Merge pull request #32 from canmod/leaving

This pull request is not really ready but we need to merge now and clean up issues later.

Author: stevencarlislewalker

.github/workflows/R-CMD-check-iidda.analysis.yaml

@@ -49,4 +49,4 @@ jobs:
         with:
           upload-snapshots: true
           working-directory: ./R/iidda.analysis
-          error-on: '"warning"'
+          error-on: '"error"'

R/iidda.analysis/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iidda.analysis
 Type: Package
 Title: Tools for Analyzing IIDDA Datasets
-Version: 1.0.0
+Version: 2.0.0
 Author: Steven Walker
 Maintainer: Steven Walker <[email protected]>
 Description: This package contains tools for working with data
@@ -25,7 +25,8 @@ Imports:
   scales, 
   tidyr, 
   tidyselect,
-  patchwork
+  patchwork,
+  curl
 Suggests:
   knitr,
   rmarkdown,

R/iidda.analysis/NAMESPACE

@@ -1,55 +1,94 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(iidda_defaults,"function")
+S3method(iidda_defaults,data.frame)
+S3method(iidda_defaults,environment)
+S3method(iidda_title,gg)
+S3method(iidda_title,patchwork)
+S3method(variable_guess,"NULL")
+S3method(variable_guess,character)
+S3method(variable_guess,data.frame)
+S3method(variable_guess,list)
 export("%>%")
+export(AttachAvailability)
+export(BasalGroupAdder)
 export(ComputeMovingAverage)
+export(CountAggregator)
+export(CustomDataPrep)
+export(DataDictionaryConverter)
+export(Deheaper)
 export(HandleMissingValues)
 export(HandleZeroValues)
+export(HierarchicalBalancer)
+export(HierarchyNormalizer)
 export(PeriodAggregator)
+export(PeriodDescriber)
 export(SeriesHarmonizer)
+export(Skipper)
+export(TimeRangeDescriber)
 export(TimeScalePicker)
+export(TimeVariableConverter)
+export(TitleGuesser)
 export(TrimSeries)
-export(WaveletDeheaper)
-export(WaveletInterpolator)
-export(WaveletJoiner)
-export(WaveletNormalizer)
-export(WaveletTransformer)
 export(add_user_entries)
+export(basal_group)
 export(browse_pipeline_dependencies)
 export(ca_iso_3166_2)
 export(check_date)
 export(clean_canmod_cdi)
+export(compute_moving_average_default)
+export(count_aggregator_default)
 export(create_bin_desc)
+export(deheaper_default)
 export(factor_time_scale)
 export(find_unaccounted_cases)
 export(generate_empty_df)
 export(generate_user_table)
+export(get_iidda_attr)
 export(get_implied_zeros)
 export(get_unit_labels)
 export(grid_dates)
+export(handle_missing_values_default)
+export(handle_zero_values_default)
+export(harmonize_plots)
+export(iidda_attach_availability)
+export(iidda_attach_bar)
+export(iidda_attach_series)
+export(iidda_availability)
+export(iidda_bar)
+export(iidda_defaults)
+export(iidda_defaults_rm)
 export(iidda_get_metadata)
+export(iidda_ma)
 export(iidda_plot_bar)
 export(iidda_plot_box)
 export(iidda_plot_heatmap)
 export(iidda_plot_highlight)
 export(iidda_plot_ma)
 export(iidda_plot_rohani_heatmap)
-export(iidda_plot_scales)
 export(iidda_plot_settings)
 export(iidda_plot_wavelet)
+export(iidda_prep_availabiliy)
 export(iidda_prep_bar)
 export(iidda_prep_box)
 export(iidda_prep_ma)
 export(iidda_prep_rohani)
 export(iidda_prep_seasonal_heatmap)
 export(iidda_prep_series)
 export(iidda_prep_wavelet)
+export(iidda_render_plot)
+export(iidda_series)
+export(iidda_set_column_types)
 export(iidda_theme)
 export(iidda_theme_above)
+export(iidda_theme_availability_bars)
+export(iidda_theme_availability_heatmap)
 export(iidda_theme_heat)
 export(join_lookup_table)
 export(join_user_table)
 export(log1p_modified_trans)
 export(lookup_join)
+export(magnitude)
 export(make_time_trans)
 export(mid_dates)
 export(mid_times)
@@ -62,12 +101,15 @@ export(normalize_population)
 export(normalize_time_scales)
 export(num_days)
 export(num_days_util)
+export(period_aggregator_default)
 export(period_averager)
+export(period_describer_default)
 export(quantile_trans)
 export(read_iidda_dataset)
 export(resolve_join)
-export(time_scale_picker)
+export(series_harmonizer_default)
 export(titleize)
+export(trim_series_default)
 export(union_series)
 export(valid_time_vars)
 export(year_end_fix)
@@ -82,7 +124,6 @@ importFrom(dplyr,cur_column)
 importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
-importFrom(dplyr,group_by_at)
 importFrom(dplyr,group_split)
 importFrom(dplyr,if_all)
 importFrom(dplyr,if_else)
@@ -101,6 +142,7 @@ importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,union)
 importFrom(ggforce,geom_mark_rect)
+importFrom(ggplot2,aes)
 importFrom(ggplot2,dup_axis)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,geom_boxplot)
@@ -111,12 +153,14 @@ importFrom(ggplot2,geom_polygon)
 importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggplot_build)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_fill_distiller)
 importFrom(ggplot2,scale_fill_gradientn)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_date)
 importFrom(ggplot2,scale_x_datetime)
 importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_continuous)
@@ -128,10 +172,13 @@ importFrom(ggplot2,ylab)
 importFrom(grDevices,axisTicks)
 importFrom(grDevices,rainbow)
 importFrom(iidda,is_empty)
+importFrom(iidda,parse_columns)
 importFrom(iidda,source_from_digitization_id)
 importFrom(iidda,sprintf_named)
+importFrom(iidda,summarise_dates)
 importFrom(iidda,write_data_frame)
 importFrom(janitor,compare_df_cols_same)
+importFrom(lubridate,as_date)
 importFrom(lubridate,as_datetime)
 importFrom(lubridate,days)
 importFrom(lubridate,dhours)
@@ -157,12 +204,14 @@ importFrom(scales,label_number)
 importFrom(scales,rescale)
 importFrom(scales,trans_new)
 importFrom(stats,approx)
+importFrom(stats,end)
 importFrom(stats,median)
 importFrom(stats,na.fail)
 importFrom(stats,na.omit)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,spec.pgram)
+importFrom(stats,start)
 importFrom(stringr,str_ends)
 importFrom(stringr,str_match_all)
 importFrom(stringr,str_remove)

