v0.0.5-fix-comments-given-by-goodpractices

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: chirps
 Type: Package
 Title: API Client for CHIRPS
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: c(person("Kaue", "de Sousa", 
         email = "kaue.desousa@inn.no", role = c("aut", "cre"),
         comment = c(ORCID = "0000-0002-7571-7845")), 

NAMESPACE

@@ -9,9 +9,19 @@ S3method(get_esi,sf)
 export(get_chirps)
 export(get_esi)
 export(precip_indices)
-import(crul)
-import(jsonlite)
-import(methods)
-import(sf)
+importFrom(crul,HttpClient)
+importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,toJSON)
+importFrom(methods,addNextMethod)
+importFrom(methods,asMethodDefinition)
+importFrom(methods,assignClassDef)
+importFrom(sf,read_sf)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_buffer)
+importFrom(sf,st_centroid)
+importFrom(sf,st_geometry_type)
+importFrom(sf,st_point)
+importFrom(sf,st_sfc)
+importFrom(sf,st_write)
 importFrom(stats,quantile)
 importFrom(tibble,as_tibble)

NEWS.md

@@ -1,3 +1,11 @@
+chirps 0.0.5 (2020-01-09)
+=========================
+
+### ENHANCEMENTS
+
+* Fix comments given by good practice `goodpractice::gp()`. Avoid long code lines, it is bad for readability. Avoid 1:length(...), 1:nrow(...), 1:ncol(...), 1:NROW(...) and 1:NCOL(...) expressions. Not import packages as a whole, as this can cause name clashes between the imported packages. 
+
+
 chirps 0.0.4 (2020-01-03)
 =========================
 

R/GET.R

@@ -1,18 +1,19 @@
 #' General function to get data from ClimateSERV API
 #'
 #' @param object a list with geojson strings
-#' @param dates a character of start and end dates in that order in the format
-#'  MM/DD/YYYY
+#' @param dates a character of start and end dates in that order in 
+#' the format MM/DD/YYYY
 #' @param operation an integer that represents which type of statistical
 #'  operation to perform on the dataset
-#' @param datatype an integer, the unique datatype number for the dataset which
-#'  this request operates on
+#' @param datatype an integer, the unique datatype number for the dataset 
+#' which this request operates on
 #' @return A data.frame with values
 #' @details 
-#' operation: supported operations are max = 0, min = 1, median = 2, sum = 4,
-#'  average = 5
+#' operation: supported operations are max = 0, min = 1, median = 2, 
+#'  sum = 4, average = 5
 #' 
-#' datatype: supported datatypes are Global CHIRPS = 0, Global ESI 4 Week = 29
+#' datatype: supported datatypes are Global CHIRPS = 0, 
+#'  Global ESI 4 Week = 29
 #'  datatype codes are described at
 #'  <https://climateserv.readthedocs.io/en/latest/api.html>
 #' 
@@ -56,7 +57,7 @@
 
   # check request progress and wait 
   # until the request is done by the server
-  request_progress <- rep(FALSE, length(ids))
+  request_progress <- seq_along(ids) == FALSE
 
   while (!all(request_progress)) {
 
@@ -84,13 +85,20 @@
   # define ids
   ids <- NULL
   for(i in seq_along(result)) {
-    ids <- c(ids, rep(i, nrow(result[[i]])))
+
+    nr <- dim(result[[i]])[[1]]
+
+    ids <- c(ids, rep(i, nr))
+
   }
 
   result <- do.call("rbind", result)
 
-  if (nrow(result) == 0) {
-    stop("Fail to get valid values, try to increase the buffer area with 'dist' \n")
+  nr <- dim(result)[[1]]
+
+  if (nr == 0) {
+    stop("Fail to get valid values, 
+         try to increase the buffer area with 'dist' \n")
   }
 
   # add ids 
@@ -104,7 +112,7 @@
 
   names(result) <- c("date", "value", "id")
 
-  rownames(result) <- 1:nrow(result)
+  rownames(result) <- seq_len(nr)
 
   result <- result[, c("id", "date", "value")]
 

