and NResource(). Here we reduce t_save to 0.5, meaning that the effort and abundance information is stored at t = 1.0, 1.5, 2.0 etc.
    
 
    sim <- project(NS_params, effort = 1, t_max = 10, dt = 0.1, t_save = 0.5)
-head(effort(sim))
    
+head(getEffort(sim))
    ##      gear
 ## time  Industrial Pelagic Beam Otter
 ##   0            1       1    1     1
@@ -215,7 +267,7 @@ 
    
 
    effort <- c(Industrial = 0, Pelagic = 1, Beam = 0.3, Otter = 0.7)
    
 
    We then call project() with this effort and inspect the resulting effort matrix (again we use the head() function to just show the first few lines):
    
 
    sim <- project(NS_params, effort = effort, t_max = 10, dt = 1, t_save = 1)
-head(effort(sim))
    
+head(getEffort(sim))
    ##     gear
 ## time Industrial Pelagic Beam Otter
 ##    0          0       1  0.3   0.7
@@ -288,14 +340,27 @@ 
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
 
 
   
-
-
-  
+
+
 
diff --git a/docs/articles/trait_model.html b/docs/articles/trait_model.html
index f9bf1933b..47863606b 100644
--- a/docs/articles/trait_model.html
+++ b/docs/articles/trait_model.html
@@ -11,7 +11,9 @@
 
 
 
-
+
+
+
 
 
   
 
@@ -279,14 +331,27 @@ 
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
 
 
   
-
-
-  
+
+
 
diff --git a/docs/articles/working_with_git.html b/docs/articles/working_with_git.html
index 2fb5a8521..c15127b45 100644
--- a/docs/articles/working_with_git.html
+++ b/docs/articles/working_with_git.html
@@ -11,7 +11,9 @@
 
 
 
-
+
+
+
 
 
   
 
@@ -213,14 +265,27 @@ 
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
 
 
   
-
-
-  
+
+
 
diff --git a/docs/authors.html b/docs/authors.html
index 4642a4746..d92f8db5b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -37,6 +37,12 @@
 
 
 
+
+
+
+
+
+
 
 
 
@@ -71,7 +77,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -89,8 +95,52 @@
 
  • 
   Reference
 
    • 
-
  • 
-  Guides
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -108,6 +158,12 @@
 
    • 
       
       
+      
+      
     
   
 
@@ -173,13 +229,30 @@ 
    Authors
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/docsearch.json b/docs/docsearch.json
new file mode 100644
index 000000000..a133a5d4f
--- /dev/null
+++ b/docs/docsearch.json
@@ -0,0 +1,95 @@
+{
+  "index_name": "sizespectrum_mizer",
+  "start_urls": [
+    {
+      "url": "https://sizespectrum.org/mizer/index.html",
+      "selectors_key": "homepage",
+      "tags": [
+        "homepage"
+      ]
+    },
+    {
+      "url": "https://sizespectrum.org/mizer/reference",
+      "selectors_key": "reference",
+      "tags": [
+        "reference"
+      ]
+    },
+    {
+      "url": "https://sizespectrum.org/mizer/articles",
+      "selectors_key": "articles",
+      "tags": [
+        "articles"
+      ]
+    }
+  ],
+  "stop_urls": [
+    "/reference/$",
+    "/reference/index.html",
+    "/articles/$",
+    "/articles/index.html"
+  ],
+  "sitemap_urls": [
+    "https://sizespectrum.org/mizer/sitemap.xml"
+  ],
+  "selectors": {
+    "homepage": {
+      "lvl0": {
+        "selector": ".contents h1",
+        "default_value": "mizer Home page"
+      },
+      "lvl1": {
+        "selector": ".contents h2"
+      },
+      "lvl2": {
+        "selector": ".contents h3",
+        "default_value": "Context"
+      },
+      "lvl3": ".ref-arguments td, .ref-description",
+      "text": ".contents p, .contents li, .contents .pre"
+    },
+    "reference": {
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+        "selector": ".contents .name",
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+        "selector": ".ref-arguments th",
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+      "lvl3": ".ref-arguments td, .ref-description",
+      "text": ".contents p, .contents li"
+    },
+    "articles": {
+      "lvl0": {
+        "selector": ".contents h1"
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+      "lvl1": {
+        "selector": ".contents .name"
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+        "selector": ".contents h2, .contents h3",
+        "default_value": "Context"
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+      "text": ".contents p, .contents li"
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+  "selectors_exclude": [
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+  "min_indexed_level": 2,
+  "custom_settings": {
+    "separatorsToIndex": "_",
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+      "hierarchy",
+      "content",
+      "anchor",
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+      "url_without_anchor"
+    ]
+  }
+}
+
diff --git a/docs/index.html b/docs/index.html
index b96c31b1a..e8d8b0c7b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -11,7 +11,9 @@
 
 
 
-
+
+
+
 
@@ -33,7 +35,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -51,8 +53,52 @@
 
  • 
   Reference
 
    • 
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -69,7 +115,13 @@
   
 
    • 
       
+
+      
+    
 
   
 
@@ -184,14 +236,27 @@ 
    Dev status
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
 
 
   
-
-
-  
+
+
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 7ebd9a66c..30e942f70 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -37,6 +37,12 @@
 
 
 
+
+
+
+
+
+
 
 
 
@@ -71,7 +77,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -89,8 +95,52 @@
 
  • 
   Reference
 
    • 
-
  • 
-  Guides
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -108,6 +158,12 @@
 
    • 
       
       
+      
+      
     
   
 
@@ -123,14 +179,59 @@ 
    Changelog 
    
       Source: NEWS.md
     
 
-    
    
-
    
-mizer 2.0.1 Unreleased 
+    
    
+
    
+mizer 2.0.2 Unreleased 
 
    
 
    
 
    
 Bug fixes
    
 
      
+
    • 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 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.
      • 
+
    
+
    
+
    
+
    
+Name changes
    
+
+
    
+
    
+
    
+Minor enhancements
    
+
      
+
    • Some improvements to documentation.
      • 
+
    • More unit tests.
      • 
+
    • Uses less memory when time step is very small by not creating array with effort values at each time step.
      • 
+
    • 
+getDiet() also takes into account possible contributions by user-defined other components.
      • 
+
    • In extension mechanism, now the name of a component is also passed to the functions implementing dynamics, encounter and mortality.
      • 
+
    • If project() is called with t_max < t_save then t_save is automatically reduced so that the result at t_max will get saved.
      • 
+
    • Start showing progress bar earlier during project().
      • 
+
    • New helper function project_simple() that projects a given number of 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 by using project_simple().
      • 
+
    • Documentation on mizer website now has a search bar.
      • 
+
    
+
    
+
    
+    
    
+
    
+mizer 2.0.1 2020-05-05 
+
    
+
    
+
    
+Bug fixes
    
+
      
 
    • 
 summary() now also works with non-default feeding kernels. #159
      • 
 
    • 
@@ -141,9 +242,9 @@ 
      
 resource_params()<- now works and has unit tests.
      • 
 
    
 
    
-
    
+
    
 
    
-Naming changes
    
+Name changes
    
 
    Some inconsistencies in the choice of names for parameters was removed by renaming
    
 
      
 
    • 
@@ -157,9 +258,9 @@ 
      
 
      • 
 
    
 
    
-
    
+
    
 
    
-New functionality
    
+Minor enhancements

    -
    +

    -Bug fixes

    +Bug fixes
    • In getSSB(), the calculation of the spawning stock biomass is done correctly using the maturity ogive instead of the proportion of energy allocated to reproduction. (#47)
    • The fast FFT method and the old method for calculating integrals now give the same numerical results. (#39)
      • @@ -511,13 +612,30 @@

      Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c01e5923b..1273238dd 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 74a0144f3..39812c081 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,6 @@ pandoc: 2.7.3 -pkgdown: 1.5.1 -pkgdown_sha: ~ +pkgdown: 1.5.1.9000 +pkgdown_sha: 3b74d8860686ed6d63e536d7ec4971fbbde5faff articles: _build_model_1: Lysekil/_build_model_1.html _build_model_2: Lysekil/_build_model_2.html @@ -12,6 +12,7 @@ articles: developer_vignette: developer_vignette.html editing_website: editing_website.html exploring_the_simulation_results: exploring_the_simulation_results.html + making_modifications: making_modifications.html mizer: mizer.html model_description: model_description.html multispecies_model: multispecies_model.html @@ -20,7 +21,7 @@ articles: running_a_simulation: running_a_simulation.html trait_model: trait_model.html working_with_git: working_with_git.html -last_built: 2020-05-05T17:14Z +last_built: 2020-06-08T15:57Z urls: reference: https://sizespectrum.org/mizer/reference article: https://sizespectrum.org/mizer/articles diff --git a/docs/reference/BevertonHoltRDD.html b/docs/reference/BevertonHoltRDD.html index 234ecff87..7855c8454 100644 --- a/docs/reference/BevertonHoltRDD.html +++ b/docs/reference/BevertonHoltRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -191,13 +247,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/MizerParams-class.html b/docs/reference/MizerParams-class.html index 70c70c2bb..3cb4f2e64 100644 --- a/docs/reference/MizerParams-class.html +++ b/docs/reference/MizerParams-class.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -143,7 +199,7 @@

    Slots

    - +
    w

    The size grid for the fish part of the spectrum. An increasing vector of weights (in grams) running from the smallest egg size to the largest asymptotic size.

