in process with generating layers.Global[2012|2013].v2013web
added datasets layers.* and scores.* for www 2012 & 2013. updated SelectLayers() to plyr::rename() layers if fed a named character vector
added datasets layers.* and scores.* for www 2012 & 2013. updated SelectLayers() to plyr::rename() layers if fed a named character vector
Merge branch 'master' of https://github.com/bbest/ohicore

Conflicts:
	inst/extdata/layers.Global2012.vWeb2012b/FIS_Trend_2012a_lyr.csv
	inst/extdata/layers.Global2012.vWeb2012b/GL_NCEAS_MAR_Trend_v2012a_lyr.csv
	inst/extdata/layers.Global2012.vWeb2012b/cc_acid_2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/cc_slr_2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/cntry_georegions_long_2013b.csv
	inst/extdata/layers.Global2012.vWeb2012b/cntry_rgn_2013.csv
	inst/extdata/layers.Global2012.vWeb2012b/cp_habitat_extent_rank.csv
	inst/extdata/layers.Global2012.vWeb2012b/cs_habitat_extent.csv
	inst/extdata/layers.Global2012.vWeb2012b/fp_art_lb_2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/hab_habitat_extent.csv
	inst/extdata/layers.Global2012.vWeb2012b/hab_habitat_health_disaggregatedNature2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/hab_habitat_presence.csv
	inst/extdata/layers.Global2012.vWeb2012b/hab_habitat_trend_disaggregatedNature2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/ico_spp_extinction_status.csv
	inst/extdata/layers.Global2012.vWeb2012b/ico_spp_popn_trend.csv
	inst/extdata/layers.Global2012.vWeb2012b/le_sector_weight_disaggregateNature2012b.csv
	inst/extdata/layers.Global2012.vWeb2012b/lsp_prot_area_inland1km.csv
	inst/extdata/layers.Global2012.vWeb2012b/lsp_prot_area_offshore3nmb.csv
	inst/extdata/layers.Global2012.vWeb2012b/np_harvest_relative_v2013a_updated_lyr_NAmanualoverride.csv
	inst/extdata/layers.Global2012.vWeb2012b/np_sustainability_v2012a_updated_lyr.csv
	inst/extdata/layers.Global2012.vWeb2012b/np_weight_combo_2012a_updated_lyr.csv
	inst/extdata/layers.Global2012.vWeb2012b/p_fp_art_hb_disaggregateNature2012.csv
	inst/extdata/layers.Global2012.vWeb2012b/p_hd_subtidal_hb_v2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/p_sp_alien_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/po_pathogens_trend_sanitation2008to2011_popninland25km2008to2013.csv
	inst/extdata/layers.Global2012.vWeb2012b/po_rgn_hd_subtidal_sb_2012a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_alien_species_Nature2012disaggregated.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_cites_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_fishing_v1_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_fishing_v1_eez_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_fishing_v2_eez_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_fishing_v3_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_fishing_v3_eez_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_habitat_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_habitat_combo_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_habitat_combo_eez_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_li_sector_evenness_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_mariculture_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_mora_s4_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_msi_gov_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_tourism_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/r_water_2013a.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_area_inland1km.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_area_offshore3nm.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_fao_gcs_area.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_georegions_labels_long_2013b.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_georegions_long_2013b.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_global.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_labels.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_spp_score_offshore3nm_2013.csv
	inst/extdata/layers.Global2012.vWeb2012b/rgn_spp_trend_2012.csv
	inst/extdata/layers.Global2012.www2013/FIS_Status_2012a_lyr.csv
	inst/extdata/layers.Global2012.www2013/FIS_Trend_2012a_lyr.csv
	inst/extdata/layers.Global2012.www2013/GL-NCEAS_CW_Fertilizers_trend_v2012a.csv
	inst/extdata/layers.Global2012.www2013/GL-NCEAS_CW_Pesticides_trend_v2012a.csv
	inst/extdata/layers.Global2012.www2013/GL_FP_wildcaught_weight_v2012a_lyr.csv
	inst/extdata/layers.Global2012.www2013/GL_NCEAS_MAR_Status_v2012a_lyr.csv
	inst/extdata/layers.Global2012.www2013/GL_NCEAS_MAR_Trend_v2012a_lyr.csv
	inst/extdata/layers.Global2012.www2013/GenEsc_v2012a.csv
