#' gfplot package
#'
#' gfplot package
#'
#' See the README on
#' \href{https://github.com/seananderson/gfplot#readme}{GitHub}
#'
#' @docType package
#' @name gfplot
#' @importFrom dplyr distinct filter mutate summarise select group_by n arrange ungroup
#' @importFrom dplyr inner_join left_join right_join anti_join full_join
#' @importFrom dplyr semi_join
#' @importFrom dplyr bind_rows case_when pull contains tibble rename as_tibble
#' @importFrom rlang enquo quo_name ":=" "!!" .data sym
#' @importFrom forcats fct_reorder
#' @importFrom assertthat assert_that are_equal
#' @importFrom RColorBrewer brewer.pal
#' @importFrom ggplot2 ggplot aes aes_string geom_hline geom_vline scale_fill_manual
#' scale_colour_manual scale_x_continuous scale_size_area coord_cartesian
#' guides geom_point facet_wrap xlab ylab geom_col ylim xlim geom_rect
#' geom_text scale_fill_continuous geom_line labs scale_y_continuous
#' guide_legend geom_ribbon element_text scale_shape_manual element_line
#' geom_path geom_polygon coord_equal stat_summary_hex facet_grid
#' position_identity coord_fixed scale_color_viridis_d scale_colour_viridis_d
#' @importFrom stats coef model.matrix lm binomial rnorm
#' update.formula formula as.formula density sd
#' @importFrom methods as
#' @importFrom grDevices chull
#' @importFrom stats t.test
#' @importFrom utils read.csv
#' @importFrom rosettafish en2fr
# avoid R CMD check warning; import something:
#' @importFrom PBSdata .PBSdataEnv
NULL
# from: https://github.com/jennybc/googlesheets/blob/master/R/googlesheets.R
# quiets concerns of R CMD check re: the .'s that appear in pipelines
if (getRversion() >= "2.15.1") utils::globalVariables(c("."))
if (getRversion() >= "2.15.1") {
utils::globalVariables(c(
"SURVEY_SERIES_TYPE_CODE", "trip_start_date", "SPECIES_CODE",
"SPECIES_COMMON_NAME", "SPECIES_DESC", "SPECIES_SCIENCE_NAME",
"SURVEY_SERIES_DESC", "SURVEY_SERIES_ID", "SURVEY_SERIES_TYPE_CODE",
"discarded_kg", "discarded_pcs", "gear", "landed_kg",
"landed_pcs", "species_common_name", "species_desc", "species_science_name",
"trip_start_date", "year",
# weighting:
"month", "freq", "trip_id", "sample_id", "survey_id", "value", "prop",
"annual_prop", "quarter", "sum_freq",
"adult",
"area_km2",
"catch_weight",
"count",
"cutoff_day",
"day_of_year",
"density_kgpm2",
"est_sample_mass",
"fe_end_date",
"fishing_event_id",
"grouping1",
"grouping_code",
"landed_kg_quarter",
"landed_kg_year",
"mass_ratio",
"mass_ratio_mature",
"maturity_mass",
"measured_weight",
"method",
"n_mature",
"n_sampled",
"n_weights",
"new_mass",
"samp_catch_weight_quarter",
"samp_trip_catch_weight",
"sum_weighted_freq1",
"threshold",
"weight",
"weighted_freq1",
"weighted_freq1_scaled",
"weighted_freq2",
"weighted_freq2_scaled",
"weighting1",
"weighting1_total",
"weighting2",
"weighting2_total",
# plotting:
"age",
"maturity_code",
"n_spp",
"sex",
"survey",
"variable",
"survey_series_desc",
"survey_abbrev",
# lengths:
"bin_size", "counts", "proportion", "total",
# aging precision:
"age_reading_id", "age_reading_type_code", "ageing_method_desc",
"ageing_param", "employee_id", "female", "glmm", "has_precision", "mature",
"mature_at", "maturity_convention_desc", "maturity_convention_description",
"maturity_convention_maxvalue", "n_employee", "p", "species_code",
"specimen_id", "specimen_sex_code",
# maturity:
"n_scaled",
# cpue:
"best_date", "best_depth", "fe_start_date", "hours_fished", "latitude",
"locality_code", "longitude", "n_trips_per_year", "n_years", "pos_catch",
"scrambled_vessel", "species_category_code", "spp_catch", "spp_in_fe",
"spp_in_row", "sum_catch", "total_positive_tows", "trips_over_thresh",
"trips_over_treshold_this_year", "vessel_name",
"est", "est_log", "lwr", "se_log", "upr", "est_link", "model", "se_link",
"n_date", "pars", "par_name", "par_group", "par_name_short", "se",
"vessel", "pred", "term",
"PID", "SID", "nepacLLhigh", "isobath",
# surveys:
"Var1", "Var2", "X", "Y", "akima_depth", "depth", "depth_m",
"depth_mean", "depth_scaled", "depth_sd", "present", "species", "start_lat",
"start_lon", "x", "y", "z", "bctopo",
# survey ts:
"num_pos_sets", "biomass", "lowerci", "mean_cv", "num_pos_sets",
"num_sets", "re", "surv_order", "survey_name", "upperci",
"maturity_convention_code",
"total_month", "month_jitter", "maturity_name_short", "survey_series_id",
".n", "maturity", "maturity_name",
"ageing_method", "length_bin", "weighted_prop", "year_jitter",
"vessel_effect", "year_effect",
"sample_source_code", "keeper", "area",
"totcatch_kg", "fyear", "SURVEY_ABBREV", "vessel_registration_number",
"sampling_desc", "mean_num_pos_sets", "cv", "sets",
"true_b", "true", "mean_num_sets",
# IPHC survey calculations
"C_it", "C_it20", "E_it", "E_it20", "H_it", "N_it", "N_it20", "bait",
"block", "chumCountPerSkate", "chumCountPerSkate20", "chumObsHooksPerSkate",
"chumObsHooksPerSkate20", "countPerSkate", "countPerSkate20",
"deplHooksPerSkate", "effSkateIPHC", "firstHook", "hook", "hook20",
"hooksChumRatio", "hooksChumRatio20", "iphcUsabilityCode", "lastHook",
"lastHookTemp", "lat", "long", "numOnHook", "numOnHook20", "obsHooksPerSkate",
"obsHooksPerSkate20", "usable", "setID", "skateID",
"I_t20BootHigh", "I_t20BootLow", "I_t20BootMean", "I_t20SampleMean",
"I_tBootCV", "I_tBootHigh", "I_tBootLow", "I_tBootMean", "I_tSampleMean",
"num_pos", "num_pos20", "num_pos_sets",
"everything", "prop_empty_sets", "wcvi",
"catchCount", "effSkate",
"lon", "spNameIPHC", "specCount", "station",
"countData1995", "countData2013", "data1996to2002",
"setData1995", "setData2013", "spNameIPHC", "Sets",
# others
"parent_rsty_id", "parent_taxonomic_unit", "row_version", "rsty_id",
"species_grouping", "taxonomic_rank",
# other
"usability_code",
".time_diff",
".year_start_date",
"action_start_date",
"common_df",
"count_surveys_since_2008",
# historical CPUE tidy
"best_depth_m", "locality", "locality_description", "mean_depth",
"species_ageing_group",
"avg_value", "min_value", "max_value", "parameter", "type",
"each_specimen_collected",
"temp",
"maturity_assignment",
"maturity_short_names",
# cpue map stuff
"label", "major"
))
}
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