CRAN resubmission updates (#83)

* CRAN resubmission updates * removing vignette builder field since there are no more vignettes * fixing an error in the documentation * fixing an error in the hbr documentation as of #73 * fixing typo in and documentation as of #76 --------- Co-authored-by: Allison Horst <[email protected]> Co-authored-by: Julien Brun <[email protected]>
lter · Mar 19, 2023 · dba1f1a · dba1f1a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: lterdatasampler
-Title: Educational dataset examples from the Long Term Ecological Research program 
+Title: Educational Dataset Examples from the Long Term Ecological Research Program 
 Version: 0.1.1
-Date: 2020-08-01
+Date: 2023-03-18
 Authors@R: c(
     person(given = "Allison",
            family = "Horst",
@@ -62,4 +62,3 @@ Suggests:
     gt
 URL: https://github.com/lter/lterdatasampler
 BugReports: https://github.com/lter/lterdatasampler/issues
-VignetteBuilder: knitr
diff --git a/R/and_vertebrates_doc.R b/R/and_vertebrates_doc.R
@@ -17,10 +17,10 @@
 #'   \item{length_1_mm}{a number denoting vertebrate length in millimeters; total or snout-fork length for trout, and snout-vent length for salamanders}
 #'   \item{length_2_mm}{a number denoting snout-tail length in millimeters (for Coastal giant salamander only)}
 #'   \item{weight_g}{a number denoting vertebrate mass in grams}
-#'   \item{clip}{a character denoting the fin clip type for cutthroat trout, ended in 2006 (LV = left ventrical fin; LVRV = left and right ventrical fins; RV = right ventrical fin; NONE = no ventral fin clip)}
+#'   \item{clip}{a character denoting the fin clip type for cutthroat trout, ended in 2006 (LV = left ventral fin; LVRV = left and right ventral fins; RV = right ventral fin; NONE = no ventral fin clip)}
 #'   \item{sampledate}{a date denoting the date of observation}
 #'   \item{notes}{a character denoting additional comments}
 #'   }
 #' @source {Gregory, S.V. and I. Arismendi. 2020. Aquatic Vertebrate Population Study in Mack Creek, Andrews Experimental Forest, 1987 to present ver 14. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/7c78d662e847cdbe33584add8f809165}
+#' \doi{10.6073/pasta/7c78d662e847cdbe33584add8f809165}
 "and_vertebrates"
diff --git a/R/arc_weather_doc.R b/R/arc_weather_doc.R
@@ -10,7 +10,7 @@
 #'   \item{daily_precip}{a number denoting total daily precipitation in millimeters}
 #'   \item{mean_windspeed}{a number denoting daily mean windspeed in meters per second}
 #' }
-#' @source {Shaver, G. 2019. A multi-year DAILY weather file for the Toolik Field Station at Toolik Lake, AK starting 1988 to present. ver 4. Environmental Data Initiative.} \url{https://doi.org/10.6073/pasta/ce0f300cdf87ec002909012abefd9c5c}
+#' @source {Shaver, G. 2019. A multi-year DAILY weather file for the Toolik Field Station at Toolik Lake, AK starting 1988 to present. ver 4. Environmental Data Initiative.} \doi{10.6073/pasta/ce0f300cdf87ec002909012abefd9c5c}
 #' @source {Arctic LTER website:} \url{https://arc-lter.ecosystems.mbl.edu/}
 "arc_weather"
 
diff --git a/R/hbr_maples_doc.R b/R/hbr_maples_doc.R
@@ -6,7 +6,7 @@
 #' \describe{
 #'   \item{year}{a number denoting the year that the sample was taken}
 #'   \item{watershed}{a factor denoting the watershed where the sample was collected; W1 = calcium-treated, Reference = reference}
-#'   \item{elevation}{a factor describing the sample staion where the fecal sample was collected}
+#'   \item{elevation}{a factor describing the Elevation of transect; Low = low elevation, Mid = mid elevation}
 #'   \item{transect}{a factor denoting the transect number within the watershed}
 #'   \item{sample}{a factor denoting the sample number within transect. There are twenty samples in each transect}
 #'   \item{stem_length}{a number denoting the height of the seedling in millimeters}
@@ -17,6 +17,6 @@
 #'   \item{corrected_leaf_area}{a number denoting the area of both leaves in addition to the area removed for chlorophyll measurements in square centimeters}
 #' }
 #' @source {Juice, S. and T. Fahey. 2019. Health and mycorrhizal colonization response of sugar maple (Acer saccharum) seedlings to calcium addition in Watershed 1 at the Hubbard Brook Experimental Forest ver 3. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/0ade53ede9a916a36962799b2407097e}
+#' \doi{10.6073/pasta/0ade53ede9a916a36962799b2407097e}
 
 "hbr_maples"
diff --git a/R/knz_bison_doc.R b/R/knz_bison_doc.R
@@ -14,6 +14,6 @@
 #'   \item{animal_yob}{a number denoting the year animal was born}
 #'   }
 #' @source {EBlair, J. 2021. CBH01 Konza Prairie bison herd information ver 12. Environmental Data Initiative. https://doi.org/10.6073/pasta/9c641b35695abc5889edd64c3950517f (Accessed 2021-05-10).}
-#' \url{https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-knz.78.12}
+#' \doi{10.6073/pasta/9c641b35695abc5889edd64c3950517f}
 
