add custom rounding function

NAMESPACE

@@ -13,6 +13,7 @@ export(growth)
 export(growth_log)
 export(growth_one_group)
 export(pick_new_bugs)
+export(roundVectorPreservingSum)
 export(simulate_timeseries)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,transpose)

R/RcppExports.R

@@ -20,18 +20,18 @@ pick_new_bugs <- function(arr, size, replace, prob) {
 #' function calculates the probability of growth for each organism based on
 #' their current abundance and any specified interactions between organisms. The
 #' function then randomly selects organisms to grow based on these probabilities
-#' and increases their abundance by grow_step (1 by default).
+#' and increases their abundance by growth_step (1 by default).
 #' The function takes four arguments:
 #' @param this_timestep A numeric vector representing the current abundance of
 #' each organism in the population.
-#' @param grow_step An integer representing the growth step for organisms in
+#' @param growth_step An integer representing the growth step for organisms in
 #' the community, 1 by default.
 #' @param interactions An optional numeric matrix representing the interaction
 #' between organisms in the population. This argument is set to R_NilValue by
 #' default.
 #' @export
-growth_one_group <- function(this_timestep, grow_step, interactions = NULL) {
-    .Call(`_dilgrowth_growth_one_group`, this_timestep, grow_step, interactions)
+growth_one_group <- function(this_timestep, growth_step, interactions = NULL) {
+    .Call(`_dilgrowth_growth_one_group`, this_timestep, growth_step, interactions)
 }
 
 #' growth
@@ -47,17 +47,17 @@ growth_one_group <- function(this_timestep, grow_step, interactions = NULL) {
 #'
 #' As opposed to growth_one_group(), the growth rate (probability of being
 #' picked for growth) is determined for each individual by the carrying
-#' capacity of its group(\[grow_step * group's % of total carrying capacity]).
+#' capacity of its group(\[growth_step * group's % of total carrying capacity]).
 #' An optionally passed interactions matrix has an effect as well. Every group
-#' will have grow_step (by default 1) of its present individuals grow in each
+#' will have growth_step (by default 1) of its present individuals grow in each
 #' run, and they can be from the same ASV/OTU/species or not. Also, growth step
 #' is proportional to the carrying capacity of its group. This is to avoid group
 #' extinction and also to ensure growth has a similar, proportional rate for
 #' each group so all groups reach their CC at the same time.
 #'`
 #' @export
-growth <- function(x, carrying_capacities, grow_step, interactions = NULL) {
-    .Call(`_dilgrowth_growth`, x, carrying_capacities, grow_step, interactions)
+growth <- function(x, carrying_capacities, growth_step, interactions = NULL) {
+    .Call(`_dilgrowth_growth`, x, carrying_capacities, growth_step, interactions)
 }
 
 #' growth_log
@@ -72,13 +72,13 @@ growth <- function(x, carrying_capacities, grow_step, interactions = NULL) {
 #' only on their abundances but also on their carrying capacity.
 #'
 #' As opposed to growth_one_group(), the growth rate is given by a logistic
-#' function and not grow_step. Another difference is that growing species are
+#' function and not growth_step. Another difference is that growing species are
 #' not chosen one by one by sampling, but with a binomial function. That means
 #' that the number of different species and the number of individuals that can
 #' grow in each iteration of this function is not limited.
 #'
 #' The difference with growth() is that growth is logistic in this function and
-#' there is not grow_step here.
+#' there is not growth_step here.
 #'
 #' If the carrying capacity for a group was surpassed before starting the
 #' growth cycle, the species of that group will die at a proportionate rate,
@@ -91,25 +91,25 @@ growth_log <- function(x, carrying_capacities, interactions = NULL) {
 
