========
-`rCAX` is an R client for the [Coordinated Assessments API](https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/). Coordinated Assessments data eXchange (CAX) is developed by the Coordinated Assessments Partnership (CAP). CAP is a collaborative process to efficiently share and provide access to standardized derived information, such as fish population-scale high-level indicators (HLIs) and supporting metrics. Participants in CAP include state fish and wildlife management agencies, tribes, federal agencies such as National Oceanic and Atmospheric Administration Fisheries (NOAA Fisheries) and Bonneville Power Administration (BPA), and others. CAP is co-sponsored by StreamNet and Pacific Northwest Aquatic Monitoring Partnership (PNAMP). Make sure to review the [StreamNet Terms of Use](https://nwfsc-math-bio.github.io/rCAX/articles/terms.html) for these data, the [StreamNet Data Policy](https://www.streamnet.org/resources/exchange-tools/data-agreements/) and the citation information from [StreamNet](https://www.streamnet.org/resources/citing-sn/) and [PNAMP](https://www.pnamp.org/project/data-citation-and-attribution) for database queries. *rCAX authors: Eli Holmes and Mari Williams, Northwest Fisheries Science Center, NOAA Fisheries.*
+`rCAX` is an R client for the [Coordinated Assessments API](https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/). Coordinated Assessments data eXchange (CAX) is developed by the Coordinated Assessments Partnership (CAP). CAP is a collaborative process to efficiently share and provide access to standardized derived information, such as fish population-scale high-level indicators (HLIs) and supporting metrics. Participants in CAP include state fish and wildlife management agencies, tribes, federal agencies such as National Oceanic and Atmospheric Administration Fisheries (NOAA Fisheries) and Bonneville Power Administration (BPA), and others. CAP is co-sponsored by StreamNet and Pacific Northwest Aquatic Monitoring Partnership (PNAMP). Make sure to review the [StreamNet Terms of Use](https://nwfsc-cb.github.io/rCAX/articles/terms.html) for these data, the [StreamNet Data Policy](https://www.streamnet.org/resources/exchange-tools/data-agreements/) and the citation information from [StreamNet](https://www.streamnet.org/resources/citing-sn/) and [PNAMP](https://www.pnamp.org/project/data-citation-and-attribution) for database queries. *rCAX authors: Eli Holmes and Mari Williams, Northwest Fisheries Science Center, NOAA Fisheries.*
## Installation
@@ -34,11 +34,11 @@ You can check your installed version versus that on GitHub at any time using `rc
## Contributing
-Fork and put in a pull request!
+Fork and put in a pull request! The documentation is provided via a pkgdown site. After changing files run `pkgdown::build_site()`.
## Contributors
-[](https://github.com/nwfsc-cb/rCAX/graphs/contributors)
+[](https://github.com/nwfsc-cb/rCAX/graphs/contributors)
See also
Returns the base HLI table which is missing the -additional metadata (such as NMFS_PopID and update dates) found in the XPort tables.
-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(esu_dps="Salmon, Chinook (Snake River spring/summer-run ESU)")return values for one ESU. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
If you want to see only the column names use
-type="colnames.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return popid of first record
-# Note the part after $ is case sensitive
-id <- rcax_pni(qlist=list(limit=1))$popid
-
-# Return the table for this id
-a <- rcax_pni(
- flist=list(popid=id),
- cols=c("popid", "spawningyear", "pniej")
- )
-head(a)
-#> popid spawningyear pniej
-#> 1 15 1985 1.00
-#> 2 15 1986 1.00
-#> 3 15 1987 1.00
-#> 4 15 1988 1.00
-#> 5 15 1989 0.98
-#> 6 15 1990 0.69
-
-# First 3 columns
-rcax_pni(qlist=list(limit=3))[,1:3]
-#> popid metriclocation
-#> 1 15
-#> 2 47
-#> 3 512 https://docs.cbfwl.org/StreamNet_References/WAsn17274.pdf
-#> popfitnotes
-#> 1
-#> 2 Nason Creek Spring Chinook Portion of Wenatchee Spring Chinook
-#> 3 Whole population
-
-# to print the first column names and definitions
-head(rcax_pni(type="colnames"))
-#> name
-#> 1 popid
-#> 2 metriclocation
-#> 3 popfitnotes
-#> 4 datastatus
-#> 5 cbfwapopname
-#> 6 methodnumber
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 Where this supporting metric is maintained at the source.
