function to compute neighbor stats. Related to #9

R/neighborSpecies_stats.R

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+#' Summarizes neighbor species data 
+#' 
+#' This function takes a data frame or tibble and groups it by neighbor species 
+#' (`especie_vecina`). For each neighbor species, the function calculates the 
+#' number of plots where each species has been recorded, as well as several 
+#' statistics for the neighbor species: the mean, standard error, minimum, 
+#' and maximum abundance of the neighbor species in the plots where it is present.
+#'
+#' @param data A data frame or tibble containing the data to be summarized.
+#'
+#' @return A tibble with the following columns:
+#'   - especie_vecina: The grouping variable (neighbor species).
+#'   - ab_mean: The mean abundance of the neighbor species.
+#'   - ab_se: The standard error of the mean abundance.
+#'   - ab_min: The minimum abundance of the neighbor species.
+#'   - ab_max: The maximum abundance of the neighbor species.
+#'   - present_at: The count of plots where each neighbor species is recorded.
+#'   - present_at_per: The percentage of the sampled plots (`individuo`) where each 
+#'   neighbor species is recorded.
+#'
+#' @export
+neighborSpecies_stats <- function(data) {
+  # Check if 'data' is a data frame or tibble
+  if (!is.data.frame(data) && !is.data.frame(as.data.frame(data))) {
+    stop("Input 'data' must be a data frame or tibble.")
+  }
+
+  # Check if 'especie_vecina' and 'n_vecino' columns exist 
+  required_cols <- c("especie_vecina", "n_vecino", "individuo")
+  missing_cols <- setdiff(required_cols, colnames(data))
+
+  if (length(missing_cols) > 0) {
+    stop(paste("Required columns missing:", paste(missing_cols, collapse = ", ")))
+  }
+
+  nplots <- length(unique(f$vecindad$individuo))
+
+  result <- data %>%
+    group_by(especie_vecina) %>%
+    summarise(ab_mean = mean(n_vecino), 
+              ab_se = sd(n_vecino) / sqrt(length(n_vecino)),
+              ab_min = min(n_vecino), 
+              ab_max = max(n_vecino),
+              present_at = length(n_vecino), 
+              present_at_per = round((present_at / nplots)*100, 2))
+
+  return(result)
+}