diff --git a/NAMESPACE b/NAMESPACE index 797d355..1069658 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -46,7 +46,9 @@ export(get_survey_gear_types) export(get_survey_ids) export(get_survey_index) export(get_survey_samples) +export(get_survey_samples2) export(get_survey_sets) +export(get_survey_sets2) export(get_survey_stomachs) export(get_table) export(inject_filter) diff --git a/man/get_data.Rd b/man/get_data.Rd index c6835ad..04b660e 100644 --- a/man/get_data.Rd +++ b/man/get_data.Rd @@ -1,5 +1,6 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/get-dat.R, R/get-hake-dat.R, R/get-sablefish.R +% Please edit documentation in R/get-dat.R, R/get-hake-dat.R, R/get-sablefish.R, +% R/get-survey-samples.R, R/get-survey-sets.R \name{get_data} \alias{get_data} \alias{get_survey_sets} @@ -26,6 +27,8 @@ \alias{get_hake_survey_samples} \alias{get_hake_catch} \alias{get_sablefish_surveys} +\alias{get_survey_samples2} +\alias{get_survey_sets2} \title{Get PBS data} \usage{ get_survey_sets( @@ -33,6 +36,7 @@ get_survey_sets( ssid = c(1, 3, 4, 16, 2, 14, 22, 36, 39, 40), join_sample_ids = FALSE, verbose = FALSE, + remove_false_zeros = FALSE, sleep = 0.05 ) @@ -123,6 +127,35 @@ get_hake_survey_samples() get_hake_catch(end_date = format(Sys.Date(), "\%d/\%m/\%Y")) get_sablefish_surveys() + +get_survey_samples2( + species, + ssid = NULL, + remove_bad_data = TRUE, + unsorted_only = TRUE, + usability = NULL, + major = NULL +) + +get_commercial_samples( + species, + unsorted_only = TRUE, + return_all_lengths = FALSE, + major = NULL, + usability = NULL +) + +get_catch(species, major = NULL) + +get_survey_sets2( + species, + ssid = c(1, 3, 4, 16, 2, 14, 22, 36, 39, 40), + join_sample_ids = FALSE, + verbose = FALSE, + sleep = 0.05 +) + +get_ll_hook_data(species = NULL, ssid = NULL) } \arguments{ \item{species}{One or more species common names (e.g. \code{"pacific ocean perch"}) or one or more species codes (e.g. \code{396}). Species codes can be @@ -144,6 +177,10 @@ different survey stratifications.} \item{verbose}{If \code{TRUE} then extra messages were reprinted during data extraction. Useful to monitor progress.} +\item{remove_false_zeros}{If \code{TRUE} will make sure weights > 0 don't have +associated counts of 0 and vice versa. Only applies to trawl data where +counts are only taken for small catches.} + \item{sleep}{System sleep in seconds between each survey-year to be kind to the server.} @@ -156,9 +193,9 @@ and unknown). Default = TRUE.} \item{usability}{A vector of usability codes to include. Defaults to all. IPHC codes may be different to other surveys.} -\item{major}{To select only the inside population (Strait of Georgia, area -4B only), set inside = 1. To select only the outside population, set inside -= 0.} +\item{major}{Character string (or vector, though doesn't work yet with +\code{cache_pbs_data}) of major stat area code to include (characters). Use +get_major_areas() to lookup area codes with descriptions.} \item{return_all_lengths}{Include all length types, rather than just with most common measurement. Default = FALSE.}