diff --git a/DESCRIPTION b/DESCRIPTION index 545d453..922f95f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,8 +17,8 @@ Suggests: VignetteBuilder: knitr Type: Package Title: Fire weather index calculation from station and model data -Version: 1.0.2 -Date: 2017-04-07 +Version: 1.0.3 +Date: 2017-07-10 Authors@R: as.person(c( "Santander Meteorology Group [aut]", "Joaquin Bedia [ctb, cre]", diff --git a/NEWS b/NEWS index e68a712..39dce87 100644 --- a/NEWS +++ b/NEWS @@ -1,5 +1,5 @@ New in fireDanger ================= -* Added package vignette +* Added CITATION file * Documentation updates \ No newline at end of file diff --git a/R/onAttach.R b/R/onAttach.R index 1c938ff..1189409 100644 --- a/R/onAttach.R +++ b/R/onAttach.R @@ -21,7 +21,7 @@ packageStartupMessage(ver.mess) } } - packageStartupMessage("Type for package overview and examples") + packageStartupMessage("Type for package overview and examples\nPlease use citation(\"fireDanger\") to cite this package.") } # End diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..9a3a0ee --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,13 @@ +bibentry(bibtype = "Article", + title = "Seasonal predictions of Fire Weather Index: Paving the way for their operational applicability in Mediterranean Europe", + author = c(person(given = "Joaquin", family = "Bedia", role = "aut"), + person(given = "Nicola", family = "Golding", role = "aut"), + person(given = "Ana", family = "Casanueva", role = "aut"), + person(given = "Maialen", family = "Iturbide", role = "aut"), + person(given = "Carlo", family = "Buontempo", role = "aut"), + person(given = "Jose Manuel", family = "Gutierrez", role = "aut")), + url = "http://linkinghub.elsevier.com/retrieve/pii/S2405880716300826", + doi = "10.1016/j.cliser.2017.04.001", + journal = "Climate Services", + year = "2017" + ) diff --git a/inst/doc/Climate_Services_2017.R b/inst/doc/Climate_Services_2017.R index c02e950..3f722da 100644 --- a/inst/doc/Climate_Services_2017.R +++ b/inst/doc/Climate_Services_2017.R @@ -12,7 +12,7 @@ knitr::opts_chunk$set(echo = TRUE, ## ---- eval=FALSE--------------------------------------------------------- # devtools::install_github(c("SantanderMetGroup/loadeR.java@v1.1-0", # "SantanderMetGroup/loadeR@v1.0-7", -# "SantanderMetGroup/loadeR.ECOMS@v1.2.2")) +# "SantanderMetGroup/loadeR.ECOMS@v1.2.3")) ## ------------------------------------------------------------------------ library(loadeR.ECOMS) @@ -36,7 +36,7 @@ library(downscaleR) library(visualizeR) ## ---- eval=FALSE--------------------------------------------------------- -# devtools::install_github("SantanderMetGroup/fireDanger@v1.0.1") +# devtools::install_github("SantanderMetGroup/fireDanger@v1.0.3") ## ------------------------------------------------------------------------ library(fireDanger) diff --git a/inst/doc/Climate_Services_2017.Rmd b/inst/doc/Climate_Services_2017.Rmd index fe74626..81d4ca8 100644 --- a/inst/doc/Climate_Services_2017.Rmd +++ b/inst/doc/Climate_Services_2017.Rmd @@ -4,11 +4,10 @@ subtitle: "Companion R examples of the paper published in Climate Services (2017 author: "J. Bedia & M. Iturbide" date: "`r Sys.Date()`" abstract: | - This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package `fireDanger`, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data. + This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package `fireDanger`, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data. `fireDanger` is part of the *climate4R* Bundle (see Cofiño et al 2017, in this issue of Climate Services), thus providing a seamless R interface not only to FWI calculation, but also to harmonized climate data access, data transformation, dowscaling / bias correction and other climate analysis tasks via a number of related R packages, some of them succintly described here. In particular, packages `loadeR.ECOMS`, `downscaleR` and `easyVerification` are used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the `visualizeR` package for seasonal forecast verification and visualization. - Packages `loadeR.ECOMS`, `downscaleR` and `easyVerification` are also used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the `visualizeR` package for seasonal forecast verification and visualization. - - The code provided in this example allows the reproducibility of all the analyses presented in the paper. However, for the sake of openness, data from the CFSv2 seasonal model (Saha et al 2010) are used instead of System4 (see the paper), the first being publicly available without restrictions. The reference observations dataset (WFDEI, Weedon et al 2014) is also publicly available. + The code provided in this example allows the reproducibility of all the analyses presented in the paper. However, for the sake of openness, data from the CFSv2 seasonal model (Saha et al 2010) are used instead of System4 (see the paper), the first being publicly available without restrictions. The reference observations dataset (WFDEI, Weedon et al 2014) is also publicly available. + output: rmarkdown::html_vignette vignette: > @@ -53,7 +52,7 @@ In this example, we will first illustrate the use of `loadeR.ECOMS`, required fo ```{r, eval=FALSE} devtools::install_github(c("SantanderMetGroup/loadeR.java@v1.1-0", "SantanderMetGroup/loadeR@v1.0-7", - "SantanderMetGroup/loadeR.ECOMS@v1.2.2")) + "SantanderMetGroup/loadeR.ECOMS@v1.2.3")) ``` In case any problems arise with the installation at this point, see this [help guide](https://github.com/SantanderMetGroup/loadeR/wiki/Installation) at the loadeR's wiki page. @@ -97,7 +96,7 @@ library(visualizeR) The package `fireDanger` is used for the calculation of the FWI System from the climate data structures provided by the packages above. It is thus seamlessly integrated with the Santander MetGroup R Climate Processing Bundle. ```{r, eval=FALSE} -devtools::install_github("SantanderMetGroup/fireDanger@v1.0.1") +devtools::install_github("SantanderMetGroup/fireDanger@v1.0.3") ``` ```{r} library(fireDanger) @@ -528,6 +527,7 @@ bubblePlot(hindcast = fwimean_hind, obs = fwimean_obs, * Bedia, J., Herrera, S., Camia, A., Moreno, J.M., Gutierrez, J.M., 2014. Forest Fire Danger Projections in the Mediterranean using ENSEMBLES Regional Climate Change Scenarios. Clim Chang 122, 185--199. doi:10.1007/s10584-013-1005-z * Bedia, J., Herrera, S., Gutierrez, J.M., Benali, A., Brands, S., Mota, B., Moreno, J.M., 2015. Global patterns in the sensitivity of burned area to fire-weather: implications for climate change. Agr. Forest Meteorol. 214--215, 369--379. doi:10.1016/j.agrformet.2015.09.002 +* Cofiño A.S., Bedia J., Iturbide M., Vega M., Herrera S., Fernández J., Frías M. D., Manzanas, R. and Gutiérrez J. M., 2017. The ECOMS User Data Gateway: Towards seasonal forecast data provision and research reproducibility in the era of Climate Services. Climate Services, in press. * Saha, S., Moorthi, S., Wu, X., Wang, J., Nadiga, S., Tripp, P., Behringer, D., Hou, Y.-T., Chuang, H., Iredell, M., Ek, M., Meng, J., Yang, R., Peña Mendez, M., van den Dool, H., Zhang, Q., Wang, W., Chen, M., Becker, E., 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1 * van Wagner, C.E., 1987. Development and structure of the Canadian Forest Fire Weather Index (Forestry Tech. Rep. No. 35). Canadian Forestry Service, Ottawa, Canada. * Weedon, G.P., Balsamo, G., Bellouin, N., Gomes, S., Best, M.J., Viterbo, P., 2014. The WFDEI meteorological forcing data set: WATCH Forcing Data methodology applied to ERA-Interim reanalysis data. Water Resour. Res. 50, 7505–7514. doi:10.1002/2014WR015638 @@ -541,4 +541,4 @@ bubblePlot(hindcast = fwimean_hind, obs = fwimean_obs, sessionInfo() ``` -*** \ No newline at end of file +*** diff --git a/inst/doc/Climate_Services_2017.html b/inst/doc/Climate_Services_2017.html index 7616b04..7a42934 100644 --- a/inst/doc/Climate_Services_2017.html +++ b/inst/doc/Climate_Services_2017.html @@ -4,7 +4,7 @@ - + @@ -12,7 +12,7 @@ - + Seasonal Predictions of Fire Weather Index: Paving the Way for their operational applicability in Mediterranean Europe @@ -81,11 +81,10 @@

