Reorganization

00_preparation.R

@@ -0,0 +1,85 @@
+# *------------------------------------------------------------------
+# | PROGRAM NAME: 
+# | FILE NAME: .R
+# | DATE: 
+# | CREATED BY:  Jim Stagge         
+# *----------------------------------------------------------------
+# | PURPOSE:  Test the fundamental models, for a single distribution. Use a hurdle model to incorporate zeros
+# | 
+# |
+# *------------------------------------------------------------------
+
+###########################################################################
+###  Install and Load Devtools for custom packages
+###########################################################################
+install.packages("fs", repos = "https://cran.case.edu/")
+install.packages("usethis", repos = "https://cran.case.edu/")
+install.packages("vctrs", repos = "https://cran.case.edu/")
+install.packages("lifecycle", repos = "https://cran.case.edu/")
+
+install.packages("backports", repos = "https://cran.case.edu/")
+install.packages("rprojroot", repos = "https://cran.case.edu/")
+install.packages("devtools", repos = "https://cran.case.edu/")
+install.packages("broom", repos = "https://cran.case.edu/")
+install.packages("ggplot2", repos = "https://cran.case.edu/")
+install.packages("Rcpp", repos = "https://cran.case.edu/")
+#require(devtools)
+
+###########################################################################
+###  Install packages from R repo
+###########################################################################
+
+install.packages("dplyr", repos = "https://cran.case.edu/")
+install.packages("tibble", repos = "https://cran.case.edu/")
+install.packages("tidyverse", repos = "https://cran.case.edu/")
+install.packages("here", repos = "https://cran.case.edu/")
+
+### To access GHCND
+#install.packages("isdparser", repos = "https://cloud.r-project.org")
+#install.packages("rnoaa", repos = "https://cloud.r-project.org")
+
+### To save in SVG
+install.packages("svglite", repos = "https://cloud.r-project.org")
+install.packages("viridis", repos = "https://cloud.r-project.org")
+
+### Packages for spi
+install.packages("fitdistrplus", repos = "https://cloud.r-project.org")
+install.packages("lubridate", repos = "https://cloud.r-project.org")
+
+install.packages("mgcv", repos = "https://cloud.r-project.org")
+### There was an error message with this version
+#install_version("mgcv", version = "1.8-31", repos = "http://cran.us.r-project.org")
+#install.packages("dplyr",  repos = "https://cloud.r-project.org")
+
+install.packages("ggthemes", repos = "https://cloud.r-project.org")
+install.packages("R6", repos = "https://cloud.r-project.org")
+
+#install.packages("rgdal", repos = "https://cloud.r-project.org")
+#install.packages("ggrepel", repos = "https://cloud.r-project.org")
+#install.packages("sf", repos = "https://cloud.r-project.org")
+#install.packages("maps", repos = "https://cloud.r-project.org")
+install.packages("furrr", repos = "https://cloud.r-project.org")
+install.packages("zoo", repos = "https://cloud.r-project.org")
+#install.packages("rnaturalearth", repos = "https://cloud.r-project.org")
+
+install.packages("vroom", repos = "https://cloud.r-project.org")
+install.packages("cmdstanr", repos = "https://mc-stan.org/r-packages")
+
+require(cmdstanr)
+install_cmdstan()
+cmdstan_path()
+cmdstan_version()
+
+install.packages("rstan", repos = "https://cloud.r-project.org")
+install.packages("StanHeaders", repos = "https://cloud.r-project.org")
+
+###########################################################################
+###  Install custom spibayes package
+###########################################################################
+### For custom MLE functions
+#devtools::install_github("staggelab/spibayes",  ref= "add_variance")
+
+install.packages("/users/PAS1627/stagge11/code/spibayes", 
+repos = NULL, 
+type = "source")
+