added license & # REFERENCES (knitcitations) to v3 modules

inst/shiny/custom_modules/occs_biomodelos.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# occs_biomodelos.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 occs_biomodelos_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -34,6 +57,8 @@ occs_biomodelos_module_server <- function(input, output, session, common) {
                                      occsCleaned = occs),
                       rmm = rangeModelMetadata::rmmTemplate(),
                       rmd = list())
+    # REFERENCES ####
+    knitcitations::citep(citation("httr"))
 
     # METADATA ####
     spp[[sp]]$rmm$data$occurrence$taxon <- sp

inst/shiny/custom_modules/occs_biomodelos.yml

@@ -1,5 +1,5 @@
 component: "occs"
 short_name: "Query BioModelos"
 long_name: "Query BioModelos"
-authors: "GEPB (**)"
-package: []
+authors: "GEPB, Bethany A. Johnson"
+package: [httr]

inst/shiny/custom_modules/rep_biomodelos.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# rep_biomodelos.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 rep_biomodelos_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(

inst/shiny/modules/diver_endemism.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# diver_endemism.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 diver_endemism_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -140,10 +163,18 @@ diver_endemism_module_server <- function(input, output, session, common) {
     # FUNCTION CALL ####
     req(endemism)
     logger %>% writeLog("Species endemism calculated.")
+
     # LOAD INTO SPP ####
     multi.sp$endemism <- endemism
     multi.sp$sppEndemism <- curSp()
     common$update_component(tab = "Map")
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+    knitcitations::citep(citation("changeRangeR"))
+
+    # METADATA ####
+    # add metadata
   })
 
   output$result <- renderPrint({

inst/shiny/modules/diver_endemism.Rmd

@@ -1,5 +1,6 @@
 ```{asis, echo = {{diver_endemism_knit}}, eval = {{diver_endemism_knit}}, include = {{diver_endemism_knit}}}
-#
+### Calculate endemism
+Write something here about what is going on...
 ```
 
 ```{r, echo = {{diver_endemism_knit}}, include = {{diver_endemism_knit}}}

inst/shiny/modules/diver_richness.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# diver_richness.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 diver_richness_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -140,10 +163,17 @@ diver_richness_module_server <- function(input, output, session, common) {
 
     req(richness)
     logger %>% writeLog("Species richness calculated.")
+
     # LOAD INTO SPP ####
     multi.sp$richness <- richness
     multi.sp$sppRichness <- curSp()
     common$update_component(tab = "Map")
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+
+    # METADATA ####
+    #add metadata
   })
 
   return(list(

inst/shiny/modules/diver_richness.yml

@@ -1,5 +1,5 @@
 component: "diver"
 short_name: "Calculate Richness"
 long_name: "Calculate Richness"
-authors: "Andrea Paz"
+authors: "Andrea Paz, Bethany A. Johnson"
 package: [raster]

inst/shiny/modules/indic_overlap.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_overlap.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 indic_overlap_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -310,6 +333,13 @@ indic_overlap_module_server <- function(input, output, session, common) {
     spp[[curSp()]]$indic$overlapFields <- overlapF
     spp[[curSp()]]$indic$overlapCat <- overlapC
     common$update_component(tab = "Results")
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+    knitcitations::citep(citation("changeRangeR"))
+
+    # METADATA ####
+    # add metadata
   })
 
   output$result <- renderUI({

inst/shiny/modules/indic_range.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_range.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 indic_range_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -220,6 +243,13 @@ indic_range_module_server <- function(input, output, session, common) {
       spp[[curSp()]]$flags$indicAreaMap <- "aoo"
       common$update_component(tab = "Map")
     }
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+    knitcitations::citep(citation("changeRangeR"))
+
+    # METADATA ####
+    # add metadata
   })
 
   output$areas <- renderText({

inst/shiny/modules/indic_time.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_time.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 indic_time_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -278,6 +301,13 @@ indic_time_module_server <- function(input, output, session, common) {
     spp[[curSp()]]$indic$areaTime <- rangeArea
     spp[[curSp()]]$indic$years <- years
     common$update_component(tab = "Results")
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+    knitcitations::citep(citation("changeRangeR"))
+
+    # METADATA ####
+    # add metadata
   })
 
   output$timeAreas <- renderUI({

inst/shiny/modules/mask_expPoly.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# mask_expPoly.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 mask_expPoly_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -299,6 +322,12 @@ mask_expPoly_module_server <- function(input, output, session, common) {
         type = "error", hlSpp(curSp()),
         "The polygon was already used. Define a new one (**)")
     }
+
+    # REFERENCES ####
+    knitcitations::citep(citation("raster"))
+
+    # METADATA ####
+    #add metadata
   })
 
   # Reset prediction

inst/shiny/modules/mask_spatial.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# mask_spatial.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 mask_spatial_module_ui <- function(id) {
   ns <- shiny::NS(id)
   tagList(
@@ -190,7 +213,12 @@ mask_spatial_module_server <- function(input, output, session, common) {
     logger %>% writeLog(
       hlSpp(curSp()), "Spatial Masked (**)")
 
+    # REFERENCES ####
+    knitcitations::citep(citation("sp"))
+    knitcitations::citep(citation("sf"))
+
     # METADATA ####
+    #add metadata
   })
 
   # Reset prediction