attempted fix for class fails

Author: matthewphamilton

NAMESPACE

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export("crs_nbr_dbl<-")
+export("merge_with_chr_vec<-")
+export("save_type<-")
 export(add_ds_to_dv_repo)
 export(add_dv_meta_to_imp_lup)
 export(add_files_to_dv)
@@ -11,6 +14,7 @@ export(assert_matches_chr)
 export(assert_single_row_tb)
 export(bind_lups)
 export(bind_lups.ready4_dictionary)
+export(crs_nbr_dbl)
 export(download_data)
 export(get_data)
 export(get_data.ready4_dv_import_lup)
@@ -44,6 +48,7 @@ export(make_pt_ready4_dist)
 export(make_pt_ready4_dv_import_lup)
 export(make_pt_ready4_par_struc_mape)
 export(make_r3_from_csv_tb)
+export(merge_with_chr_vec)
 export(read_import_from_csv)
 export(ready4_all_import_lup)
 export(ready4_dictionary)
@@ -52,6 +57,7 @@ export(ready4_dv_import_lup)
 export(ready4_par_struc_mape)
 export(remove_labels_from_ds)
 export(save_raw)
+export(save_type)
 export(transform_csv_col_to_ls_col)
 export(update_src_loc_to_url)
 export(update_src_loc_to_url.ready4_all_import_lup)
@@ -66,6 +72,7 @@ export(write_dv_ds)
 export(write_dv_ds_fls)
 export(write_dv_fl_to_loc)
 export(write_fls_to_dv_ds)
+export(write_paired_ds_fls_to_dv)
 export(write_pkg_dss_to_dv_ds_csvs)
 export(write_to_add_urls_to_dss)
 export(write_to_copy_fls_to_dv_dir)
@@ -130,3 +137,4 @@ importFrom(tidyr,gather)
 importFrom(utils,data)
 importFrom(utils,getFromNamespace)
 importFrom(utils,read.csv)
+importFrom(utils,write.csv)

R/fn_add.R

@@ -139,15 +139,14 @@ add_files_to_dv <- function (files_tb, data_dir_rt_1L_chr = ".", ds_url_1L_chr,
 #' @description add_labels_from_dictionary() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add labels from dictionary. Function argument ds_tb specifies the object to be updated. The function returns Labelled dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param dictionary_tb Dictionary (a tibble)
-#' @param remove_old_lbls_1L_lgl PARAM_DESCRIPTION, Default: F
+#' @param remove_old_lbls_1L_lgl Remove old lbls (a logical vector of length one), Default: F
 #' @return Labelled dataset (a tibble)
 #' @rdname add_labels_from_dictionary
 #' @export 
 #' @importFrom ready4fun remove_lbls_from_df
 #' @importFrom dplyr filter mutate case_when
 #' @importFrom purrr reduce
 #' @importFrom Hmisc label
-#' @keywords internal
 add_labels_from_dictionary <- function (ds_tb, dictionary_tb, remove_old_lbls_1L_lgl = F) 
 {
     if (remove_old_lbls_1L_lgl) 

R/fn_get.R

@@ -44,7 +44,6 @@ get_file_from_dv <- function (ds_ui_1L_chr, fl_nm_1L_chr, save_fmt_1L_chr, repo_
 #' @importFrom purrr map2_chr
 #' @importFrom ready4fun get_from_lup_obj
 #' @importFrom tibble as_tibble
-#' @keywords internal
 get_fl_id_from_dv_ls <- function (ds_ls, fl_nm_1L_chr, nms_chr = NA_character_) 
 {
     if (is.na(nms_chr[1])) {

R/fn_read.R

@@ -1,7 +1,7 @@
 #' Read import from comma separated variables file
 #' @description read_import_from_csv() is a Read function that reads an R script into memory. Specifically, this function implements an algorithm to read import from comma separated variables file. Function argument file_ref_chr specifies the path to object. The function returns Import (a ready4 S3).
 #' @param file_ref_chr File reference (a character vector)
-#' @param is_url_1L_lgl PARAM_DESCRIPTION, Default: F
+#' @param is_url_1L_lgl Is url (a logical vector of length one), Default: F
 #' @return Import (a ready4 S3)
 #' @rdname read_import_from_csv
 #' @export 

