Hyperlink DOIs to preferred resolver

R/data.R

@@ -53,21 +53,21 @@ pulldata <- function(x = NULL) {
 #'   Dziock F, Köhler F, Rabitsch W, Weisser WW (2015) A summary of eight traits
 #'   of Coleoptera, Hemiptera, Orthoptera and Araneae, occurring in grasslands
 #'   in Germany. Scientific Data 2: 150013.
-#'   http://dx.doi.org/10.1038/sdata.2015.13 }
+#'   https://doi.org/10.1038/sdata.2015.13 }
 #'   
 #'   Additionally, please cite the Dryad data package:
 #'   
 #'   \itemize{ \item  Gossner MM, Simons NK, Achtziger R,
 #'   Blick T, Dorow WHO, Dziock F, Köhler F, Rabitsch W, Weisser WW (2015) Data
 #'   from: A summary of eight traits of Coleoptera, Hemiptera, Orthoptera and
 #'   Araneae, occurring in grasslands in Germany. Dryad Digital Repository.
-#'   http://dx.doi.org/10.5061/dryad.53ds2 }
+#'   https://doi.org/10.5061/dryad.53ds2 }
 #'   
 #' @author Gossner MM, Simons NK, Achtziger R, Blick T, Dorow WHO, Dziock F, Köhler F, Rabitsch W, Weisser WW
 #' 
 #' @family rawdata
 #' 
-#' @source \url{http://dx.doi.org/10.5061/dryad.53ds2};
+#' @source \url{https://doi.org/10.5061/dryad.53ds2};
 #'   \href{http://creativecommons.org/publicdomain/zero/1.0/}{Creative Commons
 #'   0}. To the extent possible under law, the authors have waived all copyright
 #'   and related or neighboring rights to this data.
@@ -116,7 +116,7 @@ NULL
 #'
 #' @family rawdata
 #' 
-#' @source \url{http://dx.doi.org/10.5061/dryad.53ds2};
+#' @source \url{https://doi.org/10.5061/dryad.53ds2};
 #'   \href{http://creativecommons.org/publicdomain/zero/1.0/}{Creative Commons
 #'   0}. To the extent possible under law, the authors have waived all copyright
 #'   and related or neighboring rights to this data.

README.md

@@ -7,7 +7,7 @@
 
 
 
-Assistance for handling functional trait data and transferring them into the Ecological Trait-Data Standard (Schneider et al. 2018 Towards an Ecological Trait-data Standard, biorxiv.org DOI: [10.1101/328302](http://dx.doi.org/10.1101/328302)). 
+Assistance for handling functional trait data and transferring them into the Ecological Trait-Data Standard (Schneider et al. 2018 Towards an Ecological Trait-data Standard, biorxiv.org DOI: [10.1101/328302](https://doi.org/10.1101/328302)). 
 
 There are two major use cases for the package: 
 

vignettes/div05.bib

@@ -2228,7 +2228,7 @@ @article{brun17
   issn = {1866-3508},
   url = {https://www.earth-syst-sci-data.net/9/99/2017/},
   doi = {https://doi.org/10.5194/essd-9-99-2017},
-  abstract = {The trait-based approach is gaining increasing popularity in marine plankton ecology but the field urgently needs more and easier accessible trait data to advance. We compiled trait information on marine pelagic copepods, a major group of zooplankton, from the published literature and from experts and organized the data into a structured database. We collected 9306 records for 14 functional traits. Particular attention was given to body size, feeding mode, egg size, spawning strategy, respiration rate, and myelination (presence of nerve sheathing). Most records were reported at the species level, but some phylogenetically conserved traits, such as myelination, were reported at higher taxonomic levels, allowing the entire diversity of around 10 800 recognized marine copepod species to be covered with a few records. Aside from myelination, data coverage was highest for spawning strategy and body size, while information was more limited for quantitative traits related to reproduction and physiology. The database may be used to investigate relationships between traits, to produce trait biogeographies, or to inform and validate trait-based marine ecosystem models. The data can be downloaded from PANGAEA, $<$a href="http://dx.doi.org/10.1594/PANGAEA.862968" target="\_blank"$>$doi:10.1594/PANGAEA.862968$<$/a$>$.},
+  abstract = {The trait-based approach is gaining increasing popularity in marine plankton ecology but the field urgently needs more and easier accessible trait data to advance. We compiled trait information on marine pelagic copepods, a major group of zooplankton, from the published literature and from experts and organized the data into a structured database. We collected 9306 records for 14 functional traits. Particular attention was given to body size, feeding mode, egg size, spawning strategy, respiration rate, and myelination (presence of nerve sheathing). Most records were reported at the species level, but some phylogenetically conserved traits, such as myelination, were reported at higher taxonomic levels, allowing the entire diversity of around 10 800 recognized marine copepod species to be covered with a few records. Aside from myelination, data coverage was highest for spawning strategy and body size, while information was more limited for quantitative traits related to reproduction and physiology. The database may be used to investigate relationships between traits, to produce trait biogeographies, or to inform and validate trait-based marine ecosystem models. The data can be downloaded from PANGAEA, $<$a href="https://doi.org/10.1594/PANGAEA.862968" target="\_blank"$>$doi:10.1594/PANGAEA.862968$<$/a$>$.},
   number = {1},
   journaltitle = {Earth System Science Data},
   urldate = {2017-12-13},

vignettes/traitdataform.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(traitdataform)
 ```
 
-Assistance for handling functional trait data and transferring them into the Ecological Trait-data Standard (Schneider et al. 2018, https://terminologies.gfbio.org/terms/ets/pages/ doi: [10.5281/zenodo.1485739](http://dx.doi.org/10.5281/zenodo.1485739)). 
+Assistance for handling functional trait data and transferring them into the Ecological Trait-data Standard (Schneider et al. 2018, https://terminologies.gfbio.org/terms/ets/pages/ doi: [10.5281/zenodo.1485739](https://doi.org/10.5281/zenodo.1485739)). 
 
 There are two major use cases for the package: 
 
@@ -31,7 +31,7 @@ The toolset of the package includes
 4. Merging and handling compiled trait-data, while keeping track of the metadata for each original dataset (see section [4. Working with trait-datasets](#working-with-trait-datasets)) 
 5. saving trait dataset into a desired format using templates (e.g. for project-specific databases or online repositories) (see section [5. Writing data](#writing-data)) 
 
-This vignette contains step-by step instructions for transferring own data into a standardized trait-dataset for upload to public databases. See Schneider et al. 2018 'Towards an Ecological Trait-data Standard' (pre-print on biorxiv.org, doi: [10.1101/328302](http://dx.doi.org/10.1101/328302) ) for a discussion of the rationale. 
+This vignette contains step-by step instructions for transferring own data into a standardized trait-dataset for upload to public databases. See Schneider et al. 2018 'Towards an Ecological Trait-data Standard' (pre-print on biorxiv.org, doi: [10.1101/328302](https://doi.org/10.1101/328302) ) for a discussion of the rationale. 
 
 ---