R/chirps.R

@@ -9,8 +9,11 @@
 #' @seealso
 #'\strong{Useful links:}
 #' \itemize{
-#' \item{Development repository: \url{https://github.com/agrobioinfoservices/chirps}}
-#' \item{Static documentation: \url{https://agrobioinfoservices.github.io/chirps/}}
-#' \item{Report bugs: \url{https://github.com/agrobioinfoservices/chirps/issues}}
+#' \item{Development repository: 
+#'  \url{https://github.com/agrobioinfoservices/chirps}}
+#' \item{Static documentation: 
+#'  \url{https://agrobioinfoservices.github.io/chirps/}}
+#' \item{Report bugs: 
+#'  \url{https://github.com/agrobioinfoservices/chirps/issues}}
 #' }
-"_PACKAGE"
+"_PACKAGE"

R/get_chirps.R

@@ -5,8 +5,8 @@
 #'  ClimateSERV works with geojson of type 'Polygon'. The input \code{object}
 #'  is then transformed into polygons with a small buffer area around the point.
 #' 
-#' @param object input, an object of class \code{\link[base]{data.frame}},\code{geojson} or
-#'  \code{\link[sf]{sf}}
+#' @param object input, an object of class \code{\link[base]{data.frame}},
+#' \code{geojson} or \code{\link[sf]{sf}}
 #' @param dates a character of start and end dates in that order in the format
 #'  "YYYY-MM-DD"
 #' @param operation optional, an integer that represents which type of
@@ -125,10 +125,9 @@
 #' # as.geojson = TRUE returns an object of class 'geojson'
 #' dat <- get_chirps(object, dates, as.geojson = TRUE)
 #' 
-#' } 
-#' @import sf
-#' @import methods
-#' @import jsonlite
+#' }  
+#' @importFrom methods addNextMethod asMethodDefinition assignClassDef
+#' @importFrom sf st_centroid read_sf st_geometry_type
 #' @importFrom tibble as_tibble
 #' @export
 get_chirps <- function(object, dates, operation = 5, ...) {
@@ -194,48 +193,39 @@ get_chirps.sf <- function(object, dates, operation = 5,
 
   type <- type[which(supp_type)]
 
-  n <- nrow(object)
+  nr <- dim(object)[[1]]
 
   # find the sf_column
   index <- attr(object, "sf_column")
 
+  # get the sf column
+  lonlat <- object[[index]]
+
   if (type == "POINT") {
 
     # unlist the sf_column
     lonlat <- unlist(object[[index]])
 
-    lonlat <- matrix(lonlat,
-                     nrow = n,
-                     ncol = 2, 
-                     byrow = TRUE, 
-                     dimnames = list(1:n, c("lon","lat")))
-
-    lonlat <- as.data.frame(lonlat)
-
   }
 
   if (type == "POLYGON") {
 
-    lonlat <- object[[index]]
-
-    nl <- length(lonlat)
-
     # set centroid to validade lonlat
     lonlat <- sf::st_centroid(lonlat)
 
     # unlist the sf_column
     lonlat <- unlist(lonlat)
 
-    lonlat <- matrix(lonlat,
-                     nrow = nl,
-                     ncol = 2, 
-                     byrow = TRUE, 
-                     dimnames = list(1:nl, c("lon","lat")))
-
-    lonlat <- as.data.frame(lonlat)
-
   }
 
+  lonlat <- matrix(lonlat,
+                   nrow = nr,
+                   ncol = 2, 
+                   byrow = TRUE, 
+                   dimnames = list(seq_len(nr), c("lon","lat")))
+
+  lonlat <- as.data.frame(lonlat)
+
   # validate lonlat to check if they are within the CHIRPS range
   .validate_lonlat(lonlat, xlim = c(-180, 180), ylim = c(-50, 50))
 
@@ -253,7 +243,7 @@ get_chirps.sf <- function(object, dates, operation = 5,
   if (as.sf) {
 
     result$date <- as.integer(result$date)
-    result$date <- paste0("d_",result$date)
+    result$date <- paste0("day_",result$date)
 
     result <- split(result, result$date)
 