 #' check_step
 #'
-#' Checks if a given grow_step is ok for running a growth() function and adjusts
+#' Checks if a given growth_step is ok for running a growth() function and adjusts
 #' it accordingly if it's not (for example not allowing for it to cause too big
 #' of a growth, surpassing total wanted final community abundance).
-#' @param is_grow_step_a_perc Boolean: if false, grow_step is taken as a fixed
+#' @param is_growth_step_a_perc Boolean: if false, growth_step is taken as a fixed
 #' value, so the step will always be the same. If true, it is taken to indicate
 #' a percentage - the step will be changed proportionally to the community size.
-#' If grow_step is 0.02, 2% of the members in the community will grow the next
+#' If growth_step is 0.02, 2% of the members in the community will grow the next
 #' iteration
 #' @export
-check_step <- function(this_timestep, abun_total, grow_step, is_grow_step_a_perc = FALSE) {
-    .Call(`_dilgrowth_check_step`, this_timestep, abun_total, grow_step, is_grow_step_a_perc)
+check_step <- function(this_timestep, abun_total, growth_step, is_growth_step_a_perc = FALSE) {
+    .Call(`_dilgrowth_check_step`, this_timestep, abun_total, growth_step, is_growth_step_a_perc)
 }
 
 #' full_growth
 #'
 #' This function consists in a loop that runs growth(...)() functions as many
 #' times as needed to reach a given population size.
 #' @export
-full_growth <- function(this_timestep, abun_total, grow_step, is_grow_step_a_perc = FALSE, func = "growth", interactions = NULL, carrying_capacities = NULL) {
-    .Call(`_dilgrowth_full_growth`, this_timestep, abun_total, grow_step, is_grow_step_a_perc, func, interactions, carrying_capacities)
+full_growth <- function(this_timestep, abun_total, growth_step, is_growth_step_a_perc = FALSE, func = "growth", interactions = NULL, carrying_capacities = NULL) {
+    .Call(`_dilgrowth_full_growth`, this_timestep, abun_total, growth_step, is_growth_step_a_perc, func, interactions, carrying_capacities)
 }
 

R/roundVectorPreservingSum.R

@@ -0,0 +1,31 @@
+#' roundVectorPreservingSum
+#'
+#' This function rounds the input vector and then calculates the difference in
+#' the sum of the original vector and the rounded vector. To fix this difference,
+#' it randomly selects elements from the rounded vector and adjusts their values
+#' to preserve the sum of the original vector.
+#'
+#' This is needed to avoid decimals in the final simulated communities when
+#' simulating multiple functional groups.
+#'
+#' @param vector
+#'
+#' @return
+#' @export
+#'
+#' @examples
+roundVectorPreservingSum <- function(vector) {
+  rounded_vector <- round(vector)  # Round the vector
+  diff_sum <- sum(vector) - sum(rounded_vector)  # Calculate the difference in sum
+
+  # Adjust the rounded vector to preserve the sum
+  if (diff_sum > 0) {
+    indices <- sample(length(vector), diff_sum)
+    rounded_vector[indices] <- rounded_vector[indices] + 1
+  } else if (diff_sum < 0) {
+    indices <- sample(length(vector), -diff_sum)
+    rounded_vector[indices] <- rounded_vector[indices] - 1
+  }
+
+  return(rounded_vector)
+}

R/simulate_timeseries.R

@@ -12,7 +12,7 @@
 #' @param dilution
 #' @param no_of_dil
 #' @param fixation_at
-#' @param grow_step Number of individuals that grow each timestep (Default: 1)
+#' @param growth_step Number of individuals that grow each timestep (Default: 1)
 #' @param keep_all_timesteps
 #' @param allow_group_extinctions If TRUE, simulations will continue even if one
 #' or more groups go extinct, and the function will try to reach fixation in all
@@ -35,8 +35,8 @@ simulate_timeseries <- function (counts_data,
                                  no_of_dil=12,
                                  fixation_at=1,
                                  abun_total=NULL,
-                                 grow_step=1,
-                                 is_grow_step_a_perc=FALSE,
+                                 growth_step=1,
+                                 is_growth_step_a_perc=FALSE,
                                  keep_all_timesteps=FALSE,
                                  allow_group_extinctions=TRUE,
                                  force_continue=FALSE) {
@@ -130,7 +130,7 @@ simulate_timeseries <- function (counts_data,
       # Growth without groups (growth_one_group())
       # ==========================================
       while (sum(this_timestep) < abun_total) {
-        step          <- check_step(this_timestep, abun_total, grow_step, is_grow_step_a_perc)
+        step          <- check_step(this_timestep, abun_total, growth_step, is_growth_step_a_perc)
         this_timestep <- growth_one_group(this_timestep,
                                           step,
                                           interactions)
@@ -181,11 +181,11 @@ simulate_timeseries <- function (counts_data,
         }
       } else {
         while (round(sum(this_timestep)) < abun_total) {
-          step          <- check_step(this_timestep, abun_total, grow_step, is_grow_step_a_perc)
+          step          <- check_step(this_timestep, abun_total, growth_step, is_growth_step_a_perc)
           this_timestep <- growth(
             x = this_timestep,
             carrying_capacities = carrying_capacities,
-            grow_step = step,
+            growth_step = step,
             interactions = interactions
           )
         }
@@ -199,7 +199,7 @@ simulate_timeseries <- function (counts_data,
     if (keep_all_timesteps){
       # once the growth's finished, the next dilution can happen. But if
       # keep_all_timesteps, we have to save the abundances first
-      trajectory[as.character(dil),] <- this_timestep
+      trajectory[as.character(dil),] <- roundVectorPreservingSum(this_timestep)
     }
 
