diff --git a/Biomass_core.html b/Biomass_core.html index d1e6eb8..78f5fa7 100644 --- a/Biomass_core.html +++ b/Biomass_core.html @@ -3016,7 +3016,7 @@

Last updated: 2022-11-04

-

module-version-Badge

+

module-version-Badge

Issues-badge

Authors:

@@ -4284,7 +4284,8 @@

List of input objects

  • cohortData – a data.table containing initial cohort information per pixelGroup (see pixelGroupMap below). This table is updated during the simulation as cohort dynamics are simulated. It must contain the following -columns:

    • +columns:

    +

  • pixelGroupMap – a raster layer with pixelGroup IDs per pixel. Pixels are always grouped based on identical ecoregionGroup, speciesCode, age and B composition, even if the user supplies other initial groupings @@ -4599,9 +4601,10 @@

    List of parameters

    no longer generates initial cohort biomass conditions using a spin-up based on initial stand age like LANDIS-II ("spin-up"), nor does it attempt to fill initial cohort biomasses using biomassMap.

    -

    Plotting and saving - .plots – activates/deactivates plotting and defines -type of plotting (see ?Plots);

    +

    Plotting and saving

    -

    Other
    -- mixedType – how mixed forest stands are defined;

    +

    Other

    @@ -5607,8 +5610,7 @@

    Simulation flow and module events

    LandMine);

  • Post-disturbance mortality/regeneration (OPTIONAL) – simulated by a regeneration module (e.g., Biomass_regeneration);

    • -

  • Seed dispersal (every successionTimestep; Dispersal event):

    • - +

  • Seed dispersal (every successionTimestep; Dispersal event):

    • seed dispersal can be a slow process and has been adapted to occur every 10 years (default successionTimestep). The user can set it to occur @@ -5616,25 +5618,20 @@

      Simulation flow and module events

      to estimate species establishment probabilities, these values are integrated over 10 years.
    • see Scheller & Domingo (2012) for details on dispersal algorithms.
      • -
    -
      -
    1. Growth and mortality (mortalityAndGrowth event):
      2. -
    +
    • +

  • Growth and mortality (mortalityAndGrowth event):

    • unlike dispersal, growth and mortality always occur time step (year).
    • see Scheller & Mladenoff (2004) for further detail.
      • -
    -
      -
    1. Cohort age binning (every successionTimestep; cohortAgeReclassification -event):
      2. -
    +
    • +

  • Cohort age binning (every successionTimestep; cohortAgeReclassification +event):

    • follows the same frequency as dispersal, collapsing cohorts (i.e., summing their biomass/mortality/aNPP) to ages classes with resolution equal to successionTimestep.
    • see Scheller & Miranda (2015) for further detail.
      • -
    -
      +

    1. Summary tables of regeneration (summaryRegen event), biomass, age, growth and mortality (summaryBGM event);

    2. Plots of maps (plotMaps event) and averages (plotAvgs and @@ -5880,8 +5877,10 @@

      Set up R libraries

      .libPaths(pkgPath, include.site = FALSE) if (!require(Require, lib.loc = pkgPath)) { - remotes::install_github("PredictiveEcology/Require@5c44205bf407f613f53546be652a438ef1248147", - upgrade = FALSE, force = TRUE) + remotes::install_github( + paste0("PredictiveEcology/", + "Require@5c44205bf407f613f53546be652a438ef1248147"), + upgrade = FALSE, force = TRUE) library(Require, lib.loc = pkgPath) } @@ -5898,7 +5897,8 @@

      Get the module and module dependencies

      dependencies are installed in their correct version. SpaDES.project::packagesInModules makes a list of necessary packages for all modules in the paths$modulePath, and Require installs them.

      -
      Require("PredictiveEcology/SpaDES.project@6d7de6ee12fc967c7c60de44f1aa3b04e6eeb5db", 
+
      Require(paste0("PredictiveEcology/",
+               "SpaDES.project@6d7de6ee12fc967c7c60de44f1aa3b04e6eeb5db"), 
         require = FALSE, upgrade = FALSE, standAlone = TRUE)
 
 paths <- list(inputPath = normPath(file.path(tempDir, "inputs")), 
@@ -5988,7 +5988,7 @@ 
      Run simulation
      
                           outputs = outputs,
                           debug = TRUE)
      
 
      
-Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).
+Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).
 
      
 Figure 7: Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).
    • @@ -5204,7 +5207,7 @@

    List of parameters

    NA
    -Passed to httr::config(ssl_verifypeer = P(sim)$.sslVerify) when downloading KNN (NFI) datasets. Set to 0L if necessary to bypass checking the SSL certificate (this may be necessary when NFI’s FTP website SSL certificate is down/out-of-date). +Passed to httr::config(ssl_verifypeer = P(sim)$.sslVerify) when downloading KNN (NFI) datasets. Set to 0L if necessary to bypass checking the SSL certificate (this may be necessary when NFI’s website SSL certificate is not correctly configured).