@@ -357,7 +347,7 @@ get_chirps.geojson <- function(object, dates, operation = 5,
 
     lonlat <- as.data.frame(lonlat)
 
-    gjson <- split(object, 1:length(object))
+    gjson <- split(object, seq_along(object))
 
   }
 
@@ -377,7 +367,7 @@ get_chirps.geojson <- function(object, dates, operation = 5,
 
     result <- split(result, result$id)
 
-    object <- split(object, 1:length(object))
+    object <- split(object, seq_along(object))
 
     # add geojson properties
     result <- mapply(function(X, Y) {
@@ -411,4 +401,4 @@ get_chirps.geojson <- function(object, dates, operation = 5,
 
   return(result)
 
-}
+}

R/get_esi.R

@@ -8,7 +8,8 @@
 #'  then transformed into polygons with a small buffer area around the point.
 #' 
 #' @inheritParams get_chirps
-#' @param period an integer value for the period of ESI data, four weeks period = 1, twelve weeks = 2
+#' @param period an integer value for the period of ESI data, 
+#' four weeks period = 1, twelve weeks = 2
 #' @details
 #'  \bold{operation}: supported operations are:  
 #'  \tabular{rll}{
@@ -193,49 +194,40 @@ get_esi.sf <- function(object, dates, operation = 5, period = 1,
 
   type <- type[which(supp_type)]
 
-  n <- nrow(object)
+  nr <- dim(object)[[1]]
 
   # find the sf_column
   index <- attr(object, "sf_column")
 
+  # get the sf column
+  lonlat <- object[[index]]
+
   if (type == "POINT") {
 
     # unlist the sf_column
     lonlat <- unlist(object[[index]])
 
-    lonlat <- matrix(lonlat,
-                     nrow = n,
-                     ncol = 2, 
-                     byrow = TRUE, 
-                     dimnames = list(1:n, c("lon","lat")))
-
-    lonlat <- as.data.frame(lonlat)
-
   }
 
   if (type == "POLYGON") {
 
-    lonlat <- object[[index]]
-
-    nl <- length(lonlat)
-
     # set centroid to validade lonlat
     lonlat <- sf::st_centroid(lonlat)
 
     # unlist the sf_column
     lonlat <- unlist(lonlat)
 
-    lonlat <- matrix(lonlat,
-                     nrow = nl,
-                     ncol = 2, 
-                     byrow = TRUE, 
-                     dimnames = list(1:nl, c("lon","lat")))
-
-    lonlat <- as.data.frame(lonlat)
-
   }
 
-  # validate lonlat to check if they are within the CHIRPS range
+  lonlat <- matrix(lonlat,
+                   nrow = nr,
+                   ncol = 2, 
+                   byrow = TRUE, 
+                   dimnames = list(seq_len(nr), c("lon","lat")))
+
+  lonlat <- as.data.frame(lonlat)
+
+  # validate lonlat to check if they are within the ESI range
   .validate_lonlat(lonlat, xlim = c(-180, 180), ylim = c(-50, 50))
 
   # validate and reformat dates
@@ -260,7 +252,7 @@ get_esi.sf <- function(object, dates, operation = 5, period = 1,
   if (as.sf) {
 
     result$date <- as.integer(result$date)
-    result$date <- paste0("d_",result$date)
+    result$date <- paste0("day_",result$date)
 
     result <- split(result, result$date)
 
@@ -361,7 +353,7 @@ get_esi.geojson <- function(object, dates, operation = 5, period = 1,
 
     lonlat <- as.data.frame(lonlat)
 
-    gjson <- split(object, 1:length(object))
+    gjson <- split(object, seq_along(object))
 
   }
 
@@ -388,7 +380,7 @@ get_esi.geojson <- function(object, dates, operation = 5, period = 1,
 
     result <- split(result, result$id)
 
-    object <- split(object, 1:length(object))
+    object <- split(object, seq_along(object))
 
     # add geojson properties
     result <- mapply(function(X, Y) {
@@ -420,4 +412,4 @@ get_esi.geojson <- function(object, dates, operation = 5, period = 1,
 
   return(result)
 
-}
+}