    @@ -303,13 +359,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/MizerParams.html b/docs/reference/MizerParams.html index 49bbc0561..ce6d70cc9 100644 --- a/docs/reference/MizerParams.html +++ b/docs/reference/MizerParams.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -232,13 +288,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/MizerSim-class.html b/docs/reference/MizerSim-class.html index cd94b2415..3523feda8 100644 --- a/docs/reference/MizerSim-class.html +++ b/docs/reference/MizerSim-class.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -141,13 +197,13 @@

    Details

    As a user you should never have to access the slots of a MizerSim object directly. Instead there are a range of functions to extract the information. N() and NResource() return arrays with the saved abundances of -the species and the resource population at size respectively. effort() +the species and the resource population at size respectively. getEffort() returns the fishing effort of each gear through time. -times() returns the vector of times at which simulation results +getTimes() returns the vector of times at which simulation results were stored and idxFinalT() returns the index with which to access specifically the value at the final time in the arrays returned by the other -functions. Tparams() returns the MizerParams object that was -passed in to project(). There are also several +functions. getParams() returns the MizerParams object that was +passed to project(). There are also several summary_functions and plotting_functions available to explore the contents of a MizerSim object.

    The arrays all have named dimensions. The names of the time dimension @@ -166,7 +222,7 @@

    Slots

    - +
    params

    An object of type MizerParams.

    n

    Three-dimensional array (time x species x size) that stores the @@ -198,13 +254,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/MizerSim.html b/docs/reference/MizerSim.html index a5907d050..2ef070685 100644 --- a/docs/reference/MizerSim.html +++ b/docs/reference/MizerSim.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -178,13 +234,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/N.html b/docs/reference/N.html index fecb80a60..6434a6a45 100644 --- a/docs/reference/N.html +++ b/docs/reference/N.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/NOther.html b/docs/reference/NOther.html index 4c7d98a29..873b9a224 100644 --- a/docs/reference/NOther.html +++ b/docs/reference/NOther.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -160,13 +216,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/NS_params.html b/docs/reference/NS_params.html index 7cad2ff61..cd1ed132b 100644 --- a/docs/reference/NS_params.html +++ b/docs/reference/NS_params.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -167,13 +223,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/NS_species_params.html b/docs/reference/NS_species_params.html index 1015e863b..983f09338 100644 --- a/docs/reference/NS_species_params.html +++ b/docs/reference/NS_species_params.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -141,7 +197,7 @@

    Example species parameter set based on the North Sea

    Format

    -

    A data frame with 12 rows and 7 columns. Each row is a species.

    +

    A data frame with 12 rows and 7 columns. Each row is a species.

    species

    Name of the species

    w_inf

    The von Bertalanffy W_infinity parameter

    w_mat

    Size at maturity

    @@ -177,13 +233,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/NS_species_params_gears.html b/docs/reference/NS_species_params_gears.html index 552fd867c..3b1d2e765 100644 --- a/docs/reference/NS_species_params_gears.html +++ b/docs/reference/NS_species_params_gears.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -139,7 +195,7 @@

    Example species parameter set based on the North Sea with different gearsFormat

    -

    A data frame with 12 rows and 8 columns. Each row is a species.

    +

    A data frame with 12 rows and 8 columns. Each row is a species.

    species

    Name of the species

    w_inf

    The von Bertalanffy W_infinity parameter

    w_mat

    Size at maturity

    @@ -177,13 +233,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/RickerRDD.html b/docs/reference/RickerRDD.html index 3c14662ed..f85ac7d59 100644 --- a/docs/reference/RickerRDD.html +++ b/docs/reference/RickerRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -180,13 +236,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/SheperdRDD.html b/docs/reference/SheperdRDD.html index a2fda0ac8..2794ad622 100644 --- a/docs/reference/SheperdRDD.html +++ b/docs/reference/SheperdRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -180,13 +236,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/box_pred_kernel.html b/docs/reference/box_pred_kernel.html index 3bd70e5cc..0653efcad 100644 --- a/docs/reference/box_pred_kernel.html +++ b/docs/reference/box_pred_kernel.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -177,13 +233,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/constantRDD.html b/docs/reference/constantRDD.html index 9254ce868..fbb06f10e 100644 --- a/docs/reference/constantRDD.html +++ b/docs/reference/constantRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -176,13 +232,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/constant_other.html b/docs/reference/constant_other.html new file mode 100644 index 000000000..557d15370 --- /dev/null +++ b/docs/reference/constant_other.html @@ -0,0 +1,256 @@ + + + + + + + + +Helper function to keep other components constant — constant_other • mizer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Helper function to keep other components constant

    + Source: R/steady.R + +
    + +
    +

    Helper function to keep other components constant

    +
    + + 
    constant_other(params, n_other, component, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    params

    MizerParams object

    n_other

    Abundances of other components

    component

    Name of the component that is being updated

    ...

    Unused

    + + +
    + +
    + + + +
    + + + + + + + + + + + diff --git a/docs/reference/default_pred_kernel_params.html b/docs/reference/default_pred_kernel_params.html index 7410f0e31..a7cd2a581 100644 --- a/docs/reference/default_pred_kernel_params.html +++ b/docs/reference/default_pred_kernel_params.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/double_sigmoid_length.html b/docs/reference/double_sigmoid_length.html index d4de645fa..ecbe4ad11 100644 --- a/docs/reference/double_sigmoid_length.html +++ b/docs/reference/double_sigmoid_length.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -199,13 +255,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/emptyParams.html b/docs/reference/emptyParams.html index 4c78e5ca0..8ac36a3bc 100644 --- a/docs/reference/emptyParams.html +++ b/docs/reference/emptyParams.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -220,13 +276,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/finalN.html b/docs/reference/finalN.html index 55833e68c..fd340f525 100644 --- a/docs/reference/finalN.html +++ b/docs/reference/finalN.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -164,13 +220,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/finalNOther.html b/docs/reference/finalNOther.html index 7fdb1c3d3..f332069a4 100644 --- a/docs/reference/finalNOther.html +++ b/docs/reference/finalNOther.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -160,13 +216,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getBiomass.html b/docs/reference/getBiomass.html index 4fe9a3b18..9ec611dcc 100644 --- a/docs/reference/getBiomass.html +++ b/docs/reference/getBiomass.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -151,7 +207,7 @@

    Arg ... -

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -201,13 +257,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getBiomassFrame.html b/docs/reference/getBiomassFrame.html index a4def7111..ae310fa4d 100644 --- a/docs/reference/getBiomassFrame.html +++ b/docs/reference/getBiomassFrame.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -178,7 +234,7 @@

    Arg ... -

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -211,13 +267,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getCommunitySlope.html b/docs/reference/getCommunitySlope.html index 7b398cc15..75d538e93 100644 --- a/docs/reference/getCommunitySlope.html +++ b/docs/reference/getCommunitySlope.html @@ -37,6 +37,12 @@ + + + + + + @@ -78,7 +84,7 @@ mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -143,7 +199,7 @@

    Calculate the slope of the community abundance

    getCommunitySlope(
   sim,
-  species = seq_len(nrow(species_params(params(sim)))),
+  species = seq_len(nrow(species_params(getParams(sim)))),
   biomass = TRUE,
   ...
 )
    @@ -167,7 +223,7 @@

    Arg ... -

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -221,13 +277,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getComponent.html b/docs/reference/getComponent.html index 4fe3e224d..3aa031501 100644 --- a/docs/reference/getComponent.html +++ b/docs/reference/getComponent.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -166,13 +222,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getCriticalFeedingLevel.html b/docs/reference/getCriticalFeedingLevel.html index 8633f5fde..1675227f4 100644 --- a/docs/reference/getCriticalFeedingLevel.html +++ b/docs/reference/getCriticalFeedingLevel.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getDiet.html b/docs/reference/getDiet.html index 14b6d7ae6..b8c2d21c3 100644 --- a/docs/reference/getDiet.html +++ b/docs/reference/getDiet.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -135,6 +191,7 @@

    Get diet of predator at size, resolved by prey species

    params, n = initialN(params), n_pp = initialNResource(params), + n_other = initialNOther(params), proportion = TRUE ) @@ -143,7 +200,7 @@

    Arg params -

    A MizerParams object

    +

    A MizerParams object

    n @@ -153,6 +210,11 @@

    Arg n_pp

    A vector of the resource abundance by size

    + + n_other +

    A list of abundances for other dynamical components of the +ecosystem

    + proportion

    If TRUE (default) the function returns the diet as a @@ -164,7 +226,7 @@

    Arg

    Value

    An array (predator species x predator size x -(prey species + resource) )

