NEWS.md

In Allgeier-Lab/arrR: Individual-Based Simulation Model of Artifical Reefs in R

arrR 2.0.1

• Minor export bugfixes

arrR 2.0.0

• Split arrR into several sup-packages

arrR 1.5.2

• Update rcpp_get_adjacencies

arrR 1.5.1

• Fix bug in detritus pool consumption if pool was very low
• Remove codemeta.json

arrR 1.5

• Remove terra dependency
• Remove RcppDist dependency

arrR 1.4.3

• Allow to write results into a text file
• Renamed get_stable_values to get_req_nutrients and changes to function
• Renamed all *_var parameters to *_sd

arrR 1.4.2.1

• Better structure of rcpp_fishpop_growth()
• Adding rcpp_runif() for better RNG handling

arrR 1.4.2

• Update to "behav" movement
• Renamed pop_thres_reserves_lo/pop_thres_reserves_hi to pop_thres_reserves_mean/pop_thres_reserves_var
• Using rcpp_rnorm() for random reserves threshold value

arrR 1.4.1

• Move some pre-process code from R to Rcpp and use internal functions
• Improve documentation

arrR 1.4

• Use terra instead of raster
• Rename nutr_input to nutrients_input
• Rename nutrients_output to nutrients_loss
• Rename detritus_output to detritus_loss
• Run all seagrass/water column processes on same temporal scale
• Better global variables handling

arrR 1.3.1

• Changes to get_stable_values

arrR 1.3

• Adding pkgdown homepage
• Add detritus_output to rcpp_nutr_output
• Streamlined code for summarize_mdlrn and plot.mdl_rn
• Adding get_production and plot_production function
• Adding reset argument to filter_mdlrn

arrR 1.2

• Return pop_reserves_thres in final mdl_rn object
• Fix bug in get_density if not max_i was selected as timestep
• Return max_dist in run_simulation
• Minor bugfix in run_simulation if fishpop with 0 indiv was provided

arrR 1.1

• Fix bug in run_simulation and return of nutr_input
• Export R and Rcpp interfaces of core functions
• Renamed starting_values and parameters
• Renamed extent to dimensions

arrR 1.0

• Renamed rcpp_run_simulation to rcpp_sim_processes
• Adding all needed references
• Nested loop to diffuse values in rcpp_diffuse_values
• Improvment of get_neighbors using modular division

arrR 0.5.1

• Main simulation loop completely in Rcpp rcpp_run_simulation
• Better tracking of fish consumption and excretion
• Age counter in iterations
• Better name for pop_reserves_* parameters
• Renamed setup_seafloor_mdlrn to mdlrn_to_raster

arrR 0.5.0

• Simpler allocation rule based on curves.
• Adding new movement behaviors code based on reserve
• Minor bugfixing and rename of many functions
• New plot_threshold function.
• Fix bug in movement and specify maximum movement distance based on 95% of distribution
• Remove rlognorm again...lol
• Remove extract_result again
• Adding rcpp_shuffle
• Remove reef_dist
• Adding rcpp_update_coords
• Adding rcpp_allocation_ratio and smoother sigmoid function
• Adding get_stable_values function
• Calling all rcpp_ functions directly if possible in run_simulation
• Renamed detritus_ratio to seagrass_slough
• Renamed detritus_fish_ratio to detritus_fish_decomp
• Remove pop_want_reserves parameter. Fish always try to fill up reserves

arrR 0.4.0

• Add simulate_input and simulate_output
• Rename simulate_fishpop_growth to simulate_growth

arrR 0.3.1

• Add rlognorm for better code structure

arrR 0.3.0

• Update authors list
• Re-implement movement of fish individuals in Rcpp mainly
• Rename dead detritus to fish detritus (and all corresponding parameters)

arrR 0.2.9

• Fix bug that not all starting values are included in mdl_rn object
• Print progress each timestep because why not?
• Change to GPL3 license
• Fix bug in rcpp_calc_seagrass_growth.cpp with allocation rules

arrR 0.2.8

• Add hexlogo
• Add extract_result function and extract argument to run_simulation
• Add bg_gamma and ag_gamma to parameters. Was hard-coded previously
• Better checking if object is mdl_rn
• Renamed master branch to main

arrR 0.2.7

• Add default parameters and starting values as data
• Add structure for vignettes
• Use absolute iterations for burn-in
• Add return_burnin argument to run_simulation

arrR 0.2.6

• Renamed all pop_*grunt parameters to only pop*
• Adding burn-in option to run_simulation
• Track production, slough, nutrient uptake cumulative for each cell
• summarize_mdlrn returns burn_in column

arrR 0.2.5

• Renamed filter_result to filter_mdlrn
• Slight changes to print.mdl_rn
• Rename summarize_result to summarize_mdlrn and allow to select summary fun

arrR 0.2.4

• Better memory usage by using mainly Rcpp for core functions
• Removed pop_max_size and replace with pop_linf_grunt

arrR 0.2.3

• Add GitHub actions
• Resulting object contains parameters and starting values
• get_limits can return limits over time period
• plot.mdl_rn also takes limits if summarize = TRUE for seafloor

arrR 0.2.2

• Better plotting labels
• Renamed parameters$detritus_decomposition to parameter$detritus_mineralization

arrR 0.2.1

• Reworked seagrass growth
• Rename package to arrR
• Add pkgdown homepage

arrR 0.2.0

• Speed and RAM improvements of many function
• Including Rcpp

arrR 0.1.0

• First re-implementation of model code

Allgeier-Lab/arrR documentation built on Feb. 13, 2025, 7:44 a.m.