Seasonal Predictions of Fire Weather Index: Paving the Way for their operational applicability in Mediterranean Europe

Companion R examples of the paper published in Climate Services (2017, DOI:10.1016/j.cliser.2017.04.001)

J. Bedia & M. Iturbide

-

2017-04-07

+

2017-07-10

Abstract

-

This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package fireDanger, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data.

-

Packages loadeR.ECOMS, downscaleR and easyVerification are also used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the visualizeR package for seasonal forecast verification and visualization.

+

This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package fireDanger, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data. fireDanger is part of the climate4R Bundle (see Cofiño et al 2017, in this issue of Climate Services), thus providing a seamless R interface not only to FWI calculation, but also to harmonized climate data access, data transformation, dowscaling / bias correction and other climate analysis tasks via a number of related R packages, some of them succintly described here. In particular, packages loadeR.ECOMS, downscaleR and easyVerification are used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the visualizeR package for seasonal forecast verification and visualization.

The code provided in this example allows the reproducibility of all the analyses presented in the paper. However, for the sake of openness, data from the CFSv2 seasonal model (Saha et al 2010) are used instead of System4 (see the paper), the first being publicly available without restrictions. The reference observations dataset (WFDEI, Weedon et al 2014) is also publicly available.

@@ -109,7 +108,7 @@

Installing the R Climate Processing Bundle from the Santander MetGroup

In this example, we will first illustrate the use of loadeR.ECOMS, required for accessing the OPeNDAP server from the Santander MetGroup , storing a number of seasonal forecast datasets and variables in the so called User Data Gateway, described in the next sections. A number of dependencies are installed, although only loadeR.ECOMS is explicitly loaded by the user.

devtools::install_github(c("SantanderMetGroup/loadeR.java@v1.1-0",
                  "SantanderMetGroup/loadeR@v1.0-7",
-                 "SantanderMetGroup/loadeR.ECOMS@v1.2.2"))
+ "SantanderMetGroup/loadeR.ECOMS@v1.2.3"))

In case any problems arise with the installation at this point, see this help guide at the loadeR’s wiki page.

library(loadeR.ECOMS)

The package transformeR allows performing climate data transformations, including Principal Component/EOF analysis, subsetting, aggregation, regridding/interpolation… In this vignette, the subsetting, aggregation, detrending and visualization capabilitites of transformeR will be used.

@@ -125,7 +124,7 @@

Installing the R Climate Processing Bundle from the Santander MetGroup

Installing fireDanger

The package fireDanger is used for the calculation of the FWI System from the climate data structures provided by the packages above. It is thus seamlessly integrated with the Santander MetGroup R Climate Processing Bundle.

