From f37e3dd24ee2e6d1a059aaa0f90c2d74b93e77c7 Mon Sep 17 00:00:00 2001 From: Eli Holmes Date: Fri, 9 Dec 2022 09:57:32 -0800 Subject: [PATCH] cols did not work if you passed in 1:50 it became integer not numeric --- R/rcax_table_query.R | 12 ++++++------ docs/articles/basics.html | 12 ++++++------ docs/articles/setup.html | 3 ++- docs/pkgdown.yml | 2 +- docs/reference/rcax_hli_xport.html | 8 +++++--- man-roxygen/xportfuns.R | 8 +++++--- man/rcax_hli_xport.Rd | 6 ++++-- vignettes/basics.Rmd | 3 ++- vignettes/setup.Rmd | 2 +- 9 files changed, 32 insertions(+), 24 deletions(-) diff --git a/R/rcax_table_query.R b/R/rcax_table_query.R index b6594b9..9a64e56 100644 --- a/R/rcax_table_query.R +++ b/R/rcax_table_query.R @@ -38,10 +38,10 @@ rcax_table_query <- function( assert_is(tablename, 'character') assert_is(flist, 'list') assert_is(qlist, 'list') - assert_is(cols, c("numeric", "character")) - if(inherits(cols, "numeric")) if(any(cols<1)) stop("If cols is a number must be greater than 0.") - assert_is(sortcols, c("numeric", "character")) - if(inherits(sortcols, "numeric")) if(any(sortcols<1)) stop("If sortcols is a number must be greater than 0.") + assert_is(cols, c("integer", "numeric", "character")) + if(inherits(cols, c("integer", "numeric"))) if(any(cols<1)) stop("If cols is a number must be greater than 0.") + assert_is(sortcols, c("integer", "numeric", "character")) + if(inherits(sortcols, c("integer", "numeric"))) if(any(sortcols<1)) stop("If sortcols is a number must be greater than 0.") assert_is(GETargs, 'list') # Update GETargs list with any values that the user passed in @@ -104,7 +104,7 @@ rcax_table_query <- function( colnames(tab) <- tolower(colnames(tab)) if(!is.null(cols)){ if(inherits(cols, "character")) cols <- tolower(cols) - if(inherits(cols, "numeric")){ + if(inherits(cols, c("integer", "numeric"))){ cols <- colnames(tab)[cols] if(any(is.na(cols))) warning("cols is an integer and should be between 1 and the numbers of columns in the table. some numbers are not in the table, i.e. negative, 0, or greater than the number of columns. erroneous numbers are dropped.") cols <- cols[!is.na(cols)] @@ -112,7 +112,7 @@ rcax_table_query <- function( } if(!is.null(sortcols)){ if(inherits(sortcols, "character")) sortcols <- tolower(sortcols) - if(inherits(sortcols, "numeric")){ + if(inherits(sortcols, c("integer", "numeric"))){ sortcols <- colnames(tab)[sortcols] if(any(is.na(sortcols))) warning("sortcols is an integer and should be between 1 and the numbers of columns in the table. some numbers are not in the table, i.e. greater than the number of columns. erroneous numbers are dropped.") sortcols <- sortcols[!is.na(sortcols)] diff --git a/docs/articles/basics.html b/docs/articles/basics.html index 215a33f..d660203 100644 --- a/docs/articles/basics.html +++ b/docs/articles/basics.html @@ -115,9 +115,9 @@

Basic functions

-

See the Getting Started vignette -for instructions on installing {rCAX}. Once you have installed {rCAX}, -you can begin using the package by loading the library.

+

See the Getting Started vignette for +instructions on installing {rCAX}. Once you have installed {rCAX}, you +can begin using the package by loading the library.

