Merge pull request wallaceEcoMod#411 from danflop/licenseText

Add license text to .R files

R/custom_modules.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# custom_modules.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' Register a Wallace module
 #'
 #' Before running the Wallace application with \code{run_wallace()}, you can

R/envs_ecoClimate.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_ecoClimate.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title envs_ecoClimate Obtain ecoClimate variables
 #' @description download ecoClimate variables. See www.ecoclimate.org.

R/envs_userEnvs.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_userEnvs.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #'
 #' @title  envs_userEnvs
 #' @description Load user provided rasters

R/envs_worldclim.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_worldclim.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' @title envs_worldclim Obtain WorldClim variables
 #' @description download WorldClim variables. See www.worldclim.com.
 #'

R/espace_nicheOv.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_nicheOv.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' @title espace_nicheOv Niche Overlap
 #' @description Function evaluates niche overlap between the two species for
 #'   which the occurrence density grid was computed

R/espace_occDens.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_occDens.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title Occurrence density grid
 #' @description calculates the part of environmental space more densely

R/espace_pca.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_pca.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' @title espace_pca Principal component analysis
 #' @description Principal component analysis to reduce dimensionality of
 #'   environmental space

R/helper_functions.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# helper_functions.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 ####################### #
 # MISC #
 ####################### #

R/model_bioclim.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# model_bioclim.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title model_bioclim Generate Bioclim model
 #' @description The function generates a BIOCLIM model using

R/model_maxent.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# model_maxent.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title model_maxent Generate maxent.jar or maxnet model
 #' @description This functions generates maxent.jar or maxnet models using

R/occs_paleoDb.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# occs_paleoDb.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' #' @title `occs_paleoDb` query paleobioDB database
 #' #' @description
 #' #' query paleobioDB database and returns the complete list of data, data with

R/occs_queryDb.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# occs_queryDb.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 2 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_queryDb Query online database for species occurrence records.
 #'
 #' @description  Queries a given database for occurrence data on the provided species

R/occs_userOccs.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# occs_userOccs.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 #' @title occs_userOccs Loads user provided occurrence records
 #' @description
 #' Load user database with species occurrence records. Returns a list of lists,

R/part_partitionOccs.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# part_partitionOccs.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 2 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/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title part_partitionOccs Partition occurrence data
 #' @description This function partitions occurrence data and background points