Large update of AQ R and run scripts

[wkappel]

Updated, deleted, or renamed several R scripts. Most of the updates are minor and do not correct errors. Instead the updates unify the names of the output files between the R scripts and the run scripts.

Similar updates to the run scripts to unify the output names, add links to the data files in the output to the screen, rename several scripts, and remove a couple scripts.

Also updated/added the AMETBASE environment variable to be /home/AMETv15.

    deleted:    ../R_analysis_code/AQ_Boxplot_MDA8.R
modified:   ../R_analysis_code/AQ_Boxplot_ggplot.R
modified:   ../R_analysis_code/AQ_Kellyplot_season.R
modified:   ../R_analysis_code/AQ_Misc_Functions.R
modified:   ../R_analysis_code/AQ_Plot_Spatial_MtoM_Species.R
modified:   ../R_analysis_code/AQ_Plot_Spatial_MtoM_leaflet.R
modified:   ../R_analysis_code/AQ_Scatterplot_mtom_density.R
modified:   ../R_analysis_code/AQ_Scatterplot_multi.R
modified:   ../R_analysis_code/AQ_Stacked_Barplot_AE6_ggplot.R
modified:   ../R_analysis_code/AQ_Stacked_Barplot_AE6_ts.R
modified:   ../R_analysis_code/AQ_Stacked_Barplot_soil.R
modified:   ../R_analysis_code/AQ_Stacked_Barplot_soil_multi.R
modified:   ../R_analysis_code/AQ_Stats.R
modified:   ../R_analysis_code/AQ_Timeseries.R
modified:   ../R_analysis_code/AQ_Timeseries_MtoM.R
modified:   ../R_analysis_code/AQ_Timeseries_dygraph.R
modified:   ../R_analysis_code/AQ_Timeseries_multi_networks.R
renamed:    ../R_analysis_code/AQ_Timeseries_networks_plotly.R -> ../R_analysis_code/AQ_Timeseries_multi_networks_plotly.R
modified:   ../R_analysis_code/AQ_Timeseries_multi_species.R
renamed:    ../R_analysis_code/AQ_Timeseries_species_plotly.R -> ../R_analysis_code/AQ_Timeseries_multi_species_plotly.R
modified:   aqExample/input_files/all_scripts.input
modified:   aqExample/run_AMET_batch_scripts.csh
modified:   aqExample/run_boxplot.csh
modified:   aqExample/run_boxplot_DofW.csh
modified:   aqExample/run_boxplot_ggplot.csh
modified:   aqExample/run_boxplot_hourly.csh
modified:   aqExample/run_boxplot_plotly.csh
modified:   aqExample/run_boxplot_roselle.csh
modified:   aqExample/run_bugleplot.csh
deleted:    aqExample/run_kellyplot_multisim.csh
modified:   aqExample/run_kellyplot_region.csh
modified:   aqExample/run_kellyplot_season.csh
modified:   aqExample/run_plot_spatial_mtom_leaflet.csh
modified:   aqExample/run_plot_spatial_mtom_species.csh
modified:   aqExample/run_plot_spatial_ratio.csh
modified:   aqExample/run_raw_data.csh
modified:   aqExample/run_scatterplot_multi.csh
modified:   aqExample/run_scatterplot_multi_plotly.csh
modified:   aqExample/run_scatterplot_percentiles.csh
modified:   aqExample/run_scatterplot_plotly.csh
modified:   aqExample/run_scatterplot_single.csh
modified:   aqExample/run_scatterplot_skill.csh
modified:   aqExample/run_stacked_barplot.csh
modified:   aqExample/run_stacked_barplot_AE6.csh
modified:   aqExample/run_stacked_barplot_AE6_ts.csh
modified:   aqExample/run_stacked_barplot_soil.csh
modified:   aqExample/run_stacked_barplot_soil_multi.csh
modified:   aqExample/run_stats.csh
modified:   aqExample/run_stats_plots.csh
modified:   aqExample/run_stats_plots_leaflet.csh
modified:   aqExample/run_timeseries.csh
modified:   aqExample/run_timeseries_dygraph.csh
modified:   aqExample/run_timeseries_mtom.csh
renamed:    aqExample/run_timeseries_multi.csh -> aqExample/run_timeseries_multi_networks.csh
renamed:    aqExample/run_timeseries_multi_plotly.csh -> aqExample/run_timeseries_multi_networks_plotly.csh
modified:   aqExample/run_timeseries_multi_species.csh
renamed:    aqExample/run_timeseries_species_plotly.csh -> aqExample/run_timeseries_multi_species_plotly.csh