    +(prey species + resource + other components) )

    Details

    This function performs the same integration as @@ -197,13 +259,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getEGrowth.html b/docs/reference/getEGrowth.html index ef03f372a..d4e91f1c9 100644 --- a/docs/reference/getEGrowth.html +++ b/docs/reference/getEGrowth.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -221,13 +277,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getERepro.html b/docs/reference/getERepro.html index a98ede5b3..3c80f43f6 100644 --- a/docs/reference/getERepro.html +++ b/docs/reference/getERepro.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -215,13 +271,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getEReproAndGrowth.html b/docs/reference/getEReproAndGrowth.html index 3508d8601..9b15668ce 100644 --- a/docs/reference/getEReproAndGrowth.html +++ b/docs/reference/getEReproAndGrowth.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -235,13 +291,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getESpawning.html b/docs/reference/getESpawning.html index bdea22483..72554d044 100644 --- a/docs/reference/getESpawning.html +++ b/docs/reference/getESpawning.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -213,13 +269,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/effort.html b/docs/reference/getEffort.html similarity index 66% rename from docs/reference/effort.html rename to docs/reference/getEffort.html index e3ac9901d..d5c59b1b1 100644 --- a/docs/reference/effort.html +++ b/docs/reference/getEffort.html @@ -6,7 +6,7 @@ -Fishing effort used in simulation — effort • mizer +Fishing effort used in simulation — getEffort • mizer @@ -37,9 +37,15 @@ + + + + + - + + mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -125,7 +181,7 @@

    Fishing effort used in simulation

    Source: R/MizerSim-class.R - +
    @@ -135,7 +191,7 @@

    Fishing effort used in simulation

    t_save).

    - 
    effort(sim)
    + 
    getEffort(sim)

    Arguments

    @@ -166,13 +222,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getEncounter.html b/docs/reference/getEncounter.html index 330b1fdf0..310e3f2dc 100644 --- a/docs/reference/getEncounter.html +++ b/docs/reference/getEncounter.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + +
    + +
    + + @@ -240,13 +296,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getFMort.html b/docs/reference/getFMort.html index 1e9b34372..d52f29b75 100644 --- a/docs/reference/getFMort.html +++ b/docs/reference/getFMort.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + +
    + +
    + + @@ -240,13 +296,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getFMortGear.html b/docs/reference/getFMortGear.html index aaa31b386..6d513fa8f 100644 --- a/docs/reference/getFMortGear.html +++ b/docs/reference/getFMortGear.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -229,13 +285,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getFeedingLevel.html b/docs/reference/getFeedingLevel.html index f568356f7..6a225ab74 100644 --- a/docs/reference/getFeedingLevel.html +++ b/docs/reference/getFeedingLevel.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -246,13 +302,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getGrowthCurves.html b/docs/reference/getGrowthCurves.html index f6e0f7b16..d47126a07 100644 --- a/docs/reference/getGrowthCurves.html +++ b/docs/reference/getGrowthCurves.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -192,13 +248,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getM2.html b/docs/reference/getM2.html index e21fb4864..936a55013 100644 --- a/docs/reference/getM2.html +++ b/docs/reference/getM2.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -222,13 +278,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getM2Background.html b/docs/reference/getM2Background.html index fe65c676a..50dabdbeb 100644 --- a/docs/reference/getM2Background.html +++ b/docs/reference/getM2Background.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -213,13 +269,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getMeanMaxWeight.html b/docs/reference/getMeanMaxWeight.html index 38e292b75..618eb6584 100644 --- a/docs/reference/getMeanMaxWeight.html +++ b/docs/reference/getMeanMaxWeight.html @@ -37,6 +37,12 @@ + + + + + + @@ -78,7 +84,7 @@ mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + +
    + +
    + + @@ -143,7 +199,7 @@

    Calculate the mean maximum weight of the community

    getMeanMaxWeight(
   sim,
-  species = seq_len(nrow(species_params(params(sim)))),
+  species = seq_len(nrow(species_params(getParams(sim)))),
   measure = "both",
   ...
 )
    @@ -166,7 +222,7 @@

    Arg

    - - +
    ...

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -217,13 +273,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getMeanWeight.html b/docs/reference/getMeanWeight.html index 1d1a9943a..b8f92062d 100644 --- a/docs/reference/getMeanWeight.html +++ b/docs/reference/getMeanWeight.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + + @@ -139,7 +195,11 @@

    Calculate the mean weight of the community

    calculation.

    - 
    getMeanWeight(sim, species = seq_len(nrow(species_params(params(sim)))), ...)
    + 
    getMeanWeight(
+  sim,
+  species = seq_len(nrow(species_params(getParams(sim)))),
+  ...
+)

    Arguments

    @@ -155,7 +215,7 @@

    Arg

    - - - +
    ...

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -202,13 +262,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getMort.html b/docs/reference/getMort.html index 0369e5b22..004a5d1a5 100644 --- a/docs/reference/getMort.html +++ b/docs/reference/getMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -225,13 +281,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getN.html b/docs/reference/getN.html index 0b121c482..e7c8821fc 100644 --- a/docs/reference/getN.html +++ b/docs/reference/getN.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -148,7 +204,7 @@

    Arg

    ...

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -198,13 +254,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/params.html b/docs/reference/getParams.html similarity index 65% rename from docs/reference/params.html rename to docs/reference/getParams.html index c3409a513..81be16f2e 100644 --- a/docs/reference/params.html +++ b/docs/reference/getParams.html @@ -6,7 +6,7 @@ -Extract the parameter object underlying a simulation — params • mizer +Extract the parameter object underlying a simulation — getParams • mizer @@ -37,9 +37,15 @@ + + + + + - + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -122,14 +178,14 @@

    Extract the parameter object underlying a simulation

    Source: R/MizerSim-class.R - +

    Extract the parameter object underlying a simulation

    - 
    params(sim)
    + 
    getParams(sim)

    Arguments

    @@ -159,13 +215,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getPhiPrey.html b/docs/reference/getPhiPrey.html index 0c32ce251..19e9bf64f 100644 --- a/docs/reference/getPhiPrey.html +++ b/docs/reference/getPhiPrey.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -189,13 +245,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getPredKernel.html b/docs/reference/getPredKernel.html index d549fb753..b9ad7791a 100644 --- a/docs/reference/getPredKernel.html +++ b/docs/reference/getPredKernel.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -166,13 +222,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getPredMort.html b/docs/reference/getPredMort.html index 05b7ab4b2..2ca9bdd53 100644 --- a/docs/reference/getPredMort.html +++ b/docs/reference/getPredMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -226,13 +282,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getPredRate.html b/docs/reference/getPredRate.html index c86031c03..d86f76d10 100644 --- a/docs/reference/getPredRate.html +++ b/docs/reference/getPredRate.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + +
    + +
    + + @@ -220,13 +276,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getProportionOfLargeFish.html b/docs/reference/getProportionOfLargeFish.html index 16bac16bb..df1fcbaec 100644 --- a/docs/reference/getProportionOfLargeFish.html +++ b/docs/reference/getProportionOfLargeFish.html @@ -37,6 +37,12 @@ + + + + + + @@ -79,7 +85,7 @@ mizer - 2.0.1 + 2.0.2 @@ -97,8 +103,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -116,6 +166,12 @@
    • + +
    + +
    + + @@ -145,7 +201,7 @@

    Calculate the proportion of large fish

    getProportionOfLargeFish(
   sim,
-  species = seq_len(nrow(species_params(params(sim)))),
+  species = seq_len(nrow(species_params(getParams(sim)))),
   threshold_w = 100,
   threshold_l = NULL,
   biomass_proportion = TRUE,
@@ -181,7 +237,7 @@ 
    Arg
    - - +
    ...

