Update copyright and include a note on renv lock files being human re…

…adable.

APCD10Cr_model_20211222.slim

@@ -4,9 +4,9 @@ Author: Bryce Carson <[email protected]>
 Contributor: Clément Rougeux <clement[email protected]>
 URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
 
-APCD10Cr-2021-12-22.slim 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.
+APCD10Cr_model_20211222.slim 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.
 
-APCD10Cr-2021-12-22.slim 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.
+APCD10Cr_model_20211222.slim 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 this program. If not, see <https://www.gnu.org/licenses/>.
 */

APCD10Cr_model_20211222_job_script.sh

@@ -14,8 +14,8 @@ slim -m -l `xargs -a params_${SLURM_ARRAY_TASK_ID}` APCD10Cr_20211222.slim
 # Author: Bryce Carson <[email protected]>
 # URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
 #
-# APCD10Cr_20211222_job_script.sh 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.
+# APCD10Cr_model_20211222_job_script.sh 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.
 #
-# APCD10Cr_20211222_job_script.sh 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.
+# APCD10Cr_model_20211222_job_script.sh 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 this program. If not, see <https://www.gnu.org/licenses/>.

APCD10Cr_model_generate_parameter_files.R

@@ -1,3 +1,13 @@
+# Copyright 2021 Bryce Carson
+# Author: Bryce Carson <[email protected]>
+# URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
+#
+# APCD10Cr_model_generate_parameter_files.R 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.
+#
+# APCD10Cr_model_generate_parameter_files.R 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 this program. If not, see <https://www.gnu.org/licenses/>.
+
 library(tidyverse)
 library(glue)
 

APCD10Cr_model_generate_parameter_files.sh

@@ -3,9 +3,9 @@
 # Author: Bryce Carson <[email protected]>
 # URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
 #
-# generateParameterFiles.sh 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.
+# APCD10Cr_model_generate_parameters.sh 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.
 #
-# generateParameterFiles.sh 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.
+# APCD10Cr_model_generate_parameters.sh 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 this program. If not, see <https://www.gnu.org/licenses/>.
 

APCD10Cr_mutations_analysis_job_script.sh

@@ -19,8 +19,8 @@ R CMD BATCH --vanilla /home/bcars268/RSQLite/MeeCarsonYeaman2021.R  /home/bcars2
 # Author: Bryce Carson <[email protected]>
 # URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
 #
-# MeeCarsonYeaman2021.sh 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.
+# APCD10Cr_mutations_analysis_job_script.sh 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.
 #
-# MeeCarsonYeaman2021.sh 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.
+# APCD10Cr_mutations_analysis_job_script.sh 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 this program. If not, see <https://www.gnu.org/licenses/>.

APCD10Cr_mutations_app.R

@@ -2,12 +2,12 @@
 # Author: Bryce Carson <[email protected]>
 # URL: https://github.com/bryce-carson/APCD10Cr_Carson_2022
 #
-# APCD_app.R is free software: you can redistribute it and/or modify it under
+# APCD10Cr_mutations_app.R 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.
 #
-# APCD_app.R is distributed in the hope that it will be useful, but WITHOUT ANY
+# APCD10Cr_mutations_app.R 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.
 #

README.md

@@ -68,6 +68,8 @@ A workflow manager was not used during data production, so several scripts were
 
 A workflow manager like `targets` or `snakemake` was not used, so several scripts were written for the stages of production, validation, and analysis.
 
+[renv](https://cran.r-project.org/package=renv) is a "dependency management toolkit for R," and helps to automatically install packages listed in the json-like `.lock` files contained in the repository. *Note*: the `.lock` files are human-readable.
+
 1. Population genetic data is produced using SLiM 3 [2] with
    `APCD10Cr_model_20211222.slim` as the input model, and submitted to the SLURM
    scheduler on the academic cluster using