	inst/extdata/layers.Global2012.www2013/TourRec_Status_2012a_Sep23b.csv
	inst/extdata/layers.Global2012.www2013/TourRec_Trend_2012a_Sep23b.csv
	inst/extdata/layers.Global2012.www2013/cc_acid_2012.csv
	inst/extdata/layers.Global2012.www2013/cc_slr_2012.csv
	inst/extdata/layers.Global2012.www2013/cc_sst_2012.csv
	inst/extdata/layers.Global2012.www2013/cc_uv_2012.csv
	inst/extdata/layers.Global2012.www2013/cntry_georegions_long_2013b.csv
	inst/extdata/layers.Global2012.www2013/cntry_rgn_2013.csv
	inst/extdata/layers.Global2012.www2013/cp_habitat_extent_rank.csv
	inst/extdata/layers.Global2012.www2013/cs_habitat_extent.csv
	inst/extdata/layers.Global2012.www2013/fp_art_lb_2012.csv
	inst/extdata/layers.Global2012.www2013/fp_com_hb_2012.csv
	inst/extdata/layers.Global2012.www2013/fp_com_lb_2012.csv
	inst/extdata/layers.Global2012.www2013/hab_habitat_extent.csv
	inst/extdata/layers.Global2012.www2013/hab_habitat_health_disaggregatedNature2012.csv
	inst/extdata/layers.Global2012.www2013/hab_habitat_presence.csv
	inst/extdata/layers.Global2012.www2013/hab_habitat_trend_disaggregatedNature2012.csv
	inst/extdata/layers.Global2012.www2013/hd_intertidal_2012.csv
	inst/extdata/layers.Global2012.www2013/ico_spp_extinction_status.csv
	inst/extdata/layers.Global2012.www2013/ico_spp_popn_trend.csv
	inst/extdata/layers.Global2012.www2013/le_sector_weight_disaggregateNature2012b.csv
	inst/extdata/layers.Global2012.www2013/lsp_prot_area_inland1km.csv
	inst/extdata/layers.Global2012.www2013/lsp_prot_area_offshore3nmb.csv
	inst/extdata/layers.Global2012.www2013/np_harvest_relative_v2013a_updated_lyr_NAmanualoverride.csv
	inst/extdata/layers.Global2012.www2013/np_sustainability_v2012a_updated_lyr.csv
	inst/extdata/layers.Global2012.www2013/np_weight_combo_2012a_updated_lyr.csv
	inst/extdata/layers.Global2012.www2013/p_fp_art_hb_disaggregateNature2012.csv
	inst/extdata/layers.Global2012.www2013/p_hd_subtidal_hb_v2013a.csv
	inst/extdata/layers.Global2012.www2013/p_sp_alien_2013a.csv
	inst/extdata/layers.Global2012.www2013/po_chemicals_2012.csv
	inst/extdata/layers.Global2012.www2013/po_chemicals_3nm_2012.csv
	inst/extdata/layers.Global2012.www2013/po_nutrients_2012.csv
	inst/extdata/layers.Global2012.www2013/po_nutrients_3nm_2012.csv
	inst/extdata/layers.Global2012.www2013/po_pathogens_sanitation2008_popninland25km2008.csv
	inst/extdata/layers.Global2012.www2013/po_pathogens_trend_sanitation2008to2011_popninland25km2008to2013.csv
	inst/extdata/layers.Global2012.www2013/po_rgn_hd_subtidal_sb_2012a.csv
	inst/extdata/layers.Global2012.www2013/po_trash2011.csv
	inst/extdata/layers.Global2012.www2013/r_alien_species_Nature2012disaggregated.csv
	inst/extdata/layers.Global2012.www2013/r_cites_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_fishing_v1_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_fishing_v1_eez_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_fishing_v2_eez_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_fishing_v3_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_fishing_v3_eez_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_habitat_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_habitat_combo_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_habitat_combo_eez_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_li_gci_Nature2012disaggregated.csv
	inst/extdata/layers.Global2012.www2013/r_li_sector_evenness_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_mariculture_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_mora_s4_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_msi_gov_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_tourism_2013a.csv
	inst/extdata/layers.Global2012.www2013/r_water_2013a.csv
	inst/extdata/layers.Global2012.www2013/rgn_area_inland1km.csv
	inst/extdata/layers.Global2012.www2013/rgn_area_offshore3nm.csv
	inst/extdata/layers.Global2012.www2013/rgn_fao_gcs_area.csv
	inst/extdata/layers.Global2012.www2013/rgn_fao_targeted_2012a_rescaled.csv
	inst/extdata/layers.Global2012.www2013/rgn_georegions_labels_long_2013b.csv
	inst/extdata/layers.Global2012.www2013/rgn_georegions_long_2013b.csv
	inst/extdata/layers.Global2012.www2013/rgn_global.csv
	inst/extdata/layers.Global2012.www2013/rgn_labels.csv
	inst/extdata/layers.Global2012.www2013/rgn_popn5yrtrend_inland25mi_2007to2012.csv
	inst/extdata/layers.Global2012.www2013/rgn_spp_score_2012.csv
	inst/extdata/layers.Global2012.www2013/rgn_spp_score_offshore3nm_2013.csv
	inst/extdata/layers.Global2012.www2013/rgn_spp_trend_2012.csv
	inst/extdata/layers.Global2012.www2013/rgn_wb_gdppcppp_rescaled_year_2012b.csv
	inst/extdata/layers.Global2012.www2013/rgn_wb_wgi_2012a_rescaled.csv
