Returns the HLI table with some additional metadata, such as NMFS_PopID and update dates,
in the default tabletype="xport case.
This is the table that one can download from the
CAP Fish HLIs Tabular Query. The HLI is specified using its short code:
NOSA: Natural Origin Spawner Abundance
SAR: Smolt to Adult Ratios
PNI: Proportionate Natural Influence of supplementation hatcheries
RperS: Recruits per Spawner
JuvOut: Juvenile Outmigrants
PreSmolt: Presmolt Abundance
The query will download 1000 records by default; you can change
this by passing in qlist=list(limit=1100) for example. To make a
filtered query e.g. for one ESU or popid) pass in the flist
argument. Field names and values are case insensitive, e.g.
POPID, popid and PopID return the same result.
If your filter value is not in the table, the returned table
will be empty. Examples:
flist=list(popid=7) return values for popid 7.
flist=list(nmfs_popid=6) return values for NMFS_PopID 6.
flist=list(esu_dps="Salmon, Chinook (Snake River spring/summer-run ESU)") return values for one ESU. Use rCAX:::caxesu to see a list of ESU_DPS names.
The HLI short name: NOSA, SAR, PNI, PreSmolt, JuvOut, RperS
A filter for the query. See details and rcax_filter()
Additional query parameters. See rcax_table_query() for details.
column names to return. Use cols=NULL if you want all columns. Names are case insensitive.
The columns to sort on for the returned table. The order of sortcols indicates the order of sorting. Start with the smallest group and work outwards, e.g. c("spawningyear", "popid", "MPG"). Names are case insensitive.
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
"xport" (default) or "base". XPort has additional useful metadata.
A list of arguments for the rcax_GET() call. These do not need to be specified by the user unless the user wants to change the default values. table_id This is the CAX table id. It is looked up using tablename and rCAX:::caxpops (an internal dataset). If table_id is passed in via GETargs, it will override the default table id lookup. recordloc This is the name of the record we want in the list returned from the GET call. key is the API key.
Curl options passed to HttpClient
data frame if type="data.frame" (default) and the colnames if type="colnames"
The XPort tables have a few columns that do not appear in the Excel files that one can download from StreamNet: "species", "publish", "num", "hli", "agency", "esudps", "hli_id". "esudps" is a slight variant on "esu_dps" and is removed. "num" is a sort flag and is removed. "hli_id" is an internal reference id and is removed. "publish" will always be Yes but is left in. The other columns are left in. The colnames are re-sorted into the order found in the downloaded Excel files with the extra columns added to the end.
The table columns are sorted into the order that appears in
CAP Fish HLIs Tabular Query.
If you want to see the original columns in the original order,
use cols=1:50, say, to see the first 50 columns in the original
order.
If tabletype="base" is used, the base tables without the added metadata are
returned. The data are the same just missing the extra metadata.
If you want to see only the column names use type="colnames.
# return NMFS_PopID of second record
# Note the part after $ is case sensitive
id <- rcax_hli("NOSA", qlist=list(limit=2))$nmfs_popid[2]
a <- rcax_hli("NOSA",
flist=list(nmfs_popid=id),
cols=c("nmfs_popid", "spawningyear", "tsaej", "nosaej")
)
head(a)
#> nmfs_popid spawningyear tsaej nosaej
#> 1 185 1990 434 19
#> 2 185 1991 39 5
#> 3 185 1992 143 11
#> 4 185 1993 364 13
#> 5 185 1994 1554 91
#> 6 185 1995 1325 105
# First 3 columns
rcax_hli("NOSA", qlist=list(limit=3))[,1:3]
#> commonname run recoverydomain
#> 1 Chinook salmon Spring Interior Columbia
#> 2 Steelhead Summer Interior Columbia
#> 3 Coho salmon Fall Oregon Coast
# to print the first column names and definitions
head(rcax_hli("NOSA", type="colnames"))
#> name
#> 107 age10prop
#> 41 age10proplowerlimit
#> 24 age10propupperlimit
#> 108 age11plusprop
#> 109 age11plusproplowerlimit
#> 62 age11pluspropupperlimit
#> definition
#> 107 The proportion of natural origin fish that were age 10 (brood year +10).
#> 41 Lower limit of the confidence interval for Age10Prop.
#> 24 Upper limit of the confidence interval for Age10Prop.
#> 108 The proportion of natural origin fish that were age 11 (brood year +11) or older.
#> 109 Lower limit of the confidence interval for Age11PlusProp.
#> 62 Upper limit of the confidence interval for Age11PlusProp.