Function reference • snt

Data Integration

sn_get_map_walk_healthcare() sn_get_map_motor_healthcare(): Importation of data from MAP

sn_get_dhs(): Import DHS data from API

sn_get_files(): Smart file reader

sn_get_who_gis_adm2_shp(): Generate ADM2 shapefiles from WHO GIS Hub

sn_read_star(): Read a list of raster data

import_replace(): A helper function to import routine database

import_routine_rename: Database for Rename column names in Routine Data

import_routine_replace: Database for Replace column values in Routine Data

import_routine_replace_hfname: Database for Replace health facilities in Routine Data

import_routine_set_cluster: Database for Set Adm2 Cluster in Routine Data

bind_who_gis_adm2_shp() extract_country_from_who_gis_adm2_shp() extract_adm1_adm2_from_who_gis_adm2_shp() extract_shp_from_gishub(): Generate ADM2 shapefiles from WHO GIS Hub

smart_read_excel_by_year(): Read excel files by year

Data Cleaning

sn_check_dups(): Check for duplicates in a data frame

sn_check_fuzzy(): Fuzzy match

sn_check_laps(): Check laps

sn_check_outliers(): Find outlier

sn_clean_dups(): Merge duplicates in a data frame

sn_clean_missing(): Remove and export missing data

sn_clean_outliers(): Data.table version of find_outliers

sn_clean_str_slice_to_end(): String Util Slice a pattern and append it to the end

sn_clean_str_trim_space(): Replace double space replace two or more spaces with one space

adm_rename(): rename the administrative zone names

routine_rename(): Rename Columns in Routine data

routine_replace(): Replace routine database

Data Transformation

sn_to_lower(): Renaming the dataset to lower case

sn_to_numeric(): Transmute numeric columns to the correct type

sn_gen_assemble(): Assemble data 🈴

sn_gen_dissect(): Dissect data

sn_gen_id(): Generate ID if not exist data.table version

gen_id_if_not_exist(): Generate ID if not exist

sum_maltreat_ov5_by_sex(): Sum maltreat over 5 years old by female and male

sum_maltreat_u5_by_sex(): Sum maltreat under 5 years old by female and male

scale_numbered(): Numbered axis

sn_extract_month_from_year_week(): Extract month from year and week

sn_keep_na_sum(): Sum but keep NA

Data Reduction

sn_st_aggregate() sn_st_crop(): stars aggregate function

sn_reduce_odd_or_even(): Get odd or even rows from a tibble

fuzzy_match_enhanced(): Fuzzy match result Identify and remove duplicate reports

sn_check_fuzzy(): Fuzzy match

Databases

dbq_select(): dbp select

Analysis

sn_ana_adj1(): Calculate the adjusted incidence 1

sn_ana_adj2(): Calculate the adjusted incidence 2

sn_ana_adj3(): Calculate the adjusted incidence 3

sn_ana_report_rate(): report rate

sn_ana_report_status(): Calculate the reporting rate

adjust_incidence_1(): Adjust incidence 1

adjust_incidence_2(): Adjust incidence 2

adjust_incidence_3(): Adjust incidence 3

sn_outbreak(): Outbreak detection

get_report_duration(): Calculate the report duration Get the min max report year and month for each group based on the report status This code filters the data by the reported column to only include data that is reported, then groups the data by the variables specified in the function call. It then calculates the min and max year and month for each group, and then filters out any groups that have NA for the min year.

expected(): Calculate the expected reports

get_by_cols(): Get group by columns

sn_aggregate_by(): Aggregate_by, a helper function for generating the aggregation information

report_rate(): Calculate the reporting rate for each indicator

report_status(): Calculate the report status

sn_antijoin(): Get the anti-join from two dbs

sn_intersect(): Get the intersect from two dbs

sn_unique_diff(): Get the unique values not in compare database

Development

dev_update(): Devtools: development update function all combined in one command

update_database(): Devtools : Update SNT databases

sn_format(): Opinioned formatting function

generate_default_gitignore(): Generate Default .gitignore

mkdir(): Make Directory

type_of_path(): Check type of path

use_relative_or_absolute(): Check to use relative or absolute path

Math

sn_math_mean(): Faster Mean

Plot

sn_theme(): theme default theme for plots

sn_plot_consistency(): Consistency check plot

sn_plot_incidence_by_year(): Plot incidences

sn_plot_outliers(): Plot outliers by year

sn_plot_rainfall(): Generate a rainfall plot

sn_plot_reprat_by_adm(): Plot report rate by adm1

sn_plot_reprat_by_index(): Plot report rate by index

sn_color_false: color False

sn_color_true: color True

align_plots(): align plots Align plots in a grid, with the same width and height in the plot area. Use methods from the cowplot package.

plot_adm1_report_rate(): Plot Report Status by district month

plot_hf_report_status(): Plot Report Status

plot_indicator_report_rate(): Plot Report Status by indicators

plot_map_by_year(): Plot incidences

plot_outliers(): Plot outliers

color: color palette

complementary_color(): compute complementary color

Config

config_set_db() config_get_db() config_parallel() config_get_country(): Config database

generate_default_config(): Generate Default Config

get_os(): Get OS

get_path(): Get path

setup(): Make Structure