Merge branch 'experimental'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: feedr
 Type: Package
 Title: Transforming Raw RFID Data
-Version: 0.9.0
-Date: 2017-06-05
+Version: 0.9.1
+Date: 2017-11-03
 Authors@R: person("LaZerte", "Stefanie E", email = "[email protected]", role = c("aut","cre"))
 URL: https://github.com/animalnexus/feedr
 Description: Load, clean, transform, and visualize raw RFID data for looking at a variety of

R/data.R

@@ -1,31 +1,37 @@
-#' Finche visits to RFID-enabled feeders
+#' Finch visits to RFID-enabled feeders
 #'
 #' A small dataset containing raw reads of finches visiting feeders (RFID
 #' loggers) on Thompson Rivers University campus in Kamloops, BC, Canada
 #'
-#' @format A data frame with 412 rows and 7 variables:
+#' @format A data frame with 412 rows and 10 variables:
 #' \describe{
 #'   \item{animal_id}{Unique RFID tag attached to a finch}
+#'   \item{date}{Date of the read}
 #'   \item{time}{Time of read}
 #'   \item{logger_id}{Unique id of logger where read was made}
 #'   \item{species}{Individual species}
+#'   \item{age}{Individual age}
 #'   \item{sex}{Individual sex, if known}
+#'   \item{site_name}{Site name of the observation}
 #'   \item{lat}{Latitude}
 #'   \item{lon}{Longitude}}
 "finches"
 
-#' Large dataset of finche visits to RFID-enabled feeders
+#' Large dataset of finch visits to RFID-enabled feeders
 #'
 #' A large dataset containing raw reads of finches visiting feeders (RFID
 #' loggers) on Thompson Rivers University campus in Kamloops, BC, Canada
 #'
-#' @format A data frame with 42708 rows and 7 variables:
+#' @format A data frame with 42708 rows and 10 variables:
 #' \describe{
 #'   \item{animal_id}{Unique RFID tag attached to a finch}
+#'   \item{date}{Date of the read}
 #'   \item{time}{Time of read}
 #'   \item{logger_id}{Unique id of logger where read was made}
 #'   \item{species}{Individual species}
+#'   \item{age}{Individual age}
 #'   \item{sex}{Individual sex, if known}
+#'   \item{site_name}{Site name of the observation}
 #'   \item{lat}{Latitude}
 #'   \item{lon}{Longitude}}
 "finches_lg"
@@ -35,13 +41,13 @@
 #' A dataset containing raw reads of black-capped chickadees visiting
 #' RFID-enabled feeders (loggers) in Prince George, BC, Canada
 #'
-#' @format A data frame with 26718 rows and 7 variables:
+#' @format A data frame with 26,753 rows and 10 variables:
 #' \describe{
 #'   \item{animal_id}{Unique RFID tag attached to a chickadee}
+#'   \item{date}{Date of the read}
 #'   \item{time}{Time of read}
 #'   \item{logger_id}{Unique id of logger where read was made}
 #'   \item{experiment}{Which experiment (site) the data was collected at}
-#'   \item{date}{Date of read}
 #'   \item{lat}{Latitude of logger location}
 #'   \item{lon}{Longitude of logger location}}
 "chickadees"

R/errorchecks.R

@@ -59,7 +59,7 @@ check_input <- function(d, input = "lon", options = c("lon", "longitude", "long"
       c <- utils::combn(n, 2)
       if(ncol(c) < 10) {
         for(i in 1:ncol(c)) {
-          if(!isTRUE(all.equal(d[, c[1, i]], d[, c[2, i]]))) {
+          if(!isTRUE(all.equal(d[, c[1, i]][[1]], d[, c[2, i]][[1]]))) {
             stop("There are multiple ", input, " columns which are not equivalent\n(expects ", input, " to be one of ", paste0(options, collapse = ", "), ", but ignores case")
           }
         }

R/feedr.R

@@ -73,7 +73,7 @@ if(getRversion() >= "2.15.1")
       "site_name", "dataaccess", "count", "start", "x", "fill", "facet", "end", "y", "counts_sum", "temp", "engl_name", "val", "id", "f", "arg", "title", "lab", "site_id",
 
       # Convert functions
-      "item.number",
+      "item.number", "midnight", "time_sec", "time_rad", "data",
 
       # piping requires '.' at times
       ".")

R/load.R

@@ -172,7 +172,7 @@ load_raw <- function(r_file,
       # Convert times
       r$time <- lubridate::parse_date_time(paste(r$date, r$time), orders = time_format, tz = tz)
       if(tz_disp != tz) r$time <- lubridate::with_tz(r$time, tz_disp)
-      r$date <- as.Date(r$time)
+      r$date <- as.Date(r$time, tz = lubridate::tz(r$time))
 
       # Reorder columns
       cols <- names(r)[names(r) %in% c("animal_id", "date", "time", "logger_id", "lat", "lon")]
@@ -535,7 +535,7 @@ load_format <- function(r, tz = Sys.timezone(), tz_disp = NULL, dst = FALSE, tim
   if("time" %in% names(r)) {
     r$time <- lubridate::parse_date_time(r$time, orders = time_format, tz = tz, truncated = 1)
     if(tz != tz_disp) r$time <- lubridate::with_tz(r$time, tz_disp)
-    r$date <- as.Date(r$time)
+    r$date <- as.Date(r$time, tz = lubridate::tz(r$time))
   }
 
   # Make sure all factors are factors:
@@ -549,7 +549,7 @@ load_format <- function(r, tz = Sys.timezone(), tz_disp = NULL, dst = FALSE, tim
   }
 
   # Reorder columns
-  cols <- c("animal_id", "time", "logger_id")
+  cols <- c("animal_id", "date", "time", "logger_id")
   cols <- cols[which(cols %in% names(r))]
   r <- r[, c(cols, names(r)[!(names(r) %in% cols)])]
 

R/transformations.R

@@ -164,7 +164,7 @@ visits <- function(r, bw = 3, allow_imp = FALSE, bw_imp = 2, na_rm = FALSE, pass
     dplyr::ungroup() %>%
     dplyr::mutate(animal_n = length(unique(animal_id)),         # Get sample sizes
                  logger_n = length(unique(logger_id)),
-                 date = as.Date(start))
+                 date = as.Date(start, tz = lubridate::tz(start)))
 
   # Set timezone attributes
   attr(v$start, "tzone") <- tz
@@ -445,7 +445,7 @@ presence_single <- function(v1, bw = bw){
 
   ## Create the presence data frame.
   p <- tibble::data_frame(animal_id = v1$animal_id[1],
-                          date = as.Date(v1$start_orig[v1$start == TRUE]),
+                          date = v1$date[v1$start == TRUE],
                           logger_id = v1$logger_id[v1$start == TRUE],
                           start = v1$start_orig[v1$start == TRUE],
                           end = v1$end_orig[v1$end == TRUE],

README.md

@@ -1,5 +1,7 @@
 [![Travis-Ci Build Status](https://travis-ci.org/animalnexus/feedr.svg?branch=master)](https://travis-ci.org/animalnexus/feedr)
+
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/animalnexus/feedr?branch=master&svg=true)](https://ci.appveyor.com/project/animalnexus/feedr)
+
 # feedr
 
 `feedr` is a package for [R](https://www.r-project.org/). This collection of functions is designed to load, transform and visualize RFID data created when pit-tagged animals are detected by RFID loggers associated with static stations (e.g., seed-feeders, nestboxes, nectar-feeders, etc.).