First iteration of cap_birds

DESCRIPTION

@@ -1,61 +1,63 @@
-Package: lterdatasampler
-Title: Educational dataset examples from the Long Term Ecological Research program 
-Version: 0.1.0
-Date: 2020-08-01
-Authors@R: c(
-    person(given = "Allison",
-           family = "Horst",
-           role = c("aut", "cre"),
-           email = "ahorst@ucsb.edu",
-           comment = c(ORCID = "0000-0002-6047-5564")),
-    person(given = "Julien",
-           family = "Brun",
-           role = c("aut"),
-           email = "brun@nceas.ucsb.edu",
-           comment = c(ORCID = "0000-0002-7751-6238")),
-    person(given = "Sam",
-           family = "Guo",
-           role = c("ctb"),
-           comment = c("https://github.com/TokyoExpress")),
-    person(given = "Adhitya",
-           family = "Logan",
-           role = c("ctb"),
-           comment = c("https://github.com/adhil0")),
-    person(given = "Lian",
-           family = "Ran",
-           role = c("ctb"),
-           comment = c("https://github.com/liaaaaran")),
-    person(given = "Sophia",
-           family = "Sternberg",
-           role = c("ctb"),
-           comment = c("https://github.com/sophiasternberg")),
-    person(given = "Karen",
-           family = "Zhao",
-           role = c("ctb"),
-           comment = c("https://github.com/karenezhao"))
-           )
-Description: Selected datasets, one from each LTER site. 
-License: CC0
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
-Depends: 
-    R (>= 2.10)
-Suggests: 
-    knitr,
-    rmarkdown,
-    janitor,
-    usethis,
-    metajam,
-    tidyverse,
-    here, 
-    broom,
-    sf,
-    ggmap,
-    leaflet,
-    lubridate,
-    patchwork
-URL: https://github.com/lter/lterdatasampler
-BugReports: https://github.com/lter/lterdatasampler/issues
-VignetteBuilder: knitr
+Package: lterdatasampler
+Title: Educational dataset examples from the Long Term Ecological Research program 
+Version: 0.1.0
+Date: 2020-08-01
+Authors@R: c(
+    person(given = "Allison",
+           family = "Horst",
+           role = c("aut", "cre"),
+           email = "ahorst@ucsb.edu",
+           comment = c(ORCID = "0000-0002-6047-5564")),
+    person(given = "Julien",
+           family = "Brun",
+           role = c("aut"),
+           email = "brun@nceas.ucsb.edu",
+           comment = c(ORCID = "0000-0002-7751-6238")),
+    person(given = "Sam",
+           family = "Guo",
+           role = c("ctb"),
+           comment = c("https://github.com/TokyoExpress")),
+    person(given = "Adhitya",
+           family = "Logan",
+           role = c("ctb"),
+           comment = c("https://github.com/adhil0")),
+    person(given = "Lian",
+           family = "Ran",
+           role = c("ctb"),
+           comment = c("https://github.com/liaaaaran")),
+    person(given = "Sophia",
+           family = "Sternberg",
+           role = c("ctb"),
+           comment = c("https://github.com/sophiasternberg")),
+    person(given = "Karen",
+           family = "Zhao",
+           role = c("ctb"),
+           comment = c("https://github.com/karenezhao"))
+           )
+Description: Selected datasets, one from each LTER site. 
+License: CC0
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Depends: 
+    R (>= 2.10)
+Suggests: 
+    knitr,
+    rmarkdown,
+    janitor,
+    usethis,
+    metajam,
+    tidyverse,
+    here, 
+    broom,
+    sf,
+    ggmap,
+    leaflet,
+    lubridate,
+    patchwork,
+    gstat,
+    stars
+URL: https://github.com/lter/lterdatasampler
+BugReports: https://github.com/lter/lterdatasampler/issues
+VignetteBuilder: knitr

