update documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.4.5.9009
+Version: 0.4.5.9010
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

R/add_isotopolog_label.R

@@ -1,19 +1,16 @@
-#' Add isotopolog_label to data
+#' Add isotopolog_label to source data
 #'
 #' To convert from an isotope only dataframe to one with both isotope and
 #' isotopolog_label to satisfy MISIP requirements
 #'
-#' @param data Sample metadata (dataframe)
-#' @param isotope Column name with isotope data (string, default: "isotope")
+#' @param data (*dataframe*) Sample metadata
+#' @param isotope (*string, default: "isotope"*) Column name with isotope data
 #'
 #' @export
 #'
-#' @keywords sample_data
+#' @family "Source Data"
 #'
-#' @note This function also renames your isotope column to "isotope", if it
-#' isn't already.
-#'
-#' @return A dataframe with `isotopolog_label` column added and `isotope` column
+#' @returns A dataframe with `isotopolog_label` column added and `isotope` column
 #' modified
 
 add_isotopolog_label = function(data, isotope = "isotope") {

R/add_taxonomy.R

@@ -1,13 +1,15 @@
 #' Add a taxonomy table to qSIP abundance data
 #'
-#' @param feature_object An object of `qsip_feature_data` class
-#' @param taxa A taxa table
-#' @param id The column name for the taxa ids that match the ids in the
+#' @param feature_object (*qsip_feature_object*) An object of `qsip_feature_data` class
+#' @param taxa (*dataframe*) A taxa table
+#' @param id (*string*) The column name for the taxa ids that match the ids in the
 #' abundance table
 #'
 #' @export
 #'
-#' @keywords abundance
+#' @family "Feature Data"
+#'
+#' @returns An updated `qsip_feature_object` with the taxonomy slot populated with a taxonomy dataframe.
 
 add_taxonomy <- function(feature_object, taxa, feature_id) {
 

R/gradient_pos_density_validation.R

@@ -1,8 +1,8 @@
 #' Check the validity of density values
 #'
-#' @param gradient_pos_density Density value or values (string(s))
-#' @param high A high limit for valid density values (numeric, default: 1.8)
-#' @param low A low limit for valid density values (numeric, default: 1.55)
+#' @param gradient_pos_density (*string or strings*) Density value or values
+#' @param high (*numeric, default: 1.8*) A high limit for valid density values
+#' @param low (*numeric, default: 1.55*) A low limit for valid density values
 #'
 #' @return Returns `NULL` if the density values are valid, or a printed error
 #'

R/gradient_position_validation.R

@@ -3,13 +3,13 @@
 #' Valid gradient positions are integers. The value can be `-1` to represent
 #' "bulk" or non-qSIP samples.
 #'
-#' @param gradient_position Gradient position value or values (string(s))
+#' @param gradient_position (*string or strings*) Gradient position value or values
 #'
-#' @return Returns `NULL` if the gradient position values are valid, or a
+#' @returns `NULL` if the gradient position values are valid, or a
 #' printed error
 #'
 #' @export
-#'
+
 
 gradient_position_validation = function(gradient_position) {
   if (is.numeric(gradient_position)) {

R/isotope_validation.R

@@ -1,23 +1,21 @@
 #' Check the validity of an isotope string
 #'
-#' @param isotope Isotope value or values (string(s))
-#' @param isotope_list Isotopes to check against (strings, default: c("12C", "13C", "14N", "15N", "16O", "18O"))
+#' @param isotope (*string or strings* Isotope value or values
+#' @param isotope_list (*strings, default: c("12C", "13C", "14N", "15N", "16O", "18O")*) Isotopes to check against
 #'
-#' @return Returns `NULL` if the isotope strings are valid, or a printed error
+#' @returns Returns `NULL` if the isotope strings are valid, or a printed error
 #'
 #' @export
 #'
 #' @note The isotope_list may change if isotopolog_label stays a thing. Only the "heavy" isotopes will be allowed.
 