-#> 3 Text description of why the data are not at the scale of a single population.
-#> 4 "Draft", "Reviewed", or "Final".
-#> 5 Population name defined by CBFWA for subbasin planning.
-#> 6 When an organization provides > 1 estimate per year, this number identifies which method was used.
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_pni(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "popid" "metriclocation" "popfitnotes" "datastatus"
-#> [5] "cbfwapopname"
-
-Return PNI table from CAP Fish HLIs Tabular Query
- Source:R/rcax_pni_xport.R
- rcax_pni_xport.RdReturns the HLI table with some additional metadata (such as NMFS_PopID and update dates). -This is the table that one can download from the -CAP Fish HLIs Tabular Query.
-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. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
The XPORT tables have a few columns that do not appear in the -Excel files that -one can download from StreamNet because they come from the -html form for the HLI Tablular Query for filtering the data: -"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" -is the shortened HLI code 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.
-If you want to see the original columns in the original order,
-use type="colnames and use the name column of that output as
-the value for the cols argument.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return NMFS_PopID of first record
-# Note the part after $ is case sensitive
-id <- rcax_pni_xport(qlist=list(limit=1))$nmfs_popid
-
-# Return the table for this id
-a <- rcax_pni_xport(
- flist=list(nmfs_popid=id),
- cols=c("nmfs_popid", "spawningyear", "pniej")
- )
-head(a)
-#> nmfs_popid spawningyear pniej
-#> 1 93 1985 1.00
-#> 2 93 1986 1.00
-#> 3 93 1987 1.00
-#> 4 93 1988 1.00
-#> 5 93 1989 0.98
-#> 6 93 1990 0.69
-
-# First 3 columns
-rcax_pni_xport(qlist=list(limit=3))[,1:3]
-#> commonname run recoverydomain
-#> 1 Chinook salmon Spring Interior Columbia
-#> 2 Chinook salmon Spring Interior Columbia
-#> 3 Chinook salmon Summer Interior Columbia
-
-# to print the first column names and definitions
-head(rcax_pni_xport(type="colnames"))
-#> name
-#> 1 popid
-#> 2 metriclocation
-#> 3 popfitnotes
-#> 4 datastatus
-#> 5 species
-#> 6 hli_lastupdated
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 Where this supporting metric is maintained at the source.
-#> 3 Text description of why the data are not at the scale of a single population.
-#> 4 "Draft", "Reviewed", or "Final".
-#> 5 Species: Chinook salmon, Chum salmon, Coho salmon, Sockeye salmon, Steelhead
-#> 6 Timestamp when an HLI was last updated in a specific record.
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_pni_xport(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "commonname" "run" "recoverydomain" "esu_dps"
-#> [5] "majorpopgroup"
-
-Returns the base HLI table which is missing the -additional metadata (such as NMFS_PopID and update dates) found in the XPort tables.
-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(esu_dps="Salmon, Chinook (Snake River spring/summer-run ESU)")return values for one ESU. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
If you want to see only the column names use
-type="colnames.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return popid of first record
-# Note the part after $ is case sensitive
-id <- rcax_presmolt(qlist=list(limit=1))$popid
-
-# Make a plot of one population
-a <- rcax_presmolt(flist=list(popid=id))
-library(ggplot2)
-ggplot(a, aes(x=surveyyear, y=abundance, color=waterbody)) +
- geom_line()
-
-
-# First 3 columns
-rcax_presmolt(qlist=list(limit=3))[,1:3]
-#> popid generalapproach
-#> 1 398 Mark/recapture estimate
-#> 2 398 Mark/recapture estimate
-#> 3 1058 Snorkeling
-#> metriclocation
-#> 1 https://www.okanoganmonitoring.org/HRT/Grid/ElectroJuvenileEstimate/-1
-#> 2 https://www.okanoganmonitoring.org/HRT/Grid/ElectroJuvenileEstimate/-1
-#> 3
-
-# to print the first column names and definitions
-head(rcax_presmolt(type="colnames"))
-#> name
-#> 1 popid
-#> 2 generalapproach
-#> 3 metriclocation
-#> 4 popfitnotes
-#> 5 age0proplowerlimit
-#> 6 datastatus
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 The general class of method(s) used to make the abundance estimate.