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -231,13 +287,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getRDD.html b/docs/reference/getRDD.html index d9ae713ba..18af7e473 100644 --- a/docs/reference/getRDD.html +++ b/docs/reference/getRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -78,7 +84,7 @@ mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -220,13 +276,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getRDI.html b/docs/reference/getRDI.html index e6c90ea98..9368a15b2 100644 --- a/docs/reference/getRDI.html +++ b/docs/reference/getRDI.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -214,13 +270,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getResourceMort.html b/docs/reference/getResourceMort.html index 2d5523688..00c8667c1 100644 --- a/docs/reference/getResourceMort.html +++ b/docs/reference/getResourceMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -215,13 +271,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getSSB.html b/docs/reference/getSSB.html index 2c6011cfb..85db65edb 100644 --- a/docs/reference/getSSB.html +++ b/docs/reference/getSSB.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -179,13 +235,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/times.html b/docs/reference/getTimes.html similarity index 64% rename from docs/reference/times.html rename to docs/reference/getTimes.html index c7ae20f91..77f437e1d 100644 --- a/docs/reference/times.html +++ b/docs/reference/getTimes.html @@ -6,7 +6,7 @@ -Times for which simulation results are available — times • mizer +Times for which simulation results are available — getTimes • mizer @@ -37,9 +37,15 @@ + + + + + - + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -122,14 +178,14 @@

    Times for which simulation results are available

    Source: R/MizerSim-class.R - +

    Times for which simulation results are available

    - 
    times(sim)
    + 
    getTimes(sim)

    Arguments

    @@ -160,13 +216,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getYield.html b/docs/reference/getYield.html index 2074bb5eb..30084992e 100644 --- a/docs/reference/getYield.html +++ b/docs/reference/getYield.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -177,13 +233,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getYieldGear.html b/docs/reference/getYieldGear.html index bca7a4440..b644265a2 100644 --- a/docs/reference/getYieldGear.html +++ b/docs/reference/getYieldGear.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -178,13 +234,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/getZ.html b/docs/reference/getZ.html index a7f3e11db..db266b153 100644 --- a/docs/reference/getZ.html +++ b/docs/reference/getZ.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -221,13 +277,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_gamma_default.html b/docs/reference/get_gamma_default.html index 8b9d873b4..2ffbdddac 100644 --- a/docs/reference/get_gamma_default.html +++ b/docs/reference/get_gamma_default.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_h_default.html b/docs/reference/get_h_default.html index 698bbeae2..ddab64d98 100644 --- a/docs/reference/get_h_default.html +++ b/docs/reference/get_h_default.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + +
    + +
    + + @@ -169,13 +225,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_initial_n.html b/docs/reference/get_initial_n.html index 00d60b6cb..83bbf2874 100644 --- a/docs/reference/get_initial_n.html +++ b/docs/reference/get_initial_n.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + +
    + +
    + + @@ -179,13 +235,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_ks_default.html b/docs/reference/get_ks_default.html index 52863c1bf..d6edb87a6 100644 --- a/docs/reference/get_ks_default.html +++ b/docs/reference/get_ks_default.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + +
    + +
    + + @@ -165,13 +221,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_phi.html b/docs/reference/get_phi.html index 02e4bbebc..30be536ff 100644 --- a/docs/reference/get_phi.html +++ b/docs/reference/get_phi.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + +
    + +
    + + @@ -171,13 +227,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_required_reproduction.html b/docs/reference/get_required_reproduction.html index 32dd94db1..3ff38cd3b 100644 --- a/docs/reference/get_required_reproduction.html +++ b/docs/reference/get_required_reproduction.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -159,13 +215,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_size_range_array.html b/docs/reference/get_size_range_array.html index 7d2a73fe5..16808a0b5 100644 --- a/docs/reference/get_size_range_array.html +++ b/docs/reference/get_size_range_array.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -207,13 +263,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/get_time_elements.html b/docs/reference/get_time_elements.html index f887a18cb..89cbbaf1b 100644 --- a/docs/reference/get_time_elements.html +++ b/docs/reference/get_time_elements.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -167,13 +223,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/idxFinalT.html b/docs/reference/idxFinalT.html index 066026225..26abd96a1 100644 --- a/docs/reference/idxFinalT.html +++ b/docs/reference/idxFinalT.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -151,9 +207,9 @@

    Examp idx <- idxFinalT(sim) idx # This coincides with -length(times(sim)) +length(times(sim)) # and corresponds to the final time -times(sim)[idx] +times(sim)[idx] # We can use this index to extract the result at the final time identical(N(sim)[idx, , ], finalN(sim)) identical(NResource(sim)[idx, ], finalNResource(sim)) @@ -173,13 +229,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 1643c7392..419593583 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -37,6 +37,12 @@ + + + + + + @@ -71,7 +77,7 @@ mizer - 2.0.1 + 2.0.2 @@ -89,8 +95,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -108,6 +158,12 @@
    • + +
    + +
    + + @@ -247,18 +303,6 @@

    params()

    - -

    - - - - - - @@ -340,21 +384,15 @@

    effort()

    +

    getEffort()

    - - - - @@ -417,12 +455,6 @@

    getGrowthCurves()

    - - - - @@ -1030,6 +1062,12 @@

    emptyParams()

    + + + + @@ -1051,6 +1089,18 @@

    summary(<MizerParams>)

    + +

    + + + + + + @@ -1063,6 +1113,12 @@

    summary(<MizerSim>)

    + +

    + + @@ -1073,6 +1129,12 @@

    MizerSim()

    + + + + @@ -1155,6 +1217,12 @@

    Alias for getERepro

    + + + + @@ -1196,13 +1264,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/indicator_functions.html b/docs/reference/indicator_functions.html index bbc6cf195..3ce337d59 100644 --- a/docs/reference/indicator_functions.html +++ b/docs/reference/indicator_functions.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/initialN-set.html b/docs/reference/initialN-set.html index 7cb054ff2..2f054f519 100644 --- a/docs/reference/initialN-set.html +++ b/docs/reference/initialN-set.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -167,13 +223,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/initialNOther-set.html b/docs/reference/initialNOther-set.html index ba9509d6e..d4037de45 100644 --- a/docs/reference/initialNOther-set.html +++ b/docs/reference/initialNOther-set.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -163,13 +219,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/initialNResource-set.html b/docs/reference/initialNResource-set.html index dcf81415a..4d1bc001a 100644 --- a/docs/reference/initialNResource-set.html +++ b/docs/reference/initialNResource-set.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -167,13 +223,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/inter.html b/docs/reference/inter.html index 845ee4022..23c5e2056 100644 --- a/docs/reference/inter.html +++ b/docs/reference/inter.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + +
    + +
    + + @@ -153,13 +209,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/knife_edge.html b/docs/reference/knife_edge.html index 336de8435..2d185737a 100644 --- a/docs/reference/knife_edge.html +++ b/docs/reference/knife_edge.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -166,13 +222,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/log_breaks.html b/docs/reference/log_breaks.html index c47d79106..13c2cc812 100644 --- a/docs/reference/log_breaks.html +++ b/docs/reference/log_breaks.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -166,13 +222,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/lognormal_pred_kernel.html b/docs/reference/lognormal_pred_kernel.html index ba74300b8..caa23d435 100644 --- a/docs/reference/lognormal_pred_kernel.html +++ b/docs/reference/lognormal_pred_kernel.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -184,13 +240,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizer.html b/docs/reference/mizer.html index 724381a7e..0a6efa9ec 100644 --- a/docs/reference/mizer.html +++ b/docs/reference/mizer.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + +
    + +
    + + @@ -172,13 +228,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerEGrowth.html b/docs/reference/mizerEGrowth.html index 9e4c7d4d2..a90b9bd01 100644 --- a/docs/reference/mizerEGrowth.html +++ b/docs/reference/mizerEGrowth.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + +
    + +
    + + @@ -171,7 +227,7 @@

    Arg

    - +

    Extract the parameter object underlying a simulation

    -

    summary(<MizerParams>)

    -

    Summarize MizerParams object

    setRmax()

    Fishing effort used in simulation
    -

    times()

    +

    getTimes()

    Times for which simulation results are available

    -

    w() w_full() dw() dw_full()

    -

    Size bins

    Get growth curves giving weight as a function of age

    -

    summary(<MizerSim>)

    -

    Summarize MizerSim object

    Create empty MizerParams object of the right size

    +

    project_simple()

    +

    Project abundances by a given number of time steps into the future

    Summarize MizerParams object

    +

    w() w_full() dw() dw_full()

    +

    Size bins

    upgradeParams()

    Summarize MizerSim object

    upgradeSim()

    Constructor for the MizerSim class

    +

    getParams()

    +

    Extract the parameter object underlying a simulation
    +

    getPhiPrey()

    +

    Get available energy

    getM2()

    ...

    Unused

    Optional arguments for rate functions.
    @@ -209,13 +265,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerERepro.html b/docs/reference/mizerERepro.html index 3cc1acaa4..3c77902bd 100644 --- a/docs/reference/mizerERepro.html +++ b/docs/reference/mizerERepro.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -163,7 +219,7 @@

    Arg

    ...

    Unused

    Optional arguments for rate functions.
    @@ -207,13 +263,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerEReproAndGrowth.html b/docs/reference/mizerEReproAndGrowth.html index 73e1641e8..e1e1ef913 100644 --- a/docs/reference/mizerEReproAndGrowth.html +++ b/docs/reference/mizerEReproAndGrowth.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -170,7 +226,7 @@

    Arg

    ...

    Unused

    Optional arguments for rate functions.
    @@ -221,13 +277,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerEncounter.html b/docs/reference/mizerEncounter.html index 6f2fb8b5c..eb0d88b18 100644 --- a/docs/reference/mizerEncounter.html +++ b/docs/reference/mizerEncounter.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -155,7 +211,7 @@

    Arg

    ...

