Man pages for mrc-ide/specio
Read Spectrum Files
| calc_age_specific_fertility_rate | Calculate ASFR from TFR and fertility distribution. |
| calc_net_migration | Calculate net migration for single years using beers... |
| convert_type | Convert filtered data to correct type. |
| dimensions_age_14_hiv_population | Get dimensions for age 14 hiv population tag. |
| dimensions_agegr_sex_year | Get age group, sex and year dimensions. |
| dimensions_agegr_year | Get age groups between 15 and 49 and year dimensions. |
| dimensions_agegr_year_alternative | Get age groups between 15 and 49 and year dimensions... |
| dimensions_age_sex_year | Get single age between 0 and 80, sex and year dimensions. |
| dimensions_art | Get artdur and year dimensions. |
| dimensions_cd4 | Get CD4 stage and age category dimensions. |
| dimensions_cd4_progress | Get dimensions for adult CD4 progress data. |
| extract_incidence_prevalence | Extract incidence and prevalence for single region. |
| get_agegr_labels | Get the age group labels. |
| get_anc_data | Extract and prepare ANC related data from ProjectionSet. |
| get_array_data | Get array data for a particular property from DP data. |
| get_array_property_data | Get data for an array property from the xml_node. |
| get_art_mortality | Retrieve and tidy ART mortality data. |
| get_art_mortality_rates | Get ART mortality rate data from DP data. |
| get_cd4_array_data | Get array data for a cd4 property from DP data. |
| get_census_data | Extract and prepare census data from ProjectionSet. |
| get_concentrated_epidemic_data | Get concentrated epidemic data from EPP data set. |
| get_conversion_function | Get the relevant conversion function for an xml node. |
| get_data | Get the data from the 'Data' column and onwards if present. |
| get_default_array | Get default array data |
| get_description_indices | Get the indices for which there is a non empty field in the... |
| get_dp_data | Get data from DP file |
| get_eligibility_pop_data | Get ART eligibility population data. |
| get_enum_property | Get character value of enum property from the xml_node. |
| get_eppxml_workset | Get EPP workset from xml file. |
| get_field_data | Get field data from xml node representing serialised field. |
| get_fields | Get field data from parent node. |
| get_filename_from_extension | Get filename from extension. |
| get_hh_survey_data | Extract and prepare HH survey data from ProjectionSet. |
| get_impact_model_params | Extract AIM module parameters. |
| get_incid_prev_results | Get incidence or prevalence as a matrix from the list of... |
| get_last_non_na_column | Get the column index of the last non-NA non-empty column. |
| get_pjn_country | Get country name and code from parsed PJN |
| get_pjn_data | Get data from PJN file |
| get_pjn_metadata | Get projection metadata from PJN file data |
| get_pjn_region | Get subnational region from parsed PJN |
| get_pjn_region_code | Get subnational region code from parsed PJN |
| get_pjnz_csv_data | Get csv data from file contained within PJNZ |
| get_projection_years | Get years of the projection from dp data |
| get_property | Get data for a property in a nodeset. |
| get_property_data | Get data for a property from full dp_data via its tag. |
| get_property_tags | Get tags mapping for a property. |
| get_raw_tag_data | Get the raw data for a particular property within full... |
| get_resample_count | Pull out the count from a string e.g. "COUNT 1.0" |
| get_scale_cd4_mortality | Interpret CD4 mortality scale from version number. |
| get_tag_data | Get a tag from the DP file. |
| get_tag_notes | Get the notes column for a particular property from DP data. |
| get_vector_data | Get vector data for a particular property from DP data. |
| get_women_on_art | Get women on ART data. |
| next_index | Get the next index of a tag. |
| parse_array | Parse xml node containing array to vector. |
| parse_matrix | Parse xml node representing matrix to an R matrix. |
| parse_region_data | Tidy subpopulation data about a specific region. |
| parse_survey | Parse survey data into expected return format. |
| read_art_pop | Extract ART population data from PJNZ file |
| read_data_from_pjnz | Get data from PJNZ file for a single property |
| read_epp_data | Read EPP fitting surveillance data |
| read_epp_subpops | Read EPP subpopulation configuration. |
| read_hiv_pop | Extract people living with HIV (PLHIV) from PJNZ file |
| read_hivproj_param | Read params from DP and PJN file required for HIV model. |
| read_pjn_metadata | Get country name, iso3 code and spectrum region code from... |
| read_spt | Read best fitting HIV incidence and prevalence data from SPT... |
| read_spu | Read EPP uncertainty results from SPU file. |
| read_total_pop | Extract population data from PJNZ file |
| row_contains_data | Check whether a row contains data. |
| tidy_data_for_epp | Tidy data for EPP. |