-#> 3 Where this supporting metric is maintained at the source.
-#> 4 Text description of why the data are not at the scale of a single population.
-#> 5 Lower limit of the confidence interval for Age0Prop.
-#> 6 "Draft", "Reviewed", or "Final".
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_presmolt(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "popid" "generalapproach" "metriclocation"
-#> [4] "popfitnotes" "age0proplowerlimit"
-
-Return Presmolt Abundance table from CAP Fish HLIs Tabular Query
- Source:R/rcax_presmolt_xport.R
- rcax_presmolt_xport.RdReturns the HLI table with some additional metadata (such as NMFS_PopID and update dates). -This is the table that one can download from the -CAP Fish HLIs Tabular Query.
-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. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
The XPORT tables have a few columns that do not appear in the -Excel files that -one can download from StreamNet because they come from the -html form for the HLI Tablular Query for filtering the data: -"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" -is the shortened HLI code 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.
-If you want to see the original columns in the original order,
-use type="colnames and use the name column of that output as
-the value for the cols argument.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return NMFS_PopID of first record
-# Note the part after $ is case sensitive
-id <- rcax_presmolt_xport(qlist=list(limit=1))$nmfs_popid
-
-# Make a plot of one population
-a <- rcax_presmolt_xport(flist=list(nmfs_popid=id))
-library(ggplot2)
-ggplot(a, aes(x=surveyyear, y=abundance, color=waterbody)) +
- geom_line() +
- ggtitle(a$populationname[1])
-
-
-# First 3 columns
-rcax_presmolt_xport(qlist=list(limit=3))[,1:3]
-#> commonname run recoverydomain
-#> 1 Chinook salmon Spring Interior Columbia
-#> 2 Chinook salmon Spring Interior Columbia
-#> 3 Coho salmon Fall Oregon Coast
-
-# to print the first column names and definitions
-head(rcax_presmolt_xport(type="colnames"))
-#> name
-#> 1 popid
-#> 2 generalapproach
-#> 3 metriclocation
-#> 4 popfitnotes
-#> 5 age0proplowerlimit
-#> 6 datastatus
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 The general class of method(s) used to make the abundance estimate.
-#> 3 Where this supporting metric is maintained at the source.
-#> 4 Text description of why the data are not at the scale of a single population.
-#> 5 Lower limit of the confidence interval for Age0Prop.
-#> 6 "Draft", "Reviewed", or "Final".
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_presmolt_xport(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "commonname" "run" "recoverydomain" "esu_dps"
-#> [5] "majorpopgroup"
-
-Returns the base HLI table which is missing the -additional metadata (such as NMFS_PopID and update dates) found in the XPort tables.
-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(esu_dps="Salmon, Chinook (Snake River spring/summer-run ESU)")return values for one ESU. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
If you want to see only the column names use
-type="colnames.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return popid of first record
-# Note the part after $ is case sensitive
-id <- rcax_rpers(qlist=list(limit=1))$popid
-
-a <- rcax_rpers(
- flist=list(popid=id),
- cols=c("popid", "broodyear", "rpers")
- )
-head(a)
-#> popid broodyear rpers
-#> 1 276 1974 2.47
-#> 2 276 1975 6.53
-#> 3 276 1976 4.94
-#> 4 276 1977 80.16
-#> 5 276 1978 13.86
-#> 6 276 1979 9.94
-
-# First 3 columns
-rcax_rpers(qlist=list(limit=3))[,1:3]
-#> popid yoy metriclocation
-#> 1 29 Excel workbook maintained by biologist in contact information
-#> 2 36 Excel workbook maintained by biologist in contact information
-#> 3 276 http://odfwrecoverytracker.org/
-
-# to print the first column names and definitions
-head(rcax_rpers(type="colnames"))
-#> name
-#> 1 popid
-#> 2 yoy
-#> 3 metriclocation
-#> 4 popfitnotes
-#> 5 datastatus
-#> 6 age4adults
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 Total number of juvenile recruits (parr or smolts) at age 0 (brood year +0).
-#> 3 Where this supporting metric is maintained at the source.
-#> 4 Text description of why the data are not at the scale of a single population.