    Unused

    Optional arguments for rate functions.
    @@ -226,13 +282,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerFMort.html b/docs/reference/mizerFMort.html index c4621b68c..9746a45fd 100644 --- a/docs/reference/mizerFMort.html +++ b/docs/reference/mizerFMort.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + + @@ -153,7 +209,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -194,13 +250,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerFMortGear.html b/docs/reference/mizerFMortGear.html index afa925392..0a051085b 100644 --- a/docs/reference/mizerFMortGear.html +++ b/docs/reference/mizerFMortGear.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -151,7 +207,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -193,13 +249,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerFeedingLevel.html b/docs/reference/mizerFeedingLevel.html index 5022a8d39..51e8c298d 100644 --- a/docs/reference/mizerFeedingLevel.html +++ b/docs/reference/mizerFeedingLevel.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -145,7 +201,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -202,13 +258,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerMort.html b/docs/reference/mizerMort.html index 535774024..c148431fe 100644 --- a/docs/reference/mizerMort.html +++ b/docs/reference/mizerMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -167,7 +223,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -206,13 +262,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerPredMort.html b/docs/reference/mizerPredMort.html index 006cfca3a..cb199283e 100644 --- a/docs/reference/mizerPredMort.html +++ b/docs/reference/mizerPredMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -162,7 +218,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -201,13 +257,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerPredRate.html b/docs/reference/mizerPredRate.html index 9b362488b..f16303415 100644 --- a/docs/reference/mizerPredRate.html +++ b/docs/reference/mizerPredRate.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + + @@ -169,7 +225,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -209,13 +265,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerRDI.html b/docs/reference/mizerRDI.html index 1f4f800ec..529e74a40 100644 --- a/docs/reference/mizerRDI.html +++ b/docs/reference/mizerRDI.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -169,7 +225,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -211,13 +267,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerRates.html b/docs/reference/mizerRates.html index 4761e62f6..36f54c9b5 100644 --- a/docs/reference/mizerRates.html +++ b/docs/reference/mizerRates.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -166,7 +222,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -218,13 +274,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/mizerResourceMort.html b/docs/reference/mizerResourceMort.html index f941b8ed1..20a054c42 100644 --- a/docs/reference/mizerResourceMort.html +++ b/docs/reference/mizerResourceMort.html @@ -38,6 +38,12 @@ + + + + + + mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -164,7 +220,7 @@

    Arg ... -

    Unused

    +

    Optional arguments for rate functions.

    @@ -205,13 +261,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/newCommunityParams.html b/docs/reference/newCommunityParams.html index 8ec6f3809..4d62639af 100644 --- a/docs/reference/newCommunityParams.html +++ b/docs/reference/newCommunityParams.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -294,13 +350,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/newMultispeciesParams.html b/docs/reference/newMultispeciesParams.html index 6b172e0b4..171e12c35 100644 --- a/docs/reference/newMultispeciesParams.html +++ b/docs/reference/newMultispeciesParams.html @@ -37,6 +37,12 @@ + + + + + + @@ -78,7 +84,7 @@ mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -563,7 +619,7 @@

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/newTraitParams.html b/docs/reference/newTraitParams.html index 159ed11a1..55f43ed57 100644 --- a/docs/reference/newTraitParams.html +++ b/docs/reference/newTraitParams.html @@ -37,6 +37,12 @@ + + + + + + @@ -81,7 +87,7 @@ mizer - 2.0.1 + 2.0.2 @@ -99,8 +105,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -118,6 +168,12 @@
    • + + @@ -406,13 +462,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/noRDD.html b/docs/reference/noRDD.html index 99c6f0144..b5792cd7d 100644 --- a/docs/reference/noRDD.html +++ b/docs/reference/noRDD.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -171,13 +227,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotBiomass.html b/docs/reference/plotBiomass.html index c97ef62bc..00969b557 100644 --- a/docs/reference/plotBiomass.html +++ b/docs/reference/plotBiomass.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -208,7 +264,7 @@

    Arg ... -

    Arguments passed on to get_size_range_array

    +

    Arguments passed on to get_size_range_array

    min_w

    Smallest weight in size range. Defaults to smallest weight in the model.

    max_w

    Largest weight in size range. Defaults to largest weight in the @@ -263,13 +319,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotDiet.html b/docs/reference/plotDiet.html index 013dfe046..a2788af79 100644 --- a/docs/reference/plotDiet.html +++ b/docs/reference/plotDiet.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -140,8 +196,7 @@

    Arg species -

    Name or vector of names of the species to be plotted. By -default all species are plotted.

    +

    The name of the species whose diet should be plotted

    @@ -177,13 +232,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotFMort.html b/docs/reference/plotFMort.html index f3005fba6..0c910e15f 100644 --- a/docs/reference/plotFMort.html +++ b/docs/reference/plotFMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -75,7 +81,7 @@ mizer - 2.0.1 + 2.0.2 @@ -93,8 +99,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -112,6 +162,12 @@
    • + + @@ -207,13 +263,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotFeedingLevel-2.png b/docs/reference/plotFeedingLevel-2.png index 6d412c12e..bb32b06d7 100644 Binary files a/docs/reference/plotFeedingLevel-2.png and b/docs/reference/plotFeedingLevel-2.png differ diff --git a/docs/reference/plotFeedingLevel.html b/docs/reference/plotFeedingLevel.html index 64be46853..f3b9c9670 100644 --- a/docs/reference/plotFeedingLevel.html +++ b/docs/reference/plotFeedingLevel.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -224,7 +280,8 @@

    Examp 
    # \donttest{
 params <- suppressMessages(newMultispeciesParams(NS_species_params_gears, inter))
 sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE)
-plotFeedingLevel(sim)
    plotFeedingLevel(sim, time_range = 10:20, species = c("Cod", "Herring"))
    # }
+plotFeedingLevel(sim)
    plotFeedingLevel(sim, time_range = 10:20, species = c("Cod", "Herring"),
+                 include_critical = TRUE)
    # }
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotGrowthCurves.html b/docs/reference/plotGrowthCurves.html index 85541d682..6bc016d7f 100644 --- a/docs/reference/plotGrowthCurves.html +++ b/docs/reference/plotGrowthCurves.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + + @@ -224,13 +280,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotM2.html b/docs/reference/plotM2.html index d4442c43e..dc477e9e3 100644 --- a/docs/reference/plotM2.html +++ b/docs/reference/plotM2.html @@ -37,6 +37,12 @@ + + + + + + @@ -72,7 +78,7 @@ mizer - 2.0.1 + 2.0.2 @@ -90,8 +96,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -109,6 +159,12 @@
    • + + @@ -199,13 +255,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotMizerSim.html b/docs/reference/plotMizerSim.html index 0d4ec1af9..443e2ee91 100644 --- a/docs/reference/plotMizerSim.html +++ b/docs/reference/plotMizerSim.html @@ -37,6 +37,12 @@ + + + + + + @@ -78,7 +84,7 @@ mizer - 2.0.1 + 2.0.2 @@ -96,8 +102,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -115,6 +165,12 @@
    • + + @@ -222,13 +278,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotPredMort.html b/docs/reference/plotPredMort.html index 6106093d9..cbb8b3db2 100644 --- a/docs/reference/plotPredMort.html +++ b/docs/reference/plotPredMort.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -205,13 +261,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotSpectra.html b/docs/reference/plotSpectra.html index babb0dfee..8b22e9b25 100644 --- a/docs/reference/plotSpectra.html +++ b/docs/reference/plotSpectra.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -275,13 +331,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotYield.html b/docs/reference/plotYield.html index f0424dc03..eec329580 100644 --- a/docs/reference/plotYield.html +++ b/docs/reference/plotYield.html @@ -37,6 +37,12 @@ + + + + + + @@ -74,7 +80,7 @@ mizer - 2.0.1 + 2.0.2 @@ -92,8 +98,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -111,6 +161,12 @@
    • + + @@ -224,13 +280,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotYieldGear.html b/docs/reference/plotYieldGear.html index 167b46259..ee1a0700b 100644 --- a/docs/reference/plotYieldGear.html +++ b/docs/reference/plotYieldGear.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -207,13 +263,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/plotting_functions.html b/docs/reference/plotting_functions.html index 9c7c6254d..152471c7f 100644 --- a/docs/reference/plotting_functions.html +++ b/docs/reference/plotting_functions.html @@ -37,6 +37,12 @@ + + + + + + @@ -77,7 +83,7 @@ mizer - 2.0.1 + 2.0.2 @@ -95,8 +101,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -114,6 +164,12 @@
    • + + @@ -152,7 +208,9 @@

    Details plotFMort()Plots the total fishing mortality of each species against size. plotYield()Plots the total yield of each species across all fishing gears against time. plotYieldGear()Plots the total yield of each species by gear against time. -plot()Produces 5 plots (plotFeedingLevel(), plotBiomass(), plotPredMort(), plotFMort() and plotSpectra()) in the same window as a summary. +plotDiet()Plots the diet composition at size for a given predator species. +plotGrowthCurves()Plots the size as a function of age. +plot()Produces 5 plots (plotFeedingLevel(), plotBiomass(), plotPredMort(), plotFMort() and plotSpectra()) in the same window. @@ -226,13 +284,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/power_law_pred_kernel.html b/docs/reference/power_law_pred_kernel.html index 99df7c716..c12361871 100644 --- a/docs/reference/power_law_pred_kernel.html +++ b/docs/reference/power_law_pred_kernel.html @@ -37,6 +37,12 @@ + + + + + + @@ -73,7 +79,7 @@ mizer - 2.0.1 + 2.0.2 @@ -91,8 +97,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -110,6 +160,12 @@
    • + + @@ -200,13 +256,30 @@

    Contents

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.5.1.9000.