R/fn_transform.R

@@ -1,6 +1,6 @@
 #' Transform comma separated variables file column to list column
-#' @description transform_csv_col_to_ls_col() is a Transform function that edits an object in such a way that core object attributes - e.g. shape, dimensions, elements, type - are altered. Specifically, this function implements an algorithm to transform comma separated variables file column to list column. Function argument csv_col specifies the object to be updated. The function returns List column (a list).
-#' @param csv_col_xx PARAM_DESCRIPTION
+#' @description transform_csv_col_to_ls_col() is a Transform function that edits an object in such a way that core object attributes - e.g. shape, dimensions, elements, type - are altered. Specifically, this function implements an algorithm to transform comma separated variables file column to list column. Function argument csv_col_xx specifies the object to be updated. The function returns List column (a list).
+#' @param csv_col_xx Comma separated variables file column (an output object of multiple potential types)
 #' @return List column (a list)
 #' @rdname transform_csv_col_to_ls_col
 #' @export 

R/fn_update.R

@@ -2,8 +2,8 @@
 #' @description update_tb_src_loc_to_url_sgl_tb() is an Update function that edits an object, while preserving core object attributes. Specifically, this function implements an algorithm to update tibble source local to url sgl tibble. Function argument x specifies the object to be updated. Argument y provides the object to be updated. The function returns Updated (a tibble).
 #' @param x An object
 #' @param y PARAM_DESCRIPTION
-#' @param local_to_url_vec_chr PARAM_DESCRIPTION
-#' @param urls_vec_chr PARAM_DESCRIPTION
+#' @param local_to_url_vec_chr Local to url vec (a character vector)
+#' @param urls_vec_chr Urls vec (a character vector)
 #' @return Updated (a tibble)
 #' @rdname update_tb_src_loc_to_url_sgl_tb
 #' @export 

