using styler::tidyverse_style

R/mammalmap.R

@@ -25,70 +25,73 @@
 #' @importFrom mammalcol taxon
 #' @importFrom mammalcol colmap
 #' @export
-mammalmap <- function(species, legend=TRUE){
-
-  if (!requireNamespace("ggplot2", quietly = TRUE))
+mammalmap <- function(species, legend = TRUE) {
+  if (!requireNamespace("ggplot2", quietly = TRUE)) {
     install.packages("ggplot2")
-  if (!requireNamespace("sf", quietly = TRUE))
+  }
+  if (!requireNamespace("sf", quietly = TRUE)) {
     install.packages("sf")
-
+  }
+
   if (missing(species)) {
     stop("Argument species was not included")
   }
-  
+
   if (!is.character(species)) {
     stop(paste0("Argument species must be a character, not ", class(species)))
   }
-  
+
   if (!is.logical(legend)) {
     stop(paste0("Argument legend must be logical, not ", class(legend)))
   }
-  
+
   # require("ggplot2")
   # require("sf")
-  
-  #load("data/colmap.rda")
-  #load("data/taxon.rda")
-  
-  #data(mammalcol::taxon)
-  #data(mammalcol::colmap)
-  
+
+  # load("data/colmap.rda")
+  # load("data/taxon.rda")
+
+  # data(mammalcol::taxon)
+  # data(mammalcol::colmap)
+
   distribution_list <-
     strsplit(taxon$distribution, "\\|") # trimws () removes spaces
-  
-  deptos <- as.data.frame(cbind(Depto=unique(colmap$NAME_1), fill="white"))
+
+  deptos <- as.data.frame(cbind(Depto = unique(colmap$NAME_1), fill = "white"))
   sp_id <- which(taxon$scientificName == species)
-  unos <- trimws(distribution_list[[ sp_id ]]) # species number
-  
+  unos <- trimws(distribution_list[[sp_id]]) # species number
+
   # nested loop to get deptos
-  for (i in 1:length(deptos[,1])){
-    for (j in 1:length(unos)){
-      if(deptos$Depto[i]==unos[j]){deptos$fill[i] <- "blue"}
+  for (i in 1:length(deptos[, 1])) {
+    for (j in 1:length(unos)) {
+      if (deptos$Depto[i] == unos[j]) {
+        deptos$fill[i] <- "blue"
+      }
     }
   }
-  
+
   # make the map
-  # if legend true 
-  if(legend==TRUE) {
-    mapa <-   ggplot2::ggplot(colmap) +
+  # if legend true
+  if (legend == TRUE) {
+    mapa <- ggplot2::ggplot(colmap) +
       ggplot2::geom_sf(ggplot2::aes(fill = NAME_1)) +
       ggplot2::scale_fill_manual(values = deptos$fill) +
       # ggtitle(taxon$scientificName[25]) + #species name number
-      ggplot2::labs(subtitle = taxon$scientificName[sp_id])+
-      ggplot2::theme(legend.position="right", # location legend
-                     legend.title = ggplot2::element_blank(),#element_text(size=7),#,
-                     legend.text = ggplot2::element_text(size=8,), # text depto size
-                     plot.subtitle = ggplot2::element_text(face = "italic") # italica
+      ggplot2::labs(subtitle = taxon$scientificName[sp_id]) +
+      ggplot2::theme(
+        legend.position = "right", # location legend
+        legend.title = ggplot2::element_blank(), # element_text(size=7),#,
+        legend.text = ggplot2::element_text(size = 8, ), # text depto size
+        plot.subtitle = ggplot2::element_text(face = "italic") # italica
       )
-  }else{ # if legend false
-    mapa <-   ggplot2::ggplot(colmap) +
+  } else { # if legend false
+    mapa <- ggplot2::ggplot(colmap) +
       ggplot2::geom_sf(ggplot2::aes(fill = NAME_1), show.legend = FALSE) + # removes legend
       ggplot2::scale_fill_manual(values = deptos$fill) +
       # ggtitle(taxon$scientificName[25]) + #species name number
       ggplot2::labs(subtitle = taxon$scientificName[sp_id]) +
-      ggplot2::theme(plot.subtitle = ggplot2::element_text(face = "italic")
-                      )# italica
+      ggplot2::theme(plot.subtitle = ggplot2::element_text(face = "italic")) # italica
   }
-  
-return(mapa)
+
+  return(mapa)
 } # end function

R/onload.R

@@ -1,10 +1,9 @@
-
 .onAttach <- function(lib, pkg) {
   packageStartupMessage("This is mammalcol ",
-                        utils::packageDescription("mammalcol",
-                                                  fields = "Version"
-                        ),
-                        appendLF = TRUE
+    utils::packageDescription("mammalcol",
+      fields = "Version"
+    ),
+    appendLF = TRUE
   )
 }
 
@@ -20,7 +19,7 @@ show_progress <- function() {
 
 .onLoad <- function(libname, pkgname) {
   opt <- options()
-  opt_mammalcol<- list(
+  opt_mammalcol <- list(
     mammalcol.show_progress = TRUE
   )
   to_set <- !(names(opt_mammalcol) %in% names(opt))