     # Check again for fixation before next iteration
@@ -215,5 +215,5 @@ simulate_timeseries <- function (counts_data,
   if (keep_all_timesteps){
     return(trajectory)
   } else {
-    return(this_timestep)
+    return(roundVectorPreservingSum(this_timestep))
   }}

scripts/dilgrowth.R

@@ -107,15 +107,15 @@ option_list <- list(
   make_option(c("--save_all"), type = "logical",
               default = FALSE,
               help = "save all intermediate states of the simulations? default FALSE"),
-  make_option(c("--grow_step"), type = "double",
+  make_option(c("--growth_step"), type = "double",
               default = 1,
               help = "How many bugs are born on each iteration. 1 by default"),
-  make_option(c("--is_grow_step_a_perc"), type = "logical",
+  make_option(c("--is_growth_step_a_perc"), type = "logical",
               default = FALSE,
-              help = "If FALSE, grow_step is taken as a fixed value, so the step will always be the same. If TRUE, it's read as a percentage - the step will be changed proportionally to the community size. If grow_step is 0.02, 2% of the members in the community will grow the next iteration. FALSE by default"),
+              help = "If FALSE, growth_step is taken as a fixed value, so the step will always be the same. If TRUE, it's read as a percentage - the step will be changed proportionally to the community size. If growth_step is 0.02, 2% of the members in the community will grow the next iteration. FALSE by default"),
   make_option(c("--logistic"), type = "logical",
               default = FALSE,
-              help = "¿Should growth be logistic? If TRUE, the grow_step/growth rate of each species will change over the course of the simulation, in a logistic growth manner (see growth_log)."),
+              help = "¿Should growth be logistic? If TRUE, the growth_step/growth rate of each species will change over the course of the simulation, in a logistic growth manner (see growth_log)."),
   make_option(c("--no_of_simulations"), type = "integer",
               default = 1,
               help = "Number of simulations"),
@@ -150,12 +150,12 @@ outputname <- opt$outputname # e.g. "X2_rep4"
 cores <- opt$cores  # e.g. 16
 
 save_all  <- opt$save_all
-grow_step <- opt$grow_step
-is_grow_step_a_perc <- opt$is_grow_step_a_perc
+growth_step <- opt$growth_step
+is_growth_step_a_perc <- opt$is_growth_step_a_perc
 allow_group_extinctions <- opt$allow_group_extinctions
 
-if (is_grow_step_a_perc && (grow_step == 1)) {
-  message("WARNING: grow_step has been defined as a percentage of value 1. All organisms will duplicate every iteration. If you meant for grow_step to be a fixed value, set is_grow_step_a_perc to FALSE instead.")
+if (is_growth_step_a_perc && (growth_step == 1)) {
+  message("WARNING: growth_step has been defined as a percentage of value 1. All organisms will duplicate every iteration. If you meant for growth_step to be a fixed value, set is_growth_step_a_perc to FALSE instead.")
 }
 
 logistic <- opt$logistic
@@ -249,8 +249,8 @@ if (abun_total == 0) {
                                                              no_of_dil = no_of_dil,
                                                              fixation_at = fixation_at,
                                                              abun_total = abun_total,
-                                                             grow_step = grow_step,
-                                                             is_grow_step_a_perc = is_grow_step_a_perc,
+                                                             growth_step = growth_step,
+                                                             is_growth_step_a_perc = is_growth_step_a_perc,
                                                              keep_all_timesteps = save_all,
                                                              allow_group_extinctions = allow_group_extinctions,
                                                              force_continue = FALSE)