    + + + diff --git a/docs/reference/project.html b/docs/reference/project.html index a0038d0d8..81e9b0e6a 100644 --- a/docs/reference/project.html +++ b/docs/reference/project.html @@ -37,6 +37,12 @@ + + + + + + @@ -76,7 +82,7 @@ mizer - 2.0.1 + 2.0.2 @@ -94,8 +100,52 @@
  • Reference
    • -
  • - Guides +
  • + +
  • Publications @@ -113,6 +163,12 @@
    • + + @@ -205,12 +261,12 @@

    Arg progress_bar

    Either a boolean value to determine whether a progress -bar should be shown in the console of a shiny progress object to implement -a progress bar in a shiny app

    +bar should be shown in the console, or a shiny progress object to implement +a progress bar in a shiny app.

    ... -

    Currently unused.

    +

    Other arguments will be passed to rate functions.

    @@ -232,7 +288,7 @@

    Note

    constant through time but each gear may have a different fishing effort.

  • A numerical array with dimensions time x gear. This specifies the fishing effort of each gear at each time step. The first dimension, time, -must be named numerically and contiguously. The second dimension of the array +must be named numerically and increasing. The second dimension of the array must be named and the names must correspond to the gear names in the MizerParams argument. The value for the effort for a particular time is used during the interval from that time to the next time in the array.

    • @@ -248,10 +304,6 @@

    Note

    values for the simulation are taken from the final values in the MizerSim object and the corresponding arguments to this function will be ignored.

    -

    See also

    - -

    MizerParams(), summary_functions(), -indicator_functions() and plotting_functions()

    Examples

    if (FALSE) {
@@ -288,13 +340,30 @@ 
    Contents
    
 
    
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/project_simple.html b/docs/reference/project_simple.html
new file mode 100644
index 000000000..3ef4fbc4b
--- /dev/null
+++ b/docs/reference/project_simple.html
@@ -0,0 +1,335 @@
+
+
+
+  
+  
+
+
+
+Project abundances by a given number of time steps into the future — project_simple • mizer
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
    
+      
    
+      
+
+      
+
+      
    
+
+
    
+  
    
+    
    
+    
    Project abundances by a given number of time steps into the future
    
+    Source: R/project.R
+    
+    
    
+
+    
    
+    
    This is an internal function used by the user-facing project() function.
+It is of potential interest only to mizer extension authors.
    
+    
    
+
+    
    project_simple(
+  params,
+  n,
+  n_pp,
+  n_other,
+  t,
+  dt,
+  steps,
+  effort,
+  resource_dynamics_fn,
+  other_dynamics_fns,
+  rates_fns,
+  ...
+)
    
+
+    
    Arguments
    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
    params
    A MizerParams object.
    n
    An array (species x size) with the number density at start of
+simulation.
    n_pp
    A vector (size) with the resource number density at start of
+simulation.
    n_other
    A named list with the abundances of other components at start
+of simulation.
    t
    Time at the start of the simulation.
    dt
    Size of time step.
    steps
    The number of time steps by which to project.
    effort
    The fishing effort to be used throughout the simulation. This
+must be a vector or list with one named entry per fishing gear.
    resource_dynamics_fn
    The function for the resource
+dynamics. See Details.
    other_dynamics_fns
    List with the functions for the
+dynamics of the other components. See Details.
    rates_fns
    List with the functions for calculating
+the rates. See Details.
    ...
    Other arguments that are passed on to the rate functions.
    
+
+    
    Value
    
+
+    
    List with the final values of n, n_pp and n_other, rates.
    
+    
    Details
    
+
+    
    The function does not check its arguments because it is mean to be as fast
+as possible to allow it to be used in a loop. For example it is called in
+project() once for every saved value. The function also does not save its
+intermediate results but only returns the result at time t + dt * steps.
+During this time it uses the constant fishing effort effort.
    
+
    The functional arguments can be calculated from slots in the params object
+with
    resource_dynamics_fn <- get(params@resource_dynamics)
+other_dynamics_fns <- lapply(params@other_dynamics, get)
+rates_fns <- lapply(params@rates_funcs, get)
    
+
+
    The reason the function does not do that itself is to shave 20 microseconds
+of its running time, which pays when the function is called hundreds of
+times in a row.
    
+
    This function is also used in steady(). In between calls to
+project_simple() the steady() function checks whether the values are
+still changing significantly, so that it can stop when a steady state has
+been approached. Mizer extension packages might have a similar need to run
+a simulation repeatedly for short periods to run some other code in
+between. Because this code may want to use the values of the rates at the
+final time step, these too are included in the returned list.
    
+
+  
    
+  
+
    
+
+
+      
+   
    
+
+  
+
+
+
+
+
+  
+
+
+
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index e8462dda2..3c42563cb 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -37,6 +37,12 @@
 
 
 
+
+
+
+
+
+
 
 
 
@@ -77,7 +83,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -95,8 +101,52 @@
 
  • 
   Reference
 
    • 
-
  • 
-  Guides
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -114,6 +164,12 @@
 
    • 
       
       
+      
+      
     
   
 
@@ -133,7 +189,7 @@ 
    Objects exported from other packages
    
     
    
     
    These objects are imported from other packages. Follow the links
 below to see their documentation.
    
-
+
    
   
    reshape2
    melt
    
 
 
    
@@ -157,13 +213,30 @@ 
    Contents
    
 
    
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/resource_constant.html b/docs/reference/resource_constant.html
index fad27fbf6..4ebcc9904 100644
--- a/docs/reference/resource_constant.html
+++ b/docs/reference/resource_constant.html
@@ -37,6 +37,12 @@
 
 
 
+
+
+
+
+
+
 
 
 
@@ -74,7 +80,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -92,8 +98,52 @@
 
  • 
   Reference
 
    • 
-
  • 
-  Guides
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -111,6 +161,12 @@
 
    • 
       
       
+      
+      
     
   
 
@@ -196,13 +252,30 @@ 
    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/resource_encounter.html b/docs/reference/resource_encounter.html
new file mode 100644
index 000000000..e6090b85c
--- /dev/null
+++ b/docs/reference/resource_encounter.html
@@ -0,0 +1,260 @@
+
+
+
+  
+  
+
+
+
+Dummy function used during testing only — resource_encounter • mizer
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
    
+      
    
+      
+
+      
+
+      
    
+
+
    
+  
    
+    
    
+    
    Dummy function used during testing only
    
+    Source: R/extension.R
+    
+    
    
+
+    
    
+    
    Dummy function used during testing only
    
+    
    
+
+    
    resource_encounter(params, n, n_pp, n_other, ...)
    
+
+    
    Arguments
    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
    params
    A MizerParams object
    n
    A matrix of species abundances (species x size)
    n_pp
    A vector of the resource abundance by size
    n_other
    A list with the abundances of other components
    ...
    Unused
    
+
+
+  
    
+  
+
    
+
+
+      
+   
    
+
+  
+
+
+
+
+
+  
+
+
+
diff --git a/docs/reference/resource_semichemostat.html b/docs/reference/resource_semichemostat.html
index b85f83697..e968a2108 100644
--- a/docs/reference/resource_semichemostat.html
+++ b/docs/reference/resource_semichemostat.html
@@ -37,6 +37,12 @@
 
 
 
+
+
+
+
+
+
 
 
 
@@ -72,7 +78,7 @@
       
       
         mizer
-        2.0.1
+        2.0.2
       
     
 
@@ -90,8 +96,52 @@
 
  • 
   Reference
 
    • 
-
  • 
-  Guides
+
  • 
+  
+  
 
    • 
 
  • 
   Publications
@@ -109,6 +159,12 @@
 
    • 
       
       
+      
+      
     
   
 
@@ -192,13 +248,30 @@ 
    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/retune_erepro.html b/docs/reference/retune_erepro.html
index b731fca3a..5f7ac3a5c 100644
--- a/docs/reference/retune_erepro.html
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+
+
+
 
 
   
diff --git a/docs/reference/semichemostat.html b/docs/reference/semichemostat.html
new file mode 100644
index 000000000..cad9d41b6
--- /dev/null
+++ b/docs/reference/semichemostat.html
@@ -0,0 +1,264 @@
+
+
+
+  
+  
+
+
+
+Dummy function used during testing only — semichemostat • mizer
+
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+    
    
+      
    
+      
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+  
    
+    
    
+    
    Dummy function used during testing only
    
+    Source: R/extension.R
+    
+    
    
+
+    
    
+    
    Dummy function used during testing only
    
+    
    
+
+    
    semichemostat(params, n_other, rates, dt, component, ...)
    