R/search_mammalcol.R

@@ -30,26 +30,30 @@ search_mammalcol <- function(splist, max_distance = 0.2) {
   if (missing(splist)) {
     stop("Argument splist was not defined")
   }
-  
+
   if (is.factor(splist)) {
     splist <- as.character(splist)
   }
   # Fix species name
   splist_st <- standardize_names(splist)
   dupes_splist_st <- find_duplicates(splist_st)
 
-  if(length(dupes_splist_st) != 0 ){
-    message("The following names are repeated in the 'splist': ",
-            paste(dupes_splist_st, collapse = ", "))
+  if (length(dupes_splist_st) != 0) {
+    message(
+      "The following names are repeated in the 'splist': ",
+      paste(dupes_splist_st, collapse = ", ")
+    )
   }
   splist_std <- unique(splist_st)
 
   # create an output data container
   output_matrix <- matrix(nrow = length(splist_std), ncol = 21) # two more
-  colnames(output_matrix) <- c("name_submitted",
-                               names(taxon), 
-                               "Distance")
-
+  colnames(output_matrix) <- c(
+    "name_submitted",
+    names(taxon),
+    "Distance"
+  )
+
   # loop code to find the matching string
 
   for (i in seq_along(splist_std)) {
@@ -62,32 +66,31 @@ search_mammalcol <- function(splist, max_distance = 0.2) {
 
     # fuzzy and exact match
     matches <- agrep(splist_std[i],
-                     taxon$scientificName, # base data column
-                     max.distance = max_distance_fixed,
-                     value = TRUE)
+      taxon$scientificName, # base data column
+      max.distance = max_distance_fixed,
+      value = TRUE
+    )
 
     # check non matching result
     if (length(matches) == 0) {
       row_data <- rep("nill", 19) # number of columns
-    }
-    else if (length(matches) != 0){ # match result
+    } else if (length(matches) != 0) { # match result
       dis_value <- as.numeric(utils::adist(splist_std[i], matches))
       matches1 <- matches[dis_value <= max_distance_fixed]
       dis_val_1 <- dis_value[dis_value <= max_distance_fixed]
 
-      if (length(matches1) == 0){
+      if (length(matches1) == 0) {
         row_data <- rep("nill", 19) # number of columns
-      }
-      else if (length(matches1) != 0){
-        row_data <- as.matrix(taxon[taxon$scientificName %in% matches1,])
+      } else if (length(matches1) != 0) {
+        row_data <- as.matrix(taxon[taxon$scientificName %in% matches1, ])
       }
     }
 
     # distance value
-    if(is.null(nrow(row_data))){
+    if (is.null(nrow(row_data))) {
       dis_value_1 <- "nill"
-    } else{
-      dis_value_1 <- utils::adist(splist_std[i], row_data[,2])
+    } else {
+      dis_value_1 <- utils::adist(splist_std[i], row_data[, 2])
     }
 
     output_matrix[i, ] <-
@@ -97,7 +100,6 @@ search_mammalcol <- function(splist, max_distance = 0.2) {
   # Output
   output <- as.data.frame(output_matrix)
   # rownames(output) <- NULL
-  output <- output[,-2]# delete the id column
-  return(output[output$scientificName != "nill",])
+  output <- output[, -2] # delete the id column
+  return(output[output$scientificName != "nill", ])
 }
-

R/sp_by_depto.R

@@ -31,12 +31,12 @@ sp_by_depto <- function(states, type = c("any", "only", "all"), taxa = NULL) {
   if (length(states) == 0) stop("Please provide at least one Colombian Departamento")
   type <- match.arg(type)
   states <- sort(states)
-  
+
   # states <- paste("BR-", states, sep = "")
   if (length(states) == 0) stop("Please provide at least one Colombian Departamento")
   # res <- lapply(occurrences, match, states)
   if (type == "any") {
-    #res <- lapply(res, function(x) any(!is.na(x)))
+    # res <- lapply(res, function(x) any(!is.na(x)))
     res <- subset(distribution, grepl(paste(states, collapse = "|"), locality))
   }
   if (type == "only") {
@@ -50,10 +50,10 @@ sp_by_depto <- function(states, type = c("any", "only", "all"), taxa = NULL) {
     return(NA)
   }
   if (is.null(taxa)) {
-    merge(taxon[, c("scientificName", "family", "order",  "id")], res[, c("id", "locality")], by = "id")[,-1]
+    merge(taxon[, c("scientificName", "family", "order", "id")], res[, c("id", "locality")], by = "id")[, -1]
     # removes id
   } else {
-    merge(taxon[taxon$order %in% taxa, c("scientificName", "family", "order",  "id" )], res[, c("id", "locality")], by = "id")[,-1]
+    merge(taxon[taxon$order %in% taxa, c("scientificName", "family", "order", "id")], res[, c("id", "locality")], by = "id")[, -1]
     # removes id
   }
 }