-
 isotope_validation = function(isotope, isotope_list = c("12C", "13C", "14N", "15N", "16O", "18O")) {
 
   if (length(setdiff(isotope, isotope_list)) == 0) {
     return(NULL)
   } else {
     for (error in setdiff(isotope, isotope_list)) {
       message(glue::glue(crayon::red("Invalid isotope found: {error}")))
-
     }
     return("Please fix the isotope names and try again")
   }

R/qsip_feature_data.R

@@ -2,14 +2,14 @@
 #'
 #' A class to hold and validate a feature abundance table
 #'
-#' @slot data A dataframe or tibble
-#' @slot feature_id Column name with unique taxa IDs
+#' @slot data (*dataframe*) ASV/OTU table or equivalent
+#' @slot feature_id (*string*) Column name with unique taxa IDs
 #'
 #' @export
 #' @family "qSIP classes"
 #'
 #' @keywords object
-#' @returns A `qsip_feature_data` that holds a validated feature abundance table.
+#' @returns A validated object of the `qsip_feature_data` type
 
 qsip_feature_data <- S7::new_class(
   "qsip_feature_data",

R/qsip_sample_data.R

@@ -2,21 +2,21 @@
 #'
 #' A class to hold and validate sample data.
 #'
-#' @slot data A dataframe or tibble
-#' @slot sample_id The unique ID for the sample/fraction
-#' @slot source_mat_id The unique ID for the biological subject or replicate
-#' @slot gradient_position Column name with the fraction position
-#' @slot gradient_pos_density Column name with the gradient density
-#' @slot gradient_pos_amt Column name with a total amount per fraction, either
+#' @slot data (*dataframe*) Metadata for samples/fractions
+#' @slot sample_id (*string*) The unique sample ID
+#' @slot source_mat_id (*string*) The unique ID for the biological subject or replicate
+#' @slot gradient_position (*string*) Column name with the fraction position
+#' @slot gradient_pos_density (*string*) Column name with the gradient density
+#' @slot gradient_pos_amt (*string*) Column name with a total amount per fraction, either
 #' qPCR copies or DNA
-#' @slot gradient_pos_rel_amt Column name with the relative fraction abundance
+#' @slot gradient_pos_rel_amt (*string*) Column name with the relative fraction abundance
 #'  compared to the total
-#' @slot fraction_volume The volume loaded onto the column. Required if the `gradient_pos_amt` is reported as a concentration
+#' @slot fraction_volume (*string*) The volume loaded onto the column. Required if the `gradient_pos_amt` is reported as a concentration
 #'
 #' @export
 #' @family "qSIP classes"
 #'
-#' @keywords object
+#' @returns A validated object of the `qsip_sample_data` type
 
 qsip_sample_data <- S7::new_class(
   "qsip_sample_data",

R/qsip_source_data.R

@@ -6,17 +6,16 @@
 #' to also calculate growth then you should use the `qsip_source_data_growth`
 #' object.
 #'
-#' @slot data Source metadata (dataframe)
-#' @slot isotope Isotope name (string)
-#' @slot isotopolog Isotopolog data (string)
-#' @slot source_mat_id The unique ID for the biological subject or source (string)
+#' @slot data (*dataframe*) Source metadata
+#' @slot isotope (*string*) Isotope name
+#' @slot isotopolog (*string*)  Isotopolog data
+#' @slot source_mat_id (*string*) The unique ID for the biological subject or source
 #'
 #' @export
 #'
-#' @keywords object
 #' @family "qSIP classes"
 #'
-#' @return A `qsip_source_data` object
+#' @return A validated `qsip_source_data` object
 
 qsip_source_data <- S7::new_class(
   "qsip_source_data",

_pkgdown.yml

@@ -9,16 +9,25 @@ reference:
   - qsip_source_data
   - qsip_sample_data
   - qsip_feature_data
+
+- title: Source Data
+  contents:
+  - add_isotopolog_data
+  - remove_isotopolog_data
+  - show_comparison_groups
+
 - title: Sample Data
   contents:
-  - has_keyword("sample_data")
   - add_gradient_pos_rel_amt
-- title: Abundance Data
+
+- title: Feature Data
   contents:
-  - has_keyword("abundance")
+  - add_taxonomy
+
 - title: Data
   contents:
   - has_keyword("data")
+
 - title: internal
   contents:
   - abundance_validation