- Split
arrR
into several sup-packages
- Update
rcpp_get_adjacencies
- Fix bug in detritus pool consumption if pool was very low
- Remove
codemeta.json
- Remove
terra
dependency - Remove
RcppDist
dependency
- Allow to write results into a text file
- Renamed
get_stable_values
toget_req_nutrients
and changes to function - Renamed all
*_var
parameters to*_sd
- Better structure of
rcpp_fishpop_growth()
- Adding
rcpp_runif()
for better RNG handling
- Update to "behav" movement
- Renamed
pop_thres_reserves_lo
/pop_thres_reserves_hi
topop_thres_reserves_mean
/pop_thres_reserves_var
- Using
rcpp_rnorm()
for random reserves threshold value
- Move some pre-process code from
R
toRcpp
and use internal functions - Improve documentation
- Use
terra
instead ofraster
- Rename
nutr_input
tonutrients_input
- Rename
nutrients_output
tonutrients_loss
- Rename
detritus_output
todetritus_loss
- Run all seagrass/water column processes on same temporal scale
- Better global variables handling
- Changes to
get_stable_values
- Adding
pkgdown
homepage - Add
detritus_output
torcpp_nutr_output
- Streamlined code for
summarize_mdlrn
andplot.mdl_rn
- Adding
get_production
andplot_production
function - Adding
reset
argument tofilter_mdlrn
- Return
pop_reserves_thres
in finalmdl_rn
object - Fix bug in
get_density
if notmax_i
was selected as timestep - Return
max_dist
inrun_simulation
- Minor bugfix in
run_simulation
if fishpop with 0 indiv was provided
- Fix bug in
run_simulation
and return ofnutr_input
- Export
R
andRcpp
interfaces of core functions - Renamed
starting_values
andparameters
- Renamed
extent
todimensions
- Renamed
rcpp_run_simulation
torcpp_sim_processes
- Adding all needed references
- Nested loop to diffuse values in
rcpp_diffuse_values
- Improvment of
get_neighbors
using modular division
- 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
tomdlrn_to_raster
- 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 inrun_simulation
- Renamed
detritus_ratio
toseagrass_slough
- Renamed
detritus_fish_ratio
todetritus_fish_decomp
- Remove
pop_want_reserves
parameter. Fish always try to fill up reserves
- Add
simulate_input
andsimulate_output
- Rename
simulate_fishpop_growth
tosimulate_growth
- Add
rlognorm
for better code structure
- Update authors list
- Re-implement movement of fish individuals in Rcpp mainly
- Rename dead detritus to fish detritus (and all corresponding parameters)
- 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
- Add hexlogo
- Add
extract_result
function andextract
argument torun_simulation
- Add
bg_gamma
andag_gamma
to parameters. Was hard-coded previously - Better checking if object is
mdl_rn
- Renamed master branch to main
- Add default parameters and starting values as data
- Add structure for vignettes
- Use absolute iterations for burn-in
- Add
return_burnin
argument torun_simulation
- 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
returnsburn_in
column
- Renamed filter_result to
filter_mdlrn
- Slight changes to
print.mdl_rn
- Rename
summarize_result
tosummarize_mdlrn
and allow to select summary fun
- Better memory usage by using mainly Rcpp for core functions
- Removed
pop_max_size
and replace withpop_linf_grunt
- Add GitHub actions
- Resulting object contains parameters and starting values
get_limits
can return limits over time periodplot.mdl_rn
also takes limits ifsummarize = TRUE
for seafloor
- Better plotting labels
- Renamed
parameters$detritus_decomposition
toparameter$detritus_mineralization
- Reworked seagrass growth
- Rename package to
arrR
- Add
pkgdown
homepage
- Speed and RAM improvements of many function
- Including
Rcpp
- First re-implementation of model code