-
devtools::install_github("SantanderMetGroup/fireDanger@v1.0.1")
+
devtools::install_github("SantanderMetGroup/fireDanger@v1.0.3")
library(fireDanger)
@@ -386,6 +385,7 @@

References

  • Bedia, J., Herrera, S., Camia, A., Moreno, J.M., Gutierrez, J.M., 2014. Forest Fire Danger Projections in the Mediterranean using ENSEMBLES Regional Climate Change Scenarios. Clim Chang 122, 185–199. doi:10.1007/s10584-013-1005-z
  • Bedia, J., Herrera, S., Gutierrez, J.M., Benali, A., Brands, S., Mota, B., Moreno, J.M., 2015. Global patterns in the sensitivity of burned area to fire-weather: implications for climate change. Agr. Forest Meteorol. 214–215, 369–379. doi:10.1016/j.agrformet.2015.09.002
  • +
  • Cofiño A.S., Bedia J., Iturbide M., Vega M., Herrera S., Fernández J., Frías M. D., Manzanas, R. and Gutiérrez J. M., 2017. The ECOMS User Data Gateway: Towards seasonal forecast data provision and research reproducibility in the era of Climate Services. Climate Services, in press.
  • Saha, S., Moorthi, S., Wu, X., Wang, J., Nadiga, S., Tripp, P., Behringer, D., Hou, Y.-T., Chuang, H., Iredell, M., Ek, M., Meng, J., Yang, R., Peña Mendez, M., van den Dool, H., Zhang, Q., Wang, W., Chen, M., Becker, E., 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1
  • van Wagner, C.E., 1987. Development and structure of the Canadian Forest Fire Weather Index (Forestry Tech. Rep. No. 35). Canadian Forestry Service, Ottawa, Canada.
  • Weedon, G.P., Balsamo, G., Bellouin, N., Gomes, S., Best, M.J., Viterbo, P., 2014. The WFDEI meteorological forcing data set: WATCH Forcing Data methodology applied to ERA-Interim reanalysis data. Water Resour. Res. 50, 7505–7514. doi:10.1002/2014WR015638
  • @@ -395,10 +395,14 @@

    References

    Session Information


    sessionInfo()
    -
    ## R version 3.3.3 (2017-03-06)
    +
    ## R version 3.4.1 (2017-06-30)
     ## Platform: x86_64-pc-linux-gnu (64-bit)
     ## Running under: Ubuntu 14.04.5 LTS
     ## 
    +## Matrix products: default
    +## BLAS: /usr/lib/openblas-base/libblas.so.3
    +## LAPACK: /usr/lib/lapack/liblapack.so.3.0
    +## 
     ## locale:
     ##  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
     ##  [3] LC_TIME=es_ES.UTF-8           LC_COLLATE=en_US.UTF-8       
    @@ -411,29 +415,30 @@ 