+
+    
    Arguments
    
+    
+    
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+    
    params
    A MizerParams object
    n_other
    A list with the abundances of other components
    rates
    A list of rates as returned by mizerRates()
    dt
    Time step
    component
    Name of the component that is being updated
    ...
    Unused
    
+
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diff --git a/docs/reference/setColours.html b/docs/reference/setColours.html
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setComponent.html b/docs/reference/setComponent.html
index b838e6275..6ea3c4cd4 100644
--- a/docs/reference/setComponent.html
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setExtMort.html b/docs/reference/setExtMort.html
index e00da37f7..66c421456 100644
--- a/docs/reference/setExtMort.html
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@@ -37,6 +37,12 @@
 
 
 
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setFishing.html b/docs/reference/setFishing.html
index b74107554..a9b187ca2 100644
--- a/docs/reference/setFishing.html
+++ b/docs/reference/setFishing.html
@@ -37,6 +37,12 @@
 
 
 
+
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+        2.0.2
       
     
 
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-  
    Site built with pkgdown 1.5.1.
    
+  
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+
+
 
 
   
diff --git a/docs/reference/setInitialValues.html b/docs/reference/setInitialValues.html
index f8bf56429..993a2ee1a 100644
--- a/docs/reference/setInitialValues.html
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@@ -37,6 +37,12 @@
 
 
 
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setInteraction.html b/docs/reference/setInteraction.html
index a43a6197b..d59b9a4d8 100644
--- a/docs/reference/setInteraction.html
+++ b/docs/reference/setInteraction.html
@@ -37,6 +37,12 @@
 
 
 
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+        2.0.2
       
     
 
@@ -90,8 +96,52 @@
 
  • 
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+
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+      
     
   
 
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setLinetypes.html b/docs/reference/setLinetypes.html
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setMaxIntakeRate.html b/docs/reference/setMaxIntakeRate.html
index f53c58c36..cd45a9b5e 100644
--- a/docs/reference/setMaxIntakeRate.html
+++ b/docs/reference/setMaxIntakeRate.html
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+        2.0.2
       
     
 
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  • 
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setMetabolicRate.html b/docs/reference/setMetabolicRate.html
index ab678ff11..b9a762222 100644
--- a/docs/reference/setMetabolicRate.html
+++ b/docs/reference/setMetabolicRate.html
@@ -37,6 +37,12 @@
 
 
 
+
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+        2.0.2
       
     
 
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  • 
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    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 56175fa07..eb4f4e070 100644
--- a/docs/reference/setParams.html
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@@ -37,6 +37,12 @@
 
 
 
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    Arg
     
     
       ...
-      
    Arguments passed on to setPredKernel, setSearchVolume, setMaxIntakeRate, setMetabolicRate, setExtMort, setReproduction, setFishing, setResource
    
+      
    Arguments passed on to setPredKernel, setSearchVolume, setMaxIntakeRate, setMetabolicRate, setExtMort, setReproduction, setFishing, setResource
    
     
    pred_kernel
    Optional. An array (species x predator size x prey size)
 that holds the predation coefficient of each predator at size on each prey
 size. If not supplied, a default is set as described in section "Setting
@@ -249,8 +305,8 @@ 
    Details
 by themselves is not changing the model until you call setParams() or the
 appropriate one of its sub-functions. Here is an example which assumes that
 you have have a MizerParams object params in which you just want to change
-one parameter of the third species:
    params@species_params$gamma[[3]] &lt;- 1000
-params &lt;- setParams(params)
    
+one parameter of the third species:
    params@species_params$gamma[[3]] <- 1000
+params <- setParams(params)
    
 
 
    Because of the way the R language works, setParams does not make the
 changes to the params object that you pass to it but instead returns a new
@@ -271,8 +327,8 @@ 
    Details
 instead of params <- setParams(params).
    
 
    If you have added a comment to a slot of the params object, then setParams()
 and its subfunctions will not recalculate the value for that slot from the
-species parameters. For example
    comment(params@search_vol) &lt;- "This should not change"
-species_params(params)$gamma &lt;- 10
    
+species parameters. For example
    comment(params@search_vol) <- "This should not change"
+species_params(params)$gamma <- 10
    
 
 
    will just issue a warning "The search volume has been commented and therefore
 will not be recalculated from the species parameters". You can remove the
@@ -465,7 +521,7 @@ 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/setPredKernel.html b/docs/reference/setPredKernel.html
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+
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+
 
 
   
diff --git a/docs/reference/setRateFunction.html b/docs/reference/setRateFunction.html
index ab998280b..d99ebcece 100644
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diff --git a/docs/reference/setReproduction.html b/docs/reference/setReproduction.html
index 5c745b693..616764210 100644
--- a/docs/reference/setReproduction.html
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@@ -37,12 +37,18 @@
 
 
 
+
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+individual and sets additional density dependence." />
 
 
 
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    Set reproduction parameters
    
     
    
     
    Sets the proportion of the total energy available for reproduction and growth
 that is invested into reproduction as a function of the size of the
-individual and sets the reproductive efficiency.
    
+individual and sets additional density dependence.
    
     
    
 
     
    setReproduction(params, maturity = NULL, repro_prop = NULL, RDD = NULL, ...)
@@ -184,7 +240,7 @@ 
    
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diff --git a/docs/reference/setResource.html b/docs/reference/setResource.html
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diff --git a/docs/reference/setRmax.html b/docs/reference/setRmax.html
index d34cdfa37..d25068e6c 100644
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+  
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+
+
+
 
 
   
diff --git a/docs/reference/setSearchVolume.html b/docs/reference/setSearchVolume.html
index a327c53b8..3e8dda7af 100644
--- a/docs/reference/setSearchVolume.html
+++ b/docs/reference/setSearchVolume.html
@@ -37,6 +37,12 @@
 
 
 
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+  
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+
+
+
 
 
   
diff --git a/docs/reference/set_community_model.html b/docs/reference/set_community_model.html
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+  
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+
+
+
 
 
   
diff --git a/docs/reference/set_multispecies_model.html b/docs/reference/set_multispecies_model.html
index 86616ca98..a76cd4a05 100644
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+  
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+
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+
 
 
   
diff --git a/docs/reference/set_species_param_default.html b/docs/reference/set_species_param_default.html
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+  
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+
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+
 
 
   
diff --git a/docs/reference/set_trait_model.html b/docs/reference/set_trait_model.html
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+
 
 
   
diff --git a/docs/reference/sigmoid_length.html b/docs/reference/sigmoid_length.html
index eee00cd90..255330919 100644
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+        2.0.2
       
     
 
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+
 
 
   
diff --git a/docs/reference/sigmoid_weight.html b/docs/reference/sigmoid_weight.html
index a759e7f51..25cf6a104 100644
--- a/docs/reference/sigmoid_weight.html
+++ b/docs/reference/sigmoid_weight.html
@@ -37,6 +37,12 @@
 
 
 
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+  
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+
 
 
   
diff --git a/docs/reference/steady.html b/docs/reference/steady.html
index 44fb6be65..6d918eb86 100644
--- a/docs/reference/steady.html
+++ b/docs/reference/steady.html
@@ -37,6 +37,12 @@
 
 
 
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+        2.0.2
       
     
 
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@@ -140,7 +196,7 @@ 
    Set initial values to a steady state for the model
    
     
    steady(
   params,
   t_max = 100,
-  t_per = 7.5,
+  t_per = 1.5,
   tol = 10^(-2),
   dt = 0.1,
   return_sim = FALSE,
@@ -161,7 +217,7 @@ 
    Arg
     
       t_per
       
    The simulation is broken up into shorter runs of t_per years,
-after each of which we check for convergence. Default value is 7.5. This
+after each of which we check for convergence. Default value is 1.5. This
 should be chosen as an odd multiple of the timestep dt in order to be
 able to detect period 2 cycles.
    
     
@@ -212,13 +268,30 @@ 
    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/summary-MizerParams-method.html b/docs/reference/summary-MizerParams-method.html
index 3e35e0517..8870d1abb 100644
--- a/docs/reference/summary-MizerParams-method.html
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@@ -37,6 +37,12 @@
 
 
 
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+  
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+
+
+
 
 
   
diff --git a/docs/reference/summary-MizerSim-method.html b/docs/reference/summary-MizerSim-method.html
index de87ca055..3e6af612c 100644
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diff --git a/docs/reference/summary_functions.html b/docs/reference/summary_functions.html
index d6684a4e7..f11bac748 100644
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    Contents
    
 
 
 
    
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+  
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+
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+
 
 
   
diff --git a/docs/reference/test_dyn.html b/docs/reference/test_dyn.html
index 55bde9430..bb3358edf 100644
--- a/docs/reference/test_dyn.html
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    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.5.1.9000.
    
