Hyperlink DOIs to preferred resolver

protocols/manual-field-data-protocols.md

@@ -67,7 +67,7 @@ description: >-
 
 ## References
 
-* Pérez-Harguindeguy N., Díaz S., Garnier E., Lavorel S., Poorter H., Jaureguiberry P., Bret-Harte M. S., CornwellW. K., Craine J. M., Gurvich D. E., Urcelay C., Veneklaas E. J., Reich P. B., Poorter L., Wright I. J., Ray P., Enrico L.,Pausas J. G., de Vos A. C., Buchmann N., Funes G., Quétier F., Hodgson J. G., Thompson K., Morgan H. D., ter Steege H., van der Heijden M. G. A., Sack L., Blonder B., Poschlod P., Vaieretti M. V., Conti G., Staver A. C.,Aquino S., Cornelissen J. H. C. \(2013\) New handbook for standardised measurement of plant functional traits worldwide. _Australian Journal of Botany_ **61** , 167–234. [http://dx.doi.org/10.1071/BT12225](http://dx.doi.org/10.1071/BT12225)
+* Pérez-Harguindeguy N., Díaz S., Garnier E., Lavorel S., Poorter H., Jaureguiberry P., Bret-Harte M. S., CornwellW. K., Craine J. M., Gurvich D. E., Urcelay C., Veneklaas E. J., Reich P. B., Poorter L., Wright I. J., Ray P., Enrico L.,Pausas J. G., de Vos A. C., Buchmann N., Funes G., Quétier F., Hodgson J. G., Thompson K., Morgan H. D., ter Steege H., van der Heijden M. G. A., Sack L., Blonder B., Poschlod P., Vaieretti M. V., Conti G., Staver A. C.,Aquino S., Cornelissen J. H. C. \(2013\) New handbook for standardised measurement of plant functional traits worldwide. _Australian Journal of Botany_ **61** , 167–234. [https://doi.org/10.1071/BT12225](https://doi.org/10.1071/BT12225)
 * Vanderlip RL. 1993. How a sorghum plant develops. Manhattan, KS, USA: Kansas State University Cooperative Extension. Field Experiments in Crop Physiology. 2013, Jan 13. In _PrometheusWiki_. Retrieved 15:03,June 21, 2016, from [http://www.publish.csiro.au/prometheuswiki/tiki-pagehistory.php?page=Field Experiments in Crop Physiology&preview=41](http://www.publish.csiro.au/prometheuswiki/tiki-pagehistory.php?page=Field%20Experiments%20in%20Crop%20Physiology&preview=41)
 
 **Photosynthesis / leaf chemistry from hyperspectral data references:**

protocols/phenotractor-protocols.md

@@ -63,5 +63,5 @@ where $U\_y$ and $U\_x$ are latitude and longitude in USDA coordinate system, an
 
 ## References
 
-Andrade-Sanchez, Pedro, Michael A. Gore, John T. Heun, Kelly R. Thorp, A. Elizabete Carmo-Silva, Andrew N. French, Michael E. Salvucci, and Jeffrey W. White. "Development and evaluation of a field-based high-throughput phenotyping platform." Functional Plant Biology 41, no. 1 \(2014\): 68-79. [doi:10.1071/FP13126](http://dx.doi.org/10.1071/FP13126)
+Andrade-Sanchez, Pedro, Michael A. Gore, John T. Heun, Kelly R. Thorp, A. Elizabete Carmo-Silva, Andrew N. French, Michael E. Salvucci, and Jeffrey W. White. "Development and evaluation of a field-based high-throughput phenotyping platform." Functional Plant Biology 41, no. 1 \(2014\): 68-79. [doi:10.1071/FP13126](https://doi.org/10.1071/FP13126)
 

technical-documentation/data-standards/existing-data-standards.md

@@ -230,7 +230,7 @@ Cited in Kattge et al \(2011\) as an example of an ontology used in ecology and
 
 _See also:_
 
-* Kattge, J.\(2011\). [A generic structure for plant trait databases](http://doi.org/10.1111/j.2041-210X.2010.00067.x)
+* Kattge, J.\(2011\). [A generic structure for plant trait databases](https://doi.org/10.1111/j.2041-210X.2010.00067.x)
 
   </small>
 
@@ -241,7 +241,7 @@ Defines concepts/classes used to describe gene function, and relationships betwe
 See also:
 
 * [Gene Ontology](http://geneontology.org/)
-* Krajewski et al \(2015\). [Towards recommendations for metadata and data handling in plant phenotyping](http://doi.org/10.1093/jxb/erv271). Journal of Experimental Botany, 66\(18\), 5417–5427.
+* Krajewski et al \(2015\). [Towards recommendations for metadata and data handling in plant phenotyping](https://doi.org/10.1093/jxb/erv271). Journal of Experimental Botany, 66\(18\), 5417–5427.
 
   </small>
 
@@ -360,7 +360,7 @@ The data exchange format is based on a [JSON rendering of the ICASA Master Varia
 _See also_
 
 * [AgMIP Crop Expirement Database](http://www.agmip.org/it-team/)
-* Porter et al \(2014\). [Harmonization and translation of crop modeling data to ensure interoperability](http://dx.doi.org/10.1016/j.envsoft.2014.09.004). Environmental Modelling and Software. 62:495-508.
+* Porter et al \(2014\). [Harmonization and translation of crop modeling data to ensure interoperability](https://doi.org/10.1016/j.envsoft.2014.09.004). Environmental Modelling and Software. 62:495-508.
 * [AgMIP Data Products](http://research.agmip.org/download/attachments/3866652/11_+IT_Porter_10Oct.pdf) presentation
 * [AgMIP on Github](https://github.com/agmip)
 * [AgMIP Crop Experiment Database data variables](http://research.agmip.org/display/it/Data+Interoperability)

user-manual/data-products/plantcv-trait-data.md

@@ -11,7 +11,7 @@ Full documentation: [http://plantcv.readthedocs.io/en/latest](http://plantcv.rea
 Publications:
 
 * [https://doi.org/10.7717/peerj.4088](https://doi.org/10.7717/peerj.4088)
-* [http://dx.doi.org/10.1016/j.molp.2015.06.005](http://dx.doi.org/10.1016/j.molp.2015.06.005)
+* [https://doi.org/10.1016/j.molp.2015.06.005](https://doi.org/10.1016/j.molp.2015.06.005)
 
 To learn more about PlantCV, you can find examples in the [terraref/tutorials](https://github.com/terraref/tutorials) repository, which is accessible on GitHub and in the TERRA REF [workbench](https://www.workbench.terraref.org) under tutorials/plantcv