Man pages for rlglaubius/SpectrumUtils
Utilities for reading Spectrum files (Title Case)
| dp.extract.time.series | Helper function for extracting a single row of data with one... |
| dp.inputs.adult.art | Get Spectrum adult ART inputs |
| dp.inputs.adult.art.adjustment.value | Extract inputs used to adjust programmatic numbers on ART for... |
| dp.inputs.adult.art.allocation | Check parameters used to determine ART initiation timing |
| dp.inputs.adult.art.initiations | Get input numbers of adults initiating ART |
| dp.inputs.adult.art.ltfu | Get the input percentage of adults on ART who are lost to... |
| dp.inputs.adult.art.monthly | Get numbers of adults on ART by month during 2020-2021 |
| dp.inputs.adult.art.reinitiations | Get input numbers of adults who re-initiated ART |
| dp.inputs.adult.cd4.progression | Get the adult HIV disease progression rates |
| dp.inputs.adult.hiv.mortality.art | HIV-related mortality rates among adults on ART |
| dp.inputs.adult.hiv.mortality.custom | AIM advanced option configuration |
| dp.inputs.adult.hiv.mortality.nonaids | Get rates of non-AIDS excess mortality among adults with HIV |
| dp.inputs.adult.hiv.mortality.off.art | Get HIV-related mortality rates among adults not on ART |
| dp.inputs.adult.hiv.mortality.region | AIM advanced options regional configuration |
| dp.inputs.adult.initial.cd4 | Get the initial distribution of newly-infected adults by CD4... |
| dp.inputs.adult.ltfu.monthly | Get adult ART loss to follow-up inputs by month during... |
| dp.inputs.anc.testing | Get data on HIV testing during antenatal care |
| dp.inputs.art.by.age | Get Spectrum ART by age inputs |
| dp.inputs.art.transmission.reduction | Get the effect of ART on HIV transmission |
| dp.inputs.child.art | Get Spectrum child HIV treatment inputs |
| dp.inputs.child.art.initiations | Get input numbers of children initiating ART |
| dp.inputs.child.art.ltfu | Get the input percentage of children on ART who are lost to... |
| dp.inputs.child.art.reinitiations | Get input numbers of children who re-initiated ART |
| dp.inputs.child.art.uptake | ART uptake in children by age and year |
| dp.inputs.covid19.deaths | Get COVID-19 deaths inputs |
| dp.inputs.covid19.enabled | Check if COVID-19 inputs are enabled |
| dp.inputs.covid19.pattern | Get the input age distribution of COVID-19 deaths |
| dp.inputs.csavr.data.options | Check which data were selected for CSAVR incidence estimation |
| dp.inputs.csavr.deaths.source | Get input numbers of AIDS deaths used by CSAVR to estimate... |
| dp.inputs.csavr.diagnoses | Get input numbers of overall new HIV diagnoses |
| dp.inputs.csavr.diagnoses.cd4 | Get input numbers of new HIV diagnoses by CD4 category |
| dp.inputs.csavr.diagnoses.sex | Get input numbers of new HIV diagnoses by sex |
| dp.inputs.csavr.diagnoses.sex.age | Get input numbers of new HIV diagnoses by sex and age |
| dp.inputs.csavr.irr.options | Check if incidence rate ratios (IRRs) by sex or age were... |
| dp.inputs.csavr.migr.diagnoses | Get new diagnoses among in-migrants |
| dp.inputs.csavr.model | Get the model used to estimate incidence in CSAVR |
| dp.inputs.deaths.art.allcause | Get all-cause deaths among adult PLHIV on ART |
| dp.inputs.e0.default | Get the default input life expectancy at birth |
| dp.inputs.epp.adjustment.cap | Get the maximum amount that AIM can adjust incidence... |
| dp.inputs.epp.adjustment.enabled | Check if AIM is allowed to adjust HIV incidence from EPP |
| dp.inputs.epp.epidemic.first.year | Get the first year of HIV incidence estimated by EPP |
| dp.inputs.epp.epidemic.type | Get the epidemic type specified in EPP |
| dp.inputs.external.pop | Get the external population inputs used to calculate... |
| dp.inputs.first.year | Spectrum projection time span |
| dp.inputs.hiv.abortion | Data on abortions among HIV-positive women |
| dp.inputs.hiv.breastfeeding | Get breastfeeding patterns in mothers with HIV |
| dp.inputs.hiv.frr.age | Get HIV-related fertility adjustments by age |
| dp.inputs.hiv.frr.art | Get HIV-related fertility adjustments on ART |
| dp.inputs.hiv.frr.cd4 | Get HIV-related fertility adjustments by CD4 cell count |
| dp.inputs.hiv.frr.location | Get the HIV-related fertility local adjustment factor |
| dp.inputs.hiv.testing | Extract HIV testing program data |
| dp.inputs.incidence | Get Spectrum input HIV incidence |
| dp.inputs.incidence.model | Get the model used to estimate incidence in a Spectrum... |
| dp.inputs.irr.age | Get Spectrum inputs describing incidence by