Stylecleaning (#147)

Close #145. Code linting and extensive improvements to docs

DESCRIPTION

@@ -24,4 +24,5 @@ Imports:
     reshape2,
     plyr
 RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

NEWS.md

@@ -2,7 +2,9 @@
 
 Changes in this release:
 
-* Added `as.fhx()`. This takes data frames, tibbles, and lists as input. It assumes they have "year", "series", and "rec_type" elements/columns and returns an fhx object. (Issue #120).
+* Added `as.fhx()`. This takes data frames, tibbles, and lists as input. It assumes they have "year", "series", and "rec_type" elements/columns. It returns an `fhx` object. This makes life easier for people who work with the tidyverse. It helps make life easier for users who want to work with thier own non-FHX fire-history file formats. (Issue #120)
+
+* Extensive improvement to documentation (e.g. Issue #145). This includes new "See Also" sections so users can find cool functions, fixes for spelling errors, and clarifications to dyslexic prose.
 
 * Removed deprecated `run_sea()`. Be sure to use `sea()` now.
 
@@ -14,7 +16,7 @@ Changes in this release:
 
 * Added unit tests for basic plotting function options.
 
-* Minor internal code cleanup (Issue #130, Issue #88, Issue #133, Issue #136, Issue #88).
+* Minor internal code cleanup (Issue #130, Issue #88, Issue #133, Issue #136, Issue #88) and code linting.
 
 
 # burnr v0.4.0

R/data.R

@@ -1,49 +1,86 @@
 #' Los Griegos Peak plot2 fire-history data
 #'
-#' An fhx object with fire-history data from Los Griegos Peak, New Mexico.
+#' An `fhx` object with fire-history data from Los Griegos Peak, New Mexico.
 #'
-#' @format An fhx object with 26 series from 1366 to 2012 CE. Each series is a string with 5 characters.
+#' @format An fhx object with 26 series from 1366 to 2012 CE.
+#'
+#' @seealso [lgr2_meta] Los Griegos Peak metadata.
 "lgr2"
 
+
 #' Metadata for the Los Griegos Peak fire-history dataset
 #'
-#' A dataset with species information for the Los Griegos Peak plot2 fire-history dataset (`lgr2`).
+#' @description
+#' A data frame with species information for the Los Griegos Peak plot2
+#' fire-history dataset ([lgr2]).
 #'
-#' @format A data frame with 26 rows and 2 variables:
-#' \itemize{
-#'   \item TreeID: name of tree series
-#'   \item SpeciesID: abbreviated tree species
-#' }
+#' @format A `data.frame` with 26 rows and 2 variables:
+#'   * "TreeID": Name of tree series.
+#'   * "SpeciesID": Abbreviated tree species
+#'
+#' @seealso [lgr2] Log Griegos Peak fire-history data.
 "lgr2_meta"
 
+
 #' Peggy Mesa fire-history data
 #'
-#' An fhx object with fire-history data from Peggy Mesa. See dataset `pgm_meta` for metadata. Data from Guiterman, Christopher H., Ellis Q. Margolis, and Thomas W. Swetnam. 2015. "Dendroecological Methods For Reconstructing High-Severity Fire In Pine-Oak Forests." Tree-Ring Research 71 (2): 67-77. doi:10.3959/1536-1098-71.2.67.
-
+#' @description
+#' An `fhx` object with fire-history data from Peggy Mesa.
+#'
+#' @format An `fhx` object with 41 series from 1555 to 2013 CE.
+#'
+#' @source Guiterman, Christopher H., Ellis Q. Margolis, and
+#' Thomas W. Swetnam. 2015. "Dendroecological Methods For Reconstructing
+#' High-Severity Fire In Pine-Oak Forests." Tree-Ring Research 71 (2): 67-77.
+#' doi:10.3959/1536-1098-71.2.67.
 #'
-#' @format An fhx object with 41 series from 1555 to 2013 CE. Each series is a string with 5 characters.
+#' @seealso
+#'   * [pgm_meta] Peggy Mesa metadata.
+#'   * [pgm_pdsi] PDSI time-series for Peggy Mesa site.
 "pgm"
 
+
 #' Metadata for the Peggy Mesa fire-history dataset
 #'
-#' A dataset with species and location information for the Peggy Mesa fire-history dataset (`pgm`). Data from Guiterman, Christopher H., Ellis Q. Margolis, and Thomas W. Swetnam. 2015. "Dendroecological Methods For Reconstructing High-Severity Fire In Pine-Oak Forests." Tree-Ring Research 71 (2): 67-77. doi:10.3959/1536-1098-71.2.67.
+#' @description
+#' A data frame with species and location information for the Peggy Mesa
+#' fire-history dataset ([pgm]).
+#'
+#' @format A `data.frame` with 41 rows and 5 variables:
+#'   * "TreeID": Name of tree series.
+#'   * "SpeciesID": Abbreviated tree species.
+#'   * "Latitude": latitude of tree in decimal degrees.
+#'   * "Longitude": longitude of tree in decimal degrees.
+#'   * "Elevation": tree elevation in meters.
+#'
+#' @source Guiterman, Christopher H., Ellis Q. Margolis, and
+#' Thomas W. Swetnam. 2015. "Dendroecological Methods For Reconstructing
+#' High-Severity Fire In Pine-Oak Forests." Tree-Ring Research 71 (2): 67-77.
+#' doi:10.3959/1536-1098-71.2.67.
 #'
-#' @format A data frame with 41 rows and 5 variables:
-#' \itemize{
-#'   \item TreeID: name of tree series
-#'   \item SpeciesID: abbreviated tree species
-#'   \item Latitude: latitude of tree in decimal degrees
-#'   \item Longitude: longitude of tree in decimal degrees
-#'   \item Elevation: tree elevation in meters
-#' }
+#' @seealso
+#'   * [pgm] Peggy Mesa fire-history data.
+#'   * [pgm_pdsi] PDSI time-series for Peggy Mesa site.
 "pgm_meta"
 
+
 #' Reconstructed PDSI time series for the Peggy Mesa fire-history dataset
 #'
-#' A tree-ring reconstructed Palmer Drought-Severity Index time series corresponding to the Peggy Mesa fire-history dataset (`pgm`) -- specifically, the Jemez Mountains area (gridpoint 133). The reconstruction is from The North American Drought Atlas (Cook and Krusic 2004).
+#' @description
+#' A tree-ring reconstructed Palmer Drought-Severity Index time series
+#' corresponding to the Peggy Mesa fire-history dataset ([pgm]) -- specifically,
+#' the Jemez Mountains area (gridpoint 133). The reconstruction is from The
+#' North American Drought Atlas (Cook and Krusic 2004).
+#'
+#' @format A `data.frame` with 2004 rows and 1 variables. Row names give the
+#' year for the reconstructed value:
+#'   * "RECON": The reconstructed PDSI series.
+#'
+#' @source Cook, E. R., and Krusic, P. J. (2004). The North American Drought
+#' Atlas. Retrieved September 13, 2017, from
+#' http://iridl.ldeo.columbia.edu/SOURCES/.LDEO/.TRL/.NADA2004/.pdsi-atlas.html
 #'
-#' @format A data frame with 2004 rows and 1 variables. Row names give the year for the reconstructed value:
-#' \itemize{
-#'   \item RECON: The reconstructed PDSI series.
-#' }
-"pgm_pdsi"
+#' @seealso
+#'   * [pgm] Peggy Mesa fire-history data.
+#'   * [pgm_meta] Peggy Mesa metadata.
+"pgm_pdsi"