 "knz_bison"
diff --git a/R/luq_streamchem_doc.R b/R/luq_streamchem_doc.R
@@ -24,5 +24,5 @@
 #'   \item{TSS}{a number denoting the Total Suspended Sediments in mg/L}
 #' }
 #' @source {McDowell, W. 2021. Chemistry of stream water from the Luquillo Mountains ver 4923056. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/0a09f5aa2e6f11451553c92b102279a6}
+#' \doi{10.6073/pasta/0a09f5aa2e6f11451553c92b102279a6}
 "luq_streamchem"
diff --git a/R/ntl_airtemp_doc.R b/R/ntl_airtemp_doc.R
@@ -10,5 +10,5 @@
 #'   }
 
 #' @source {Anderson, L. and D. Robertson. 2020. Madison Wisconsin Daily Meteorological Data 1869 - current ver 32. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/e3ff85971d817e9898bb8a83fb4c3a8b}
+#' \doi{10.6073/pasta/e3ff85971d817e9898bb8a83fb4c3a8b}
 "ntl_airtemp"
diff --git a/R/ntl_icecover_doc.R b/R/ntl_icecover_doc.R
@@ -12,7 +12,7 @@
 #'   \item{year}{a number denoting the year of observation}
 #'   }
 #' @source {Magnuson, J.J., S.R. Carpenter, and E.H. Stanley. 2021. North Temperate Lakes LTER: Ice Duration - Madison Lakes Area 1853 - current ver 35. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/ab31f2489ee436beb73fc8f1d0213d97}
+#' \doi{10.6073/pasta/ab31f2489ee436beb73fc8f1d0213d97}
 "ntl_icecover"
 
 

diff --git a/R/nwt_pikas_doc.R b/R/nwt_pikas_doc.R
@@ -14,6 +14,6 @@
 #'   \item{elev_m}{a number denoting the elevation in meters of the sampling station where the fecal sample was collected}
 #' }
 #' @source {Whipple, A. and Niwot Ridge LTER. 2020. Physiological stress of American pika (Ochotona princeps) and associated habitat characteristics for Niwot Ridge, 2018 - 2019 ver 1. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/9f95baf55f98732f47a8844821ff690d}
+#' \doi{10.6073/pasta/9f95baf55f98732f47a8844821ff690d}
 
 "nwt_pikas"
diff --git a/R/pie_crab_doc.R b/R/pie_crab_doc.R
@@ -15,5 +15,5 @@
 #'   \item{name}{full name of research site;  LTER, Long-Term Ecological Research site; NERR, National Estuarine Research Reserve}
 #'   }
 #' @source {Johnson, D. 2019. Fiddler crab body size in salt marshes from Florida to Massachusetts, USA at PIE and VCR LTER and NOAA NERR sites during summer 2016. ver 1. Environmental Data Initiative.}
-#' \url{https://doi.org/10.6073/pasta/4c27d2e778d3325d3830a5142e3839bb}
+#' \doi{10.6073/pasta/4c27d2e778d3325d3830a5142e3839bb}
 "pie_crab"
diff --git a/README.Rmd b/README.Rmd
@@ -29,7 +29,7 @@ Site](https://github.com/lter/lterdatasampler/workflows/pkgdown/badge.svg)](http
 
 <!-- badges: end -->
 
-# lterdatasampler <a href='https://lter.github.io/lterdatasampler'><img src="man/figures/logo.png" id="home_logo" align="right" height="180"/></a>
+# lterdatasampler <a href='https://lter.github.io/lterdatasampler/'><img src="man/figures/logo.png" id="home_logo" align="right" height="180"/></a>
 
 The mission of the [Long Term Ecological Research program (LTER)
 Network](https://lternet.edu/) is to “*provide the scientific community,
@@ -54,7 +54,7 @@ We encourage you to explore existing LTER [teaching and training
 initiatives](https://lternet.edu/education-and-training/), and the
 **many** other available LTER datasets which can be accessed via the
 [Environmental Data
-Initiative](https://environmentaldatainitiative.org/). Please contact
+Initiative](https://edirepository.org). Please contact
 cited researchers directly to discuss using data for research purposes
 or in publication.
 
@@ -73,7 +73,7 @@ remotes::install_github("lter/lterdatasampler")
 Dataset samples currently included in the package are summarized below;
 see individual Articles for data and source details. Note: the three
 letter prefix for each dataset indicates the LTER site (see full list of
-site abbreviations [here](https://lternet.edu/site/)).
+[site abbreviations](https://lternet.edu/site/)).
 
 -   [`and_vertebrates`](https://lter.github.io/lterdatasampler/reference/and_vertebrates.html):
     Records for aquatic vertebrates (cutthroat trout and salamanders) in
@@ -174,7 +174,7 @@ People / organizations who supported this project:
 -   LTER Education Committee
 -   All the LTER Researchers and Site PIs
 -   Cyber-infrastructures:
-    [EDI](https://environmentaldatainitiative.org/) and
+    [EDI](https://edirepository.org/) and
     [DataONE](https://www.dataone.org/)
 
 We gratefully acknowledge all authors and contributors of the