R/fn_write.R

@@ -107,7 +107,6 @@ write_dv_fl_to_loc <- function (ds_ui_1L_chr, fl_nm_1L_chr = NA_character_, fl_i
 #' @importFrom stats setNames
 #' @importFrom purrr map_int
 #' @importFrom dataverse get_dataset
-#' @keywords internal
 write_fls_to_dv_ds <- function (dss_tb, dv_nm_1L_chr, ds_url_1L_chr, wait_time_in_secs_int = 5L, 
     make_local_copy_1L_lgl = F, parent_dv_dir_1L_chr, paths_to_dirs_chr, 
     inc_fl_types_chr = NA_character_, key_1L_chr = Sys.getenv("DATAVERSE_KEY"), 
@@ -138,6 +137,41 @@ write_fls_to_dv_ds <- function (dss_tb, dv_nm_1L_chr, ds_url_1L_chr, wait_time_i
     }
     return(ds_ls)
 }
+#' Write paired dataset files to dataverse
+#' @description write_paired_ds_fls_to_dv() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write paired dataset files to dataverse. The function is called for its side effects and does not return a value. WARNING: This function writes R scripts to your local environment. Make sure to only use if you want this behaviour
+#' @param ds_tb Dataset (a tibble)
+#' @param fl_nm_1L_chr File name (a character vector of length one)
+#' @param desc_1L_chr Description (a character vector of length one)
+#' @param ds_url_1L_chr Dataset url (a character vector of length one), Default: 'https://doi.org/10.7910/DVN/2Y9VF9'
+#' @param pkg_dv_dir_1L_chr Package dataverse directory (a character vector of length one), Default: 'data-raw/dataverse'
+#' @param data_dir_rt_1L_chr Data directory root (a character vector of length one), Default: '.'
+#' @param key_1L_chr Key (a character vector of length one), Default: Sys.getenv("DATAVERSE_KEY")
+#' @param server_1L_chr Server (a character vector of length one), Default: Sys.getenv("DATAVERSE_SERVER")
+#' @return NULL
+#' @rdname write_paired_ds_fls_to_dv
+#' @export 
+#' @importFrom utils write.csv
+#' @importFrom stats setNames
+write_paired_ds_fls_to_dv <- function (ds_tb, fl_nm_1L_chr, desc_1L_chr, ds_url_1L_chr = "https://doi.org/10.7910/DVN/2Y9VF9", 
+    pkg_dv_dir_1L_chr = "data-raw/dataverse", data_dir_rt_1L_chr = ".", 
+    key_1L_chr = Sys.getenv("DATAVERSE_KEY"), server_1L_chr = Sys.getenv("DATAVERSE_SERVER")) 
+{
+    if (!dir.exists(pkg_dv_dir_1L_chr)) 
+        dir.create(pkg_dv_dir_1L_chr)
+    pkg_dv_dir_1L_chr <- paste0(pkg_dv_dir_1L_chr, "/", fl_nm_1L_chr)
+    if (!dir.exists(pkg_dv_dir_1L_chr)) 
+        dir.create(pkg_dv_dir_1L_chr)
+    ds_tb %>% saveRDS(paste0(pkg_dv_dir_1L_chr, "/", fl_nm_1L_chr, 
+        ".RDS"))
+    readRDS(paste0(pkg_dv_dir_1L_chr, "/", fl_nm_1L_chr, ".RDS")) %>% 
+        utils::write.csv(file = paste0(pkg_dv_dir_1L_chr, "/", 
+            fl_nm_1L_chr, ".csv"), row.names = F)
+    make_files_tb(paths_to_dirs_chr = pkg_dv_dir_1L_chr, recode_ls = c(rep(desc_1L_chr, 
+        2)) %>% as.list() %>% stats::setNames(c(rep(fl_nm_1L_chr, 
+        2)))) %>% add_files_to_dv(data_dir_rt_1L_chr = data_dir_rt_1L_chr, 
+        ds_url_1L_chr = ds_url_1L_chr, key_1L_chr = key_1L_chr, 
+        server_1L_chr = server_1L_chr)
+}
 #' Write package datasets to dataverse dataset comma separated variables files
 #' @description write_pkg_dss_to_dv_ds_csvs() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write package datasets to dataverse dataset comma separated variables files. The function returns Dataset (a list).
 #' @param pkg_dss_tb Package datasets (a tibble)
@@ -156,7 +190,6 @@ write_fls_to_dv_ds <- function (dss_tb, dv_nm_1L_chr, ds_url_1L_chr, wait_time_i
 #' @importFrom utils data
 #' @importFrom dplyr mutate_if
 #' @importFrom stringr str_c
-#' @keywords internal
 write_pkg_dss_to_dv_ds_csvs <- function (pkg_dss_tb, dv_nm_1L_chr, ds_url_1L_chr, wait_time_in_secs_int = 5L, 
     dev_pkg_nm_1L_chr = ready4fun::get_dev_pkg_nm(), parent_dv_dir_1L_chr = "../../../../Data/Dataverse", 
     key_1L_chr = Sys.getenv("DATAVERSE_KEY"), server_1L_chr = Sys.getenv("DATAVERSE_SERVER")) 
@@ -177,7 +210,7 @@ write_pkg_dss_to_dv_ds_csvs <- function (pkg_dss_tb, dv_nm_1L_chr, ds_url_1L_chr
 }
 #' Write to add urls to datasets
 #' @description write_to_add_urls_to_dss() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write to add urls to datasets. The function returns Package datasets (a tibble).
-#' @param ds_url_1L_chr PARAM_DESCRIPTION
+#' @param ds_url_1L_chr Dataset url (a character vector of length one)
 #' @param pkg_dss_tb Package datasets (a tibble)
 #' @param pkg_nm_1L_chr Package name (a character vector of length one), Default: ready4fun::get_dev_pkg_nm()
 #' @return Package datasets (a tibble)