Load the library.

 library(rCAX)
@@ -214,9 +214,9 @@

Get records from the NOSA XPort t aes(x=spawningyear, y=log(tsaej), color=waterbody)) + geom_line(na.rm = TRUE) + ggtitle("log(total spawners)") -

-Keep in mind that not all ESU and DPS are in the CAX database for each -HLI. Go to https://www.streamnet.org/data/hli/ to do a search to +

+

Keep in mind that not all ESU and DPS are in the CAX database for +each HLI. Go to https://www.streamnet.org/data/hli/ to do a search to quickly see what is available in different HLI tables.

diff --git a/docs/articles/setup.html b/docs/articles/setup.html index 79b6593..f1c11c1 100644 --- a/docs/articles/setup.html +++ b/docs/articles/setup.html @@ -140,7 +140,8 @@

InstallationAPI key

{rCAX} includes a “read-only” API key. Thus you do not need an API -key to use {rCAX}. If you need to use your own key, see .

+key to use {rCAX}. If you need to use your own key, see vignette on the +API GET function.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 24507de..2d0da48 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,7 +7,7 @@ articles: basics: basics.html setup: setup.html terms: terms.html -last_built: 2022-12-09T17:35Z +last_built: 2022-12-09T17:55Z urls: reference: https://nwfsc-math-bio.github.io/rCAX/reference article: https://nwfsc-math-bio.github.io/rCAX/articles diff --git a/docs/reference/rcax_hli_xport.html b/docs/reference/rcax_hli_xport.html index a64cc3c..287ba86 100644 --- a/docs/reference/rcax_hli_xport.html +++ b/docs/reference/rcax_hli_xport.html @@ -190,9 +190,11 @@

Details

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.

+

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.

References

diff --git a/man-roxygen/xportfuns.R b/man-roxygen/xportfuns.R index 398b7ad..bb6efad 100644 --- a/man-roxygen/xportfuns.R +++ b/man-roxygen/xportfuns.R @@ -35,6 +35,8 @@ #' 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. +#' The table columns are sorted into the order that appears in +#' [CAP Fish HLIs Tabular Query](https://www.streamnet.org/data/hli/). +#' 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. diff --git a/man/rcax_hli_xport.Rd b/man/rcax_hli_xport.Rd index 6ee52a3..e4f22b5 100644 --- a/man/rcax_hli_xport.Rd +++ b/man/rcax_hli_xport.Rd @@ -75,9 +75,11 @@ 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 +\href{https://www.streamnet.org/data/hli/}{CAP Fish HLIs Tabular Query}. If you want to see the original columns in the original order, -use \verb{type="colnames} and use the name column of that output as -the value for the \code{cols} argument. +use \code{cols=1:50}, say, to see the first 50 columns in the original +order. } \examples{ # return NMFS_PopID of second record diff --git a/vignettes/basics.Rmd b/vignettes/basics.Rmd index 2137cc8..f8c3779 100644 --- a/vignettes/basics.Rmd +++ b/vignettes/basics.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( ) ``` -See the [Getting Started vignette](articles/setup.html) for instructions on installing {rCAX}. Once you have installed {rCAX}, you can begin using the package by loading the library. +See the [Getting Started vignette](setup.html) for instructions on installing {rCAX}. Once you have installed {rCAX}, you can begin using the package by loading the library. Load the library. ```{r setup} @@ -75,6 +75,7 @@ ggplot( geom_line(na.rm = TRUE) + ggtitle("log(total spawners)") ``` + Keep in mind that not all ESU and DPS are in the CAX database for each HLI. Go to https://www.streamnet.org/data/hli/ to do a search to quickly see what is available in different HLI tables. ## Filtering diff --git a/vignettes/setup.Rmd b/vignettes/setup.Rmd index 78c76f6..6d2296a 100644 --- a/vignettes/setup.Rmd +++ b/vignettes/setup.Rmd @@ -41,4 +41,4 @@ If your version is out of date, update with another call to `install_github()` ( ## API key {rCAX} includes a "read-only" API key. Thus you -do not need an API key to use {rCAX}. If you need to use your own key, see \code{vignette("api_get", package = "rCAX")}. +do not need an API key to use {rCAX}. If you need to use your own key, see vignette on the [API GET function](api_get.html).