-#> 5 "Draft", "Reviewed", or "Final".
-#> 6 Total number of adult recruits that were age 4 (brood year +4).
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_rpers(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "popid" "yoy" "metriclocation" "popfitnotes"
-#> [5] "datastatus"
-
-Return RperS table from CAP Fish HLIs Tabular Query
- Source:R/rcax_rpers_xport.R
- rcax_rpers_xport.RdReturns the HLI table with some additional metadata (such as NMFS_PopID and update dates). -This is the table that one can download from the -CAP Fish HLIs Tabular Query.
-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. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
The XPORT tables have a few columns that do not appear in the -Excel files that -one can download from StreamNet because they come from the -html form for the HLI Tablular Query for filtering the data: -"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" -is the shortened HLI code 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.
-If you want to see the original columns in the original order,
-use type="colnames and use the name column of that output as
-the value for the cols argument.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return NMFS_PopID of first record
-# Note the part after $ is case sensitive
-id <- rcax_rpers_xport(qlist=list(limit=1))$nmfs_popid
-
-a <- rcax_rpers_xport(
- flist=list(nmfs_popid=id),
- cols=c("nmfs_popid", "broodyear", "rpers")
- )
-head(a)
-#> nmfs_popid broodyear rpers
-#> 1 145 1974 2.47
-#> 2 145 1975 6.53
-#> 3 145 1976 4.94
-#> 4 145 1977 80.16
-#> 5 145 1978 13.86
-#> 6 145 1979 9.94
-
-# First 3 columns
-rcax_rpers_xport(qlist=list(limit=3))[,1:3]
-#> commonname run recoverydomain
-#> 1 Chinook salmon Spring/summer Interior Columbia
-#> 2 Chinook salmon Spring/summer Interior Columbia
-#> 3 Coho salmon Both early and late Willamette/Lower Columbia
-
-# to print the first column names and definitions
-head(rcax_rpers_xport(type="colnames"))
-#> name
-#> 1 yoy
-#> 2 metriclocation
-#> 3 popfitnotes
-#> 4 species
-#> 5 age8adults
-#> 6 totalspawnersupperlimit
-#> definition
-#> 1 Total number of juvenile recruits (parr or smolts) at age 0 (brood year +0).
-#> 2 Where this supporting metric is maintained at the source.
-#> 3 Text description of why the data are not at the scale of a single population.
-#> 4 Species: Chinook salmon, Chum salmon, Coho salmon, Sockeye salmon, Steelhead
-#> 5 Total number of adult recruits that were age 8 (brood year +8).
-#> 6 Upper limit of the confidence interval for TotalSpawners.
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_rpers_xport(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "commonname" "run" "recoverydomain" "esu_dps"
-#> [5] "majorpopgroup"
-
-Returns the base HLI table which is missing the -additional metadata (such as NMFS_PopID and update dates) found in the XPort tables.
-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(esu_dps="Salmon, Chinook (Snake River spring/summer-run ESU)")return values for one ESU. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
If you want to see only the column names use
-type="colnames.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return popid of first record
-# Note the part after $ is case sensitive
-id <- rcax_sar(qlist=list(limit=1))$popid
-
-a <- rcax_sar(
- flist=list(popid=id),
- cols=c("popid", "outmigrationyear", "sar")
- )
-head(a)
-#> popid outmigrationyear sar
-#> 1 60 2007 4.20
-#> 2 60 2007 2.45
-#> 3 60 2008 6.74
-#> 4 60 2008 3.57
-#> 5 60 2009 2.05
-#> 6 60 2009 3.77
-
-# First 3 columns
-rcax_sar(qlist=list(limit=3))[,1:3]
-#> popid tsoalpha metriclocation
-#> 1 12
-#> 2 60
-#> 3 113 0.05
-
-# to print the first column names and definitions
-head(rcax_sar(type="colnames"))
-#> name
-#> 1 popid
-#> 2 tsoalpha
-#> 3 metriclocation
-#> 4 popfitnotes
-#> 5 tar
-#> 6 datastatus
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 The significance level for the TSO confidence interval, expressed as alpha.
-#> 3 Where this supporting metric is maintained at the source.
-#> 4 Text description of why the data are not at the scale of a single population.