R/gs_crs_nbr_dbl.R renamed to R/gnrc_crs_nbr_dbl.R

@@ -1,4 +1,12 @@
 #' crs_nbr_dbl
+#' @description S4 Generic function to get the value of the slot crs_nbr_dbl
+#' @rdname crs_nbr_dbl-methods
+#' @param x An object 
+#' 
+#' @export
+
+methods::setGeneric("crs_nbr_dbl", function(x) standardGeneric("crs_nbr_dbl"))
+#' crs_nbr_dbl
 #' @name crs_nbr_dbl-ready4_script_data
 #' @description Get the value of the slot crs_nbr_dbl for S4 objects of class ready4_script_data
 #' @param x An object of class ready4_script_data
@@ -9,6 +17,15 @@ methods::setMethod("crs_nbr_dbl", methods::className("ready4_script_data"), func
     x@crs_nbr_dbl
 })
 #' crs_nbr_dbl<-
+#' @description S4 Generic function to set the value of the slot crs_nbr_dbl
+#' @rdname crs_nbr_dbl_set-methods
+#' @param x An object 
+#' @param value Value to be assigned to x
+#' 
+#' @export
+
+methods::setGeneric("crs_nbr_dbl<-", function(x, value) standardGeneric("crs_nbr_dbl<-"))
+#' crs_nbr_dbl<-
 #' @name crs_nbr_dbl<--ready4_script_data
 #' @description Set the value of the slot crs_nbr_dbl for S4 objects of class ready4_script_data
 #' @param x An object of class ready4_script_data

R/gs_merge_with_chr_vec.R renamed to R/gnrc_merge_with_chr_vec.R

@@ -1,4 +1,12 @@
 #' merge_with_chr_vec
+#' @description S4 Generic function to get the value of the slot merge_with_chr_vec
+#' @rdname merge_with_chr_vec-methods
+#' @param x An object 
+#' 
+#' @export
+
+methods::setGeneric("merge_with_chr_vec", function(x) standardGeneric("merge_with_chr_vec"))
+#' merge_with_chr_vec
 #' @name merge_with_chr_vec-ready4_local
 #' @description Get the value of the slot merge_with_chr_vec for S4 objects of class ready4_local
 #' @param x An object of class ready4_local
@@ -9,6 +17,15 @@ methods::setMethod("merge_with_chr_vec", methods::className("ready4_local"), fun
     x@merge_with_chr_vec
 })
 #' merge_with_chr_vec<-
+#' @description S4 Generic function to set the value of the slot merge_with_chr_vec
+#' @rdname merge_with_chr_vec_set-methods
+#' @param x An object 
+#' @param value Value to be assigned to x
+#' 
+#' @export
+
+methods::setGeneric("merge_with_chr_vec<-", function(x, value) standardGeneric("merge_with_chr_vec<-"))
+#' merge_with_chr_vec<-
 #' @name merge_with_chr_vec<--ready4_local
 #' @description Set the value of the slot merge_with_chr_vec for S4 objects of class ready4_local
 #' @param x An object of class ready4_local

R/gs_save_type.R renamed to R/gnrc_save_type.R

@@ -1,4 +1,12 @@
 #' save_type
+#' @description S4 Generic function to get the value of the slot save_type
+#' @rdname save_type-methods
+#' @param x An object 
+#' 
+#' @export
+
+methods::setGeneric("save_type", function(x) standardGeneric("save_type"))
+#' save_type
 #' @name save_type-ready4_local_raw
 #' @description Get the value of the slot save_type for S4 objects of class ready4_local_raw
 #' @param x An object of class ready4_local_raw
@@ -9,6 +17,15 @@ methods::setMethod("save_type", methods::className("ready4_local_raw"), function
     x@save_type
 })
 #' save_type<-
+#' @description S4 Generic function to set the value of the slot save_type
+#' @rdname save_type_set-methods
+#' @param x An object 
+#' @param value Value to be assigned to x
+#' 
+#' @export
+
+methods::setGeneric("save_type<-", function(x, value) standardGeneric("save_type<-"))
+#' save_type<-
 #' @name save_type<--ready4_local_raw
 #' @description Set the value of the slot save_type for S4 objects of class ready4_local_raw
 #' @param x An object of class ready4_local_raw