    Session Information

    ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: -## [1] RColorBrewer_1.1-2 easyVerification_0.4.0 -## [3] SpecsVerification_0.5-0 fireDanger_1.0.1 -## [5] visualizeR_0.2-1 sm_2.2-5.4 -## [7] downscaleR_2.0-1 loadeR.ECOMS_1.2.2 -## [9] loadeR_1.0-7 loadeR.java_1.1-0 -## [11] rJava_0.9-8 transformeR_0.0.8 +## [1] RColorBrewer_1.1-2 easyVerification_0.4.1 +## [3] SpecsVerification_0.5-2 fireDanger_1.0.3 +## [5] visualizeR_0.2-0 sm_2.2-5.4 +## [7] downscaleR_2.0-1 loadeR.ECOMS_1.3.0 +## [9] loadeR_1.1.0 loadeR.java_1.1-0 +## [11] rJava_0.9-8 transformeR_0.0-15 ## [13] abind_1.4-5 ## ## loaded via a namespace (and not attached): -## [1] Rcpp_0.12.10 plyr_1.8.4 bitops_1.0-6 -## [4] tools_3.3.3 vioplot_0.2 boot_1.3-17 -## [7] digest_0.6.9 evd_2.3-2 evaluate_0.10 -## [10] memoise_1.0.0 lattice_0.20-35 Matrix_1.2-8 -## [13] yaml_2.1.14 parallel_3.3.3 spam_1.4-0 -## [16] akima_0.6-2 withr_1.0.0 stringr_1.0.0 -## [19] knitr_1.15.1 mapplots_1.5 fields_8.10 -## [22] devtools_1.12.0 maps_3.1.1 rprojroot_1.2 -## [25] grid_3.3.3 dtw_1.18-1 pbapply_1.3-1 -## [28] rmarkdown_1.3 sp_1.2-4 magrittr_1.5 -## [31] scales_0.4.1 CircStats_0.2-4 backports_1.0.5 -## [34] htmltools_0.3.5 MASS_7.3-44 colorspace_1.2-6 -## [37] proxy_0.4-17 stringi_1.0-1 munsell_0.4.3 -## [40] RCurl_1.95-4.8 verification_1.42 RcppEigen_0.3.2.9.1
    +## [1] Rcpp_0.12.11 plyr_1.8.4 compiler_3.4.1 +## [4] bitops_1.0-6 tools_3.4.1 vioplot_0.2 +## [7] boot_1.3-19 digest_0.6.12 evd_2.3-2 +## [10] evaluate_0.10 memoise_1.1.0 lattice_0.20-35 +## [13] Matrix_1.2-10 yaml_2.1.14 parallel_3.4.1 +## [16] spam_1.4-0 akima_0.6-2 withr_1.0.2 +## [19] stringr_1.2.0 raster_2.5-8 knitr_1.15.1 +## [22] mapplots_1.5 fields_8.15 devtools_1.12.0 +## [25] maps_3.1.1 rprojroot_1.2 grid_3.4.1 +## [28] dtw_1.18-1 pbapply_1.3-2 rmarkdown_1.5 +## [31] sp_1.2-4 magrittr_1.5 scales_0.4.1 +## [34] CircStats_0.2-4 backports_1.0.5 htmltools_0.3.5 +## [37] MASS_7.3-47 colorspace_1.3-2 proxy_0.4-17 +## [40] stringi_1.1.5 munsell_0.4.3 RCurl_1.95-4.8 +## [43] verification_1.42 RcppEigen_0.3.2.9.1

@@ -444,7 +449,7 @@

Session Information

(function () { var script = document.createElement("script"); script.type = "text/javascript"; - script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; + script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); diff --git a/vignettes/Climate_Services_2017.Rmd b/vignettes/Climate_Services_2017.Rmd index fe74626..81d4ca8 100644 --- a/vignettes/Climate_Services_2017.Rmd +++ b/vignettes/Climate_Services_2017.Rmd @@ -4,11 +4,10 @@ subtitle: "Companion R examples of the paper published in Climate Services (2017 author: "J. Bedia & M. Iturbide" date: "`r Sys.Date()`" abstract: | - This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package `fireDanger`, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data. + This is a worked example that reproduces the steps followed in Bedia et al. 2017 using the R-package `fireDanger`, that contains functions for computing the different components of the Fire Weather Index System (FWI, van Wagner 1987) from station and numerical climate model data. `fireDanger` is part of the *climate4R* Bundle (see Cofiño et al 2017, in this issue of Climate Services), thus providing a seamless R interface not only to FWI calculation, but also to harmonized climate data access, data transformation, dowscaling / bias correction and other climate analysis tasks via a number of related R packages, some of them succintly described here. In particular, packages `loadeR.ECOMS`, `downscaleR` and `easyVerification` are used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the `visualizeR` package for seasonal forecast verification and visualization. - Packages `loadeR.ECOMS`, `downscaleR` and `easyVerification` are also used for climate data loading, manipulation, bias correction and verification. Furthermore, in the last section of this tutorial we also illustrate the use of different functionalities from the `visualizeR` package for seasonal forecast verification and visualization. - - The code provided in this example allows the reproducibility of all the analyses presented in the paper. However, for the sake of openness, data from the CFSv2 seasonal model (Saha et al 2010) are used instead of System4 (see the paper), the first being publicly available without restrictions. The reference observations dataset (WFDEI, Weedon et al 2014) is also publicly available. + The code provided in this example allows the reproducibility of all the analyses presented in the paper. However, for the sake of openness, data from the CFSv2 seasonal model (Saha et al 2010) are used instead of System4 (see the paper), the first being publicly available without restrictions. The reference observations dataset (WFDEI, Weedon et al 2014) is also publicly available. + output: rmarkdown::html_vignette vignette: > @@ -53,7 +52,7 @@ In this example, we will first illustrate the use of `loadeR.ECOMS`, required fo ```{r, eval=FALSE} devtools::install_github(c("SantanderMetGroup/loadeR.java@v1.1-0", "SantanderMetGroup/loadeR@v1.0-7", - "SantanderMetGroup/loadeR.ECOMS@v1.2.2")) + "SantanderMetGroup/loadeR.ECOMS@v1.2.3")) ``` In case any problems arise with the installation at this point, see this [help guide](https://github.com/SantanderMetGroup/loadeR/wiki/Installation) at the loadeR's wiki page. @@ -97,7 +96,7 @@ library(visualizeR) The package `fireDanger` is used for the calculation of the FWI System from the climate data structures provided by the packages above. It is thus seamlessly integrated with the Santander MetGroup R Climate Processing Bundle. ```{r, eval=FALSE} -devtools::install_github("SantanderMetGroup/fireDanger@v1.0.1") +devtools::install_github("SantanderMetGroup/fireDanger@v1.0.3") ``` ```{r} library(fireDanger) @@ -528,6 +527,7 @@ bubblePlot(hindcast = fwimean_hind, obs = fwimean_obs, * Bedia, J., Herrera, S., Camia, A., Moreno, J.M., Gutierrez, J.M., 2014. Forest Fire Danger Projections in the Mediterranean using ENSEMBLES Regional Climate Change Scenarios. Clim Chang 122, 185--199. doi:10.1007/s10584-013-1005-z * Bedia, J., Herrera, S., Gutierrez, J.M., Benali, A., Brands, S., Mota, B., Moreno, J.M., 2015. Global patterns in the sensitivity of burned area to fire-weather: implications for climate change. Agr. Forest Meteorol. 214--215, 369--379. doi:10.1016/j.agrformet.2015.09.002 +* Cofiño A.S., Bedia J., Iturbide M., Vega M., Herrera S., Fernández J., Frías M. D., Manzanas, R. and Gutiérrez J. M., 2017. The ECOMS User Data Gateway: Towards seasonal forecast data provision and research reproducibility in the era of Climate Services. Climate Services, in press. * Saha, S., Moorthi, S., Wu, X., Wang, J., Nadiga, S., Tripp, P., Behringer, D., Hou, Y.-T., Chuang, H., Iredell, M., Ek, M., Meng, J., Yang, R., Peña Mendez, M., van den Dool, H., Zhang, Q., Wang, W., Chen, M., Becker, E., 2013. The NCEP Climate Forecast System Version 2. J Clim 130925135638001. doi:10.1175/JCLI-D-12-00823.1 * van Wagner, C.E., 1987. Development and structure of the Canadian Forest Fire Weather Index (Forestry Tech. Rep. No. 35). Canadian Forestry Service, Ottawa, Canada. * Weedon, G.P., Balsamo, G., Bellouin, N., Gomes, S., Best, M.J., Viterbo, P., 2014. The WFDEI meteorological forcing data set: WATCH Forcing Data methodology applied to ERA-Interim reanalysis data. Water Resour. Res. 50, 7505–7514. doi:10.1002/2014WR015638 @@ -541,4 +541,4 @@ bubblePlot(hindcast = fwimean_hind, obs = fwimean_obs, sessionInfo() ``` -*** \ No newline at end of file +***