 
    
 
       
    
 
   
+
+
+
 
 
   
diff --git a/docs/reference/truncated_lognormal_pred_kernel.html b/docs/reference/truncated_lognormal_pred_kernel.html
index fccee5201..190201389 100644
--- a/docs/reference/truncated_lognormal_pred_kernel.html
+++ b/docs/reference/truncated_lognormal_pred_kernel.html
@@ -37,6 +37,12 @@
 
 
 
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+
 
 
   
diff --git a/docs/reference/upgradeParams.html b/docs/reference/upgradeParams.html
index 76ccee5a5..7ae80cbf0 100644
--- a/docs/reference/upgradeParams.html
+++ b/docs/reference/upgradeParams.html
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+        2.0.2
       
     
 
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    Upgrade MizerParams object from earlier mizer versions
    
     
    Occasionally during the development of new features for mizer, the
 MizerParams object gains extra slots. MizerParams objects
 created in older versions of mizer are then no longer valid in the new
-version because of the missing slots. You need to upgrade them with
    params &lt;- upgradeParams(params)
    
+version because of the missing slots. You need to upgrade them with
    params <- upgradeParams(params)
    
 
 
    where params should be replaced by the name of your MizerParams object.
 This function adds the missing slots and fills them with default values. Any
@@ -201,13 +257,30 @@ 
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+
 
 
   
diff --git a/docs/reference/upgradeSim.html b/docs/reference/upgradeSim.html
index 9f68f194b..62d8d7cbf 100644
--- a/docs/reference/upgradeSim.html
+++ b/docs/reference/upgradeSim.html
@@ -37,6 +37,12 @@
 
 
 
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+
 
 
 
@@ -44,7 +50,7 @@
 MizerSim class or the MizerParams class gains
 extra slots. MizerSim objects created in older versions of mizer are then no
 longer valid in the new version because of the missing slots. You need to
-upgrade them withsim &amp;lt;- upgradeSim(sim)
+upgrade them withsim &lt;- upgradeSim(sim)
 
 where sim should be replaced by the name of your MizerSim object." />
 
@@ -78,7 +84,7 @@
       
       
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-        2.0.1
+        2.0.2
       
     
 
@@ -96,8 +102,52 @@
 
  • 
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+
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@@ -136,7 +192,7 @@ 
    Upgrade MizerSim object from earlier mizer versions
    
 MizerSim class or the MizerParams class gains
 extra slots. MizerSim objects created in older versions of mizer are then no
 longer valid in the new version because of the missing slots. You need to
-upgrade them with
    sim &lt;- upgradeSim(sim)
    
+upgrade them with
    sim <- upgradeSim(sim)
    
 
 
    where sim should be replaced by the name of your MizerSim object.
    
     
@@ -196,13 +252,30 @@ 
    Contents
    
 
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
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+
+
 
 
   
diff --git a/docs/reference/validGearParams.html b/docs/reference/validGearParams.html
index 29c3d0eaf..095cc35d2 100644
--- a/docs/reference/validGearParams.html
+++ b/docs/reference/validGearParams.html
@@ -38,6 +38,12 @@
 
 
 
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+        2.0.2
       
     
 
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+
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+
 
 
   
diff --git a/docs/reference/validSpeciesParams.html b/docs/reference/validSpeciesParams.html
index c0a7a3667..8b07a07ec 100644
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+        2.0.2
       
     
 
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+  
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+
 
 
   
diff --git a/docs/reference/validate_effort_vector.html b/docs/reference/validate_effort_vector.html
index 21fa15686..8c530f722 100644
--- a/docs/reference/validate_effort_vector.html
+++ b/docs/reference/validate_effort_vector.html
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+        2.0.2
       
     
 
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+  
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+
 
 
   
diff --git a/docs/reference/w.html b/docs/reference/w.html
index 7808241f0..e87e67bae 100644
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+  
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+
 
 
   
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index c665a9074..47e50397c 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -46,13 +46,13 @@
     https://sizespectrum.org/mizer/reference/constantRDD.html
   
   
-    https://sizespectrum.org/mizer/reference/default_pred_kernel_params.html
+    https://sizespectrum.org/mizer/reference/constant_other.html
   
   
-    https://sizespectrum.org/mizer/reference/double_sigmoid_length.html
+    https://sizespectrum.org/mizer/reference/default_pred_kernel_params.html
   
   
-    https://sizespectrum.org/mizer/reference/effort.html
+    https://sizespectrum.org/mizer/reference/double_sigmoid_length.html
   
   
     https://sizespectrum.org/mizer/reference/emptyParams.html
@@ -93,6 +93,9 @@
   
     https://sizespectrum.org/mizer/reference/getESpawning.html
   
+  
+    https://sizespectrum.org/mizer/reference/getEffort.html
+  
   
     https://sizespectrum.org/mizer/reference/getEncounter.html
   
@@ -126,6 +129,9 @@
   
     https://sizespectrum.org/mizer/reference/getN.html
   
+  
+    https://sizespectrum.org/mizer/reference/getParams.html
+  
   
     https://sizespectrum.org/mizer/reference/getPhiPrey.html
   
@@ -153,6 +159,9 @@
   
     https://sizespectrum.org/mizer/reference/getSSB.html
   
+  
+    https://sizespectrum.org/mizer/reference/getTimes.html
+  
   
     https://sizespectrum.org/mizer/reference/getYield.html
   
@@ -267,9 +276,6 @@
   
     https://sizespectrum.org/mizer/reference/noRDD.html
   
-  
-    https://sizespectrum.org/mizer/reference/params.html
-  
   
     https://sizespectrum.org/mizer/reference/plotBiomass.html
   
@@ -312,18 +318,27 @@
   
     https://sizespectrum.org/mizer/reference/project.html
   
+  
+    https://sizespectrum.org/mizer/reference/project_simple.html
+  
   
     https://sizespectrum.org/mizer/reference/reexports.html
   
   
     https://sizespectrum.org/mizer/reference/resource_constant.html
   
+  
+    https://sizespectrum.org/mizer/reference/resource_encounter.html
+  
   
     https://sizespectrum.org/mizer/reference/resource_semichemostat.html
   
   
     https://sizespectrum.org/mizer/reference/retune_erepro.html
   
+  
+    https://sizespectrum.org/mizer/reference/semichemostat.html
+  
   
     https://sizespectrum.org/mizer/reference/setColours.html
   
@@ -405,9 +420,6 @@
   
     https://sizespectrum.org/mizer/reference/test_dyn.html
   
-  
-    https://sizespectrum.org/mizer/reference/times.html
-  
   
     https://sizespectrum.org/mizer/reference/truncated_lognormal_pred_kernel.html
   
@@ -447,6 +459,9 @@
   
     https://sizespectrum.org/mizer/articles/exploring_the_simulation_results.html
   
+  
+    https://sizespectrum.org/mizer/articles/making_modifications.html
+  
   
     https://sizespectrum.org/mizer/articles/mizer.html
   
diff --git a/vignettes/running_a_simulation.Rmd b/vignettes/running_a_simulation.Rmd
index 9756f5911..d3036f2f9 100644
--- a/vignettes/running_a_simulation.Rmd
+++ b/vignettes/running_a_simulation.Rmd
@@ -182,10 +182,10 @@ selectivity (see the fishing mortality panel). Remember that the default setting
 for the fishing gears is a knife-edge gear where the knife-edge is positioned at
 the species `w_mat` parameter.
 
-The effort through time can be inspected with `effort()` (we use the `head()`
+The effort through time can be inspected with `getEffort()` (we use the `head()`
 function to just show the first few lines).
 ```{r label=show_effort}
-head(effort(sim))
+head(getEffort(sim))
 ```
 The `effort` slot shows the effort by time and gear. In this example, we
 specified the `effort` argument as a single numeric of value 1. As you can see
@@ -207,7 +207,7 @@ to 0.5, meaning that the effort and abundance information is stored at t = 1.0,
 
 ```{r label=simple_proj_tsave05}
 sim <- project(NS_params, effort = 1, t_max = 10, dt = 0.1, t_save = 0.5)
-head(effort(sim))
+head(getEffort(sim))
 ```
 
 ### Setting constant effort for different gears {#sec:proj_diff_gears_constant_effort}
@@ -230,7 +230,7 @@ matrix (again we use the `head()` function to just show the first few lines):
 
 ```{r label=project_effort_vector}
 sim <- project(NS_params, effort = effort, t_max = 10, dt = 1, t_save = 1)
-head(effort(sim))
+head(getEffort(sim))
 ```
 
 You can see that the effort for each gear is constant but each gear has the