	inst/extdata/layers.Global2012.www2013/rgn_wb_wgi_2012a_rescaled_inverse.csv
	inst/extdata/layers.Global2013.www2013/FIS_Trend_2013a_lyr.csv
	inst/extdata/layers.Global2013.www2013/GL_NCEAS_MAR_Trend_v2013a_lyr.csv
	inst/extdata/layers.Global2013.www2013/cc_acid_2013.csv
	inst/extdata/layers.Global2013.www2013/cc_slr_2013.csv
	inst/extdata/layers.Global2013.www2013/cntry_georegions_long_2013b.csv
	inst/extdata/layers.Global2013.www2013/cntry_rgn_2013.csv
	inst/extdata/layers.Global2013.www2013/cp_habitat_extent_rank.csv
	inst/extdata/layers.Global2013.www2013/cs_habitat_extent.csv
	inst/extdata/layers.Global2013.www2013/fp_art_lb_2013.csv
	inst/extdata/layers.Global2013.www2013/hab_habitat_extent.csv
	inst/extdata/layers.Global2013.www2013/hab_habitat_health_disaggregatedNature2012.csv
	inst/extdata/layers.Global2013.www2013/hab_habitat_presence.csv
	inst/extdata/layers.Global2013.www2013/hab_habitat_trend_disaggregatedNature2012.csv
	inst/extdata/layers.Global2013.www2013/ico_spp_extinction_status.csv
	inst/extdata/layers.Global2013.www2013/ico_spp_popn_trend.csv
	inst/extdata/layers.Global2013.www2013/le_sector_weight_disaggregateNature2012b.csv
	inst/extdata/layers.Global2013.www2013/lsp_prot_area_inland1km.csv
	inst/extdata/layers.Global2013.www2013/lsp_prot_area_offshore3nmb.csv
	inst/extdata/layers.Global2013.www2013/np_harvest_relative_v2013a_updated_lyr_NAmanualoverride.csv
	inst/extdata/layers.Global2013.www2013/np_sustainability_v2013a_updated_lyr.csv
	inst/extdata/layers.Global2013.www2013/np_weight_combo_2013a_updated_lyr.csv
	inst/extdata/layers.Global2013.www2013/p_fp_art_hb_disaggregateNature2012.csv
	inst/extdata/layers.Global2013.www2013/p_hd_subtidal_hb_v2013a.csv
	inst/extdata/layers.Global2013.www2013/p_sp_alien_2013a.csv
	inst/extdata/layers.Global2013.www2013/po_pathogens_trend_sanitation2008to2011_popninland25km2008to2013.csv
	inst/extdata/layers.Global2013.www2013/po_rgn_hd_subtidal_sb_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_alien_species_Nature2012disaggregated.csv
	inst/extdata/layers.Global2013.www2013/r_cites_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_fishing_v1_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_fishing_v1_eez_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_fishing_v2_eez_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_fishing_v3_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_fishing_v3_eez_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_habitat_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_habitat_combo_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_habitat_combo_eez_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_li_sector_evenness_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_mariculture_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_mora_s4_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_msi_gov_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_tourism_2013a.csv
	inst/extdata/layers.Global2013.www2013/r_water_2013a.csv
	inst/extdata/layers.Global2013.www2013/rgn_area_inland1km.csv
	inst/extdata/layers.Global2013.www2013/rgn_area_offshore3nm.csv
	inst/extdata/layers.Global2013.www2013/rgn_fao_gcs_area.csv
	inst/extdata/layers.Global2013.www2013/rgn_georegions_labels_long_2013b.csv
	inst/extdata/layers.Global2013.www2013/rgn_georegions_long_2013b.csv
	inst/extdata/layers.Global2013.www2013/rgn_global.csv
	inst/extdata/layers.Global2013.www2013/rgn_labels.csv
	inst/extdata/layers.Global2013.www2013/rgn_spp_score_offshore3nm_2013.csv
	inst/extdata/layers.Global2013.www2013/rgn_spp_trend_2013.csv
finishing file commit for layers.Global[2012|2013].www2013
updating documentation
added Conf() class and conf.Global[2012|2013].www2013
updated SelectLayers to have conforming data.frame. test now problematic with layers.Global2012.Nature2012ftp having wrong units entry and generic category and value fields
minor documentation updates
pressures reproducing www2013 scores
Resilience ported and identical to www2013
removed calc.[FIS|MAR].Nature2012 since .www2013
almost finished with full index calculations in inst/tmp/CalculateIndexAll.R. dropped R5 class of Scores in favor of simpler scores data.frame for saving and loading of scores
premtg w/ Steve
cleaned up ICO and added test_fxns.R
interim functions.R working FIS to ICO in goals.csv. added LIV/ECO status/trend to google doc and layers.
mostly working functions to produce www scores
identical scores_www (2013-10-09) except NP (and some Index)
NP now jives with www after converting factor to character for indexing trend years. All values identical, except Index.future.0 which should've been area weighted anyways.
cleaned up CalculateIndexAll.R