R/iidda.analysis/R/api.R

@@ -8,3 +8,47 @@ need_iidda_api <- function(function_name) {
     )
   }
 }
+
+in_src_for_this_pkg = function() {
+  in_a_pkg = file.exists("DESCRIPTION")
+  if (in_a_pkg) {
+    pkg_in_wd = read.dcf("DESCRIPTION")[1L, "Package"] |> unname()
+    return(pkg_in_wd == "iidda.analysis")
+  }
+  return(FALSE)
+}
+
+cache_data_dictionary = function() {
+  if (in_src_for_this_pkg()) {
+    dict = pull_data_dictionary()
+    if (!is.null(dict)) {
+      cached_dict_path = "inst/iidda-data-dictionary.rdata"
+      saveRDS(dict, file = cached_dict_path)
+    }
+  }
+  invisible(NULL)
+}
+
+## copied from iidda.api
+set_dict_names = function(x) {
+  setNames(x, vapply(x, getElement, character(1L), "name"))
+}
+
+pull_data_dictionary = function() {
+  dict = try(iidda.api::ops_staging$data_dictionary(), silent = TRUE)
+  if (inherits(dict, "try-error")) return(NULL)
+  return(set_dict_names(dict))
+}
+read_data_dictionary = function() {
+  ("iidda-data-dictionary.rdata"
+    |> system.file(package = "iidda.analysis")
+    |> readRDS()
+  )
+}
+
+iidda_data_dictionary = function() {
+  do_pull = "iidda_try_pull_dict" |> getOption() |> isTRUE()
+  dict = if (do_pull) pull_data_dictionary() else NULL
+  if (is.null(dict)) dict = read_data_dictionary()
+  return(dict)
+}