-#> 5 Total adult return. Number of adults returning for the first time from the indicated outmigration year, or the group of marked smolts (as appropriate), to match the outmigrants in the TSO field.
-#> 6 "Draft", "Reviewed", or "Final".
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_sar(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "popid" "tsoalpha" "metriclocation" "popfitnotes"
-#> [5] "tar"
-
-Return SAR table from CAP Fish HLIs Tabular Query
- Source:R/rcax_sar_xport.R
- rcax_sar_xport.RdReturns the HLI table with some additional metadata (such as NMFS_PopID and update dates). -This is the table that one can download from the -CAP Fish HLIs Tabular Query.
-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. UserCAX:::caxesuto see a list of ESU_DPS names.
-
Arguments
-- tablename -
(character) The CAX name for the table; ignored if
GETargs$table_idpassed in.
-
-
-- flist -
A filter for the query. See details and
rcax_filter()
-
-
-- qlist -
Additional query params. See
rcax_table_query()for details.
-
-
-- cols -
column names to return. Use cols=NULL if you want all columns
-
-
-- sortcols -
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")
-
-
-- type -
whether to return the table ("data.frame") or colnames with definitions ("colnames"). Default is to return the table as a data frame.
-
-
-- GETargs -
A list of arguments for the
rcax_GET()call. These do not normally need to be specified by the user.table_idThis is the CAX table id. It is looked up usingtablenameandrCAX:::caxpops(an internal dataset).recordlocThis is the name of the record we want in the list returned from the GET call.keyis the API key. Seevignette("setup", package = "rCAX")for API key details.
-
-
-- ... -
Curl options passed to
HttpClient
-
-
Value
- - -data frame if type="data.frame" (default) and the colnames if type="colnames"
Details
-The table_id is set automatically using a saved data frame from a rcax_tables() call. The table is saved in R/sysdata.rda.
The XPORT tables have a few columns that do not appear in the -Excel files that -one can download from StreamNet because they come from the -html form for the HLI Tablular Query for filtering the data: -"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" -is the shortened HLI code 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.
-If you want to see the original columns in the original order,
-use type="colnames and use the name column of that output as
-the value for the cols argument.
References
-API docs at https://www.streamnet.org/resources/exchange-tools/rest-api-documentation/
-See also
- -Examples
-# return NMFS_PopID of first record
-# Note the part after $ is case sensitive
-id <- rcax_sar_xport(qlist=list(limit=1))$nmfs_popid
-
-a <- rcax_sar_xport(
- flist=list(nmfs_popid=id),
- cols=c("nmfs_popid", "outmigrationyear", "sar")
- )
-head(a)
-#> nmfs_popid outmigrationyear sar
-#> 1 251 2007 4.20
-#> 2 251 2007 2.45
-#> 3 251 2008 6.74
-#> 4 251 2008 3.57
-#> 5 251 2009 2.05
-#> 6 251 2009 3.77
-
-# First 3 columns
-rcax_sar_xport(qlist=list(limit=3))[,1:3]
-#> commonname run recoverydomain
-#> 1 Chinook salmon Spring Interior Columbia
-#> 2 Steelhead Winter Interior Columbia
-#> 3 Coho salmon Fall Oregon Coast
-
-# to print the first column names and definitions
-head(rcax_sar_xport(type="colnames"))
-#> name
-#> 1 popid
-#> 2 tsoalpha
-#> 3 metriclocation
-#> 4 popfitnotes
-#> 5 tar
-#> 6 datastatus
-#> definition
-#> 1 StreamNet code for the population of fish.
-#> 2 The significance level for the TSO confidence interval, expressed as alpha.
-#> 3 Where this supporting metric is maintained at the source.
-#> 4 Text description of why the data are not at the scale of a single population.
-#> 5 Total adult return. Number of adults returning for the first time from the indicated outmigration year, or the group of marked smolts (as appropriate), to match the outmigrants in the TSO field.
-#> 6 "Draft", "Reviewed", or "Final".
-
-# to print the first 5 column names as they appear
-# in Excel files downloaded from https://www.streamnet.org/data/hli/
-tab <- rcax_sar_xport(qlist=list(limit=1))
-colnames(tab)[1:5]
-#> [1] "commonname" "run" "recoverydomain" "esu_dps"
-#> [5] "majorpopgroup"
-
-