R/cap_birds_doc.R

@@ -0,0 +1,25 @@
+#' Bird Community Observations (2000 - 2019), Central Arizona - Phoenix LTER
+#'
+#' Bird count data collected in different seasons using a standardized point-count protocol.  In 2000, sites were visited twice. In 2001 each site was visited in each season by three independent observers. In 2005, sites were visited in three seasons, and from 2006 - 2019, only in spring and winter.
+#'
+#' @format A tibble with 172,175 rows and 14 variables
+#' \describe{
+#'   \item{survey_id}{a number denoting the unique identity of the bird survey}
+#'   \item{site_code}{a character denoting the identity of the survey location}
+#'   \item{survey_date}{a date denoting the date of observation}
+#'   \item{time_start}{a time denoting the start time of the observation period}
+#'   \item{time_end}{a time denoting the end time of the observation period}
+#'   \item{common_name}{a character denoting the common name of the species observed}
+#'   \item{distance}{a character denoting the distance of the observed birds from the observer in meters}
+#'   \item{bird_count}{a number denoting the count of birds observed during the survey period}
+#'   \item{seen}{a boolean denoting whether the bird was seen by the observer}
+#'   \item{heard}{a boolean denoting whether the bird was heard by the observer}
+#'   \item{direction}{a character denoting the direction of the bird from the observation point}
+#'   \item{location_type}{a character denoting the physical or research context of the site}
+#'   \item{lat}{a number denoting the latitude of the survey site in degrees}
+#'   \item{long}{a number denoting the longitude of the survey site in degrees}
+#' }
+#' @source {Warren, P., S.B. Lerman, H. Bateman, M. Katti, and E. Shochat. 2022. Point-count bird censusing: long-term monitoring of bird abundance and diversity in central Arizona-Phoenix, ongoing since 2000 ver 19. Environmental Data Initiative.}
+#' \url{https://doi.org/10.6073/pasta/4fca7c8a6cd56a6abed9834aca72e764}
+
+"cap_birds"

data-raw/cap_birds_data.R

@@ -0,0 +1,79 @@
+#' ---
+#' title: "Data Preparation"
+#' ---
+#' ### Download the raw data from EDI.org
+
+#+ download_data, eval=FALSE
+library(metajam)
+library(tidyverse)
+
+# Point-count bird censusing: long-term monitoring of bird abundance and diversity in central Arizona-Phoenix, ongoing since 2000
+# Main URL: https://doi.org/10.6073/pasta/4fca7c8a6cd56a6abed9834aca72e764
+
+# Location Data
+locations_url <-
+  "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-cap.46.19&entityid=86856afb2e6779f5acb261a2b04d1e13"
+
+
+# Sighting data
+cap_url <-
+  "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-cap.46.19&entityid=832065765ce5a9a8238a0b25cb549722"
+
+# Download the data packages with metajam
+locations_download <-
+  download_d1_data(data_url = locations_url, path = tempdir())
+
+cap_download <-
+  download_d1_data(data_url = cap_url, path = tempdir())
+
+#' ### Data cleaning
+#+ data sampling, eval=FALSE
+
+# Read in location data
+locations_files <-
+  read_d1_files(locations_download)
+locations_raw <- locations_files$data
+
+# Discard repeated site locations. Some sites were moved over the course of the study, but the changes in location were very small
+locations <- locations_raw %>%
+  select(
+    -begin_date,
+    -begin_date_month,
+    -begin_date_year,
+    -end_date,
+    -end_date_month,
+    -end_date_year,
+  ) %>%
+  mutate(
+    location_type = recode(
+      location_type,
+      "ESCA" = "Ecological Survey of Central Arizona",
+      "NDV" = "North Desert Village",
+      "riparian" = "Riparian",
+      "SRBP" = "Salt River Biodiversity Project",
+      "PASS" = "Phoenix Area Social Survey",
+      "desert_fertilization" = "Desert Fertilization"
+    )
+  ) %>%
+  group_by(site_code) %>%
+  slice_tail() %>%
+  ungroup()
+
+# Read in count data
+cap_files <- read_d1_files(cap_download)
+cap_birds_raw <- cap_files$data
+
+# Select needed variables, spell out abbreviations
+cap_birds <-
+  cap_birds_raw %>%
+  mutate(survey_date = as.Date(survey_date)) %>%
+  select(-observer, -code, -observation_notes, -qccomment) %>%
+  mutate(distance = recode(distance, "FT" = "Flying Through"))
+
+# Combine location data with count data
+cap_birds <-
+  cap_birds %>% full_join(locations, by = "site_code")
+
+#+ save data, include=FALSE, EVAL=FALSE
+## Save sample file
+usethis::use_data(cap_birds, overwrite = TRUE)