update argument names

R/bc_compaction.R

@@ -1,3 +1,5 @@
+#' @title bc_compaction
+#' 
 #' Calculates Percentage of core compression for cores
 #'
 #' Accepts a data.frame with core properties and returns a modified version
@@ -9,25 +11,25 @@
 #' @param external_distance name of the column with distance between sampler top and sediment surface
 #' @return the initial data.frame with the addition of Percentage of core compression
 
-bc_compaction <- function(
-  data,
-  sampler_length,
-  internal_distance,
-  external_distance
-){
-  if(!is.data.frame(data)){
+bc_compaction <- 
+  function(data,
+           sampler_length,
+           internal_distance,
+           external_distance) {
+
+    # Stop if data is not a data.frame
+  if (!is.data.frame(data)) {
     stop("data is not a data.frame")
   }
   # Stop if any of the required variables are not numeric
-  if(!all(is.numeric(data[, sampler_length]),
-          is.numeric(data[, internal_distance]),
-          is.numeric(data[, external_distance])
-  )){
-    non_numeric <- !sapply(
-      X = list(data[, sampler_length], data[, internal_distance], data[, external_distance]),
-      FUN = is.numeric)
+  if (!all(is.numeric(data[, sampler_length]),
+           is.numeric(data[, internal_distance]),
+           is.numeric(data[, external_distance]))) {
+    non_numeric <- !sapply(X = list(data[, sampler_length], data[, internal_distance], data[, external_distance]),
+                           FUN = is.numeric)
 
-    var_names <- c(sampler_length, internal_distance, external_distance)
+    var_names <-
+      c(sampler_length, internal_distance, external_distance)
 
     stop("The following variables are not numeric:\n",
          paste(var_names[which(non_numeric)], sep = "\n"))
@@ -36,7 +38,7 @@ bc_compaction <- function(
   # estimate compaction correction factor
   compaction_correction_factor <-
     (data[, sampler_length] - data[, internal_distance]) /
-    (data[, sampler_length] - data[,external_distance])
+    (data[, sampler_length] - data[, external_distance])
 
 
   # compaction rate as percentage

R/bc_decomp.R

@@ -3,31 +3,42 @@
 #' This function uses six arguments
 #' 
 #' @param data dataframe with the following columns "ID" "cm" "weight" "LOI" "c_org".
-#' @param tube_lenght The lenght in cm of the sampler.
-#' @param core_in The lenght in cm of the part of the sampler left outside of the sediment (from the inside of the sampler).
-#' @param core_out The lenght in cm of the part of the sampler left outside of the sediment (from the outside of the sampler).
-#' @param diameter in cm of the sampler
+#' @param sampler_lenght name of the column with the total length of the sampler tube
+#' @param internal_distance The lenght in cm of the part of the sampler left outside of the sediment (from the inside of the sampler).
+#' @param external_distance The lenght in cm of the part of the sampler left outside of the sediment (from the outside of the sampler).
+#' @param sampler_diameter diameter in cm of the sampler
 #' @param method used to estimate the decompressed depth of each section, "linear" or "exp". Default is "linear".
 #' 
 
 bc_decomp <-
-  function(data, tube_lenght, core_in, core_out, diameter, method = "linear") {
-
-    if(!(method %in% c("linear", "exp"))) {
-
-          return("Method must be either 'linear' or 'exp'")
-        }
-
-    if(method == "linear") {
+  function(data,
+           sampler_lenght,
+           internal_distance,
+           external_distance,
+           sampler_diameter,
+           method = "linear") {
+
+    # Stop if data is not a data.frame  
+    if(!is.data.frame(data)){
+      stop("data is not a data.frame")
+    }
+
+    # Stop if method is not linear or exp
+    if (!(method %in% c("linear", "exp"))) {
+      return("Method must be either 'linear' or 'exp'")
+    }
+
+    if (method == "linear") {
+
 
       decomp <- data.frame(data$ID)
-      decomp$cm_obs <- data$cm + ((tube_lenght - core_out) - (tube_lenght - core_in))
+      decomp$cm_obs <- data$cm + ((sampler_lenght - external_distance) - (sampler_lenght - internal_distance))
 
-      corr_fact <- as.numeric((tube_lenght - core_in) / (tube_lenght - core_out))
+      corr_fact <- as.numeric((sampler_lenght - internal_distance) / (sampler_lenght - external_distance))
 
       decomp$cm_deco <- decomp$cm_obs * corr_fact
       decomp$sect_h <- c(dplyr::first(decomp$cm_deco), diff(decomp$cm_deco))
-      decomp$volume <- (((pi * (diameter/2)^2) * decomp$sect_h)/2) #volume is divided by two as half section is used
+      decomp$volume <- (((pi * (sampler_diameter/2)^2) * decomp$sect_h)/2) #volume is divided by two as half section is used
       decomp$density <- data$weight/decomp$volume
 
       c <- as.numeric(stats::coef(stats::lm(c_org~LOI, data = data))[1])
@@ -41,18 +52,18 @@ bc_decomp <-
     }
 
     if(method == "exp") {
-      test <- data.frame(x = c(((tube_lenght - core_out) - (tube_lenght - core_in)), (tube_lenght - core_out)),
-                         y = c(((tube_lenght - core_out) - (tube_lenght - core_in)), 0.1))
+      test <- data.frame(x = c(((sampler_lenght - external_distance) - (sampler_lenght - internal_distance)), (sampler_lenght - external_distance)),
+                         y = c(((sampler_lenght - external_distance) - (sampler_lenght - internal_distance)), 0.1))
 
       a <- as.numeric(stats::coef(drc::drm(y~x, data=test, fct=aomisc::DRC.expoDecay()))[1])
       b <- as.numeric(stats::coef(drc::drm(y~x, data=test, fct=aomisc::DRC.expoDecay()))[2])
 
       decomp <- data.frame(data$ID)
-      decomp$cm_obs <- data$cm + ((tube_lenght - core_out) - (tube_lenght - core_in))
+      decomp$cm_obs <- data$cm + ((sampler_lenght - external_distance) - (sampler_lenght - internal_distance))
       decomp$cm_deco <- decomp$cm_obs -
         (a * exp(-b*decomp$cm_obs))
       decomp$sect_h <- c(dplyr::first(decomp$cm_deco), diff(decomp$cm_deco))
-      decomp$volume <- (((pi * (diameter/2)^2) * decomp$sect_h)/2) #volume is divided by two as half section is used
+      decomp$volume <- (((pi * (sampler_diameter/2)^2) * decomp$sect_h)/2) #volume is divided by two as half section is used
       decomp$density <- data$weight/decomp$volume
 
       c <- as.numeric(stats::coef(stats::lm(c_org~LOI, data = data))[1])