cols did not work if you passed in 1:50

it became integer not numeric

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
@@ -104,15 +104,15 @@ 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)]
     }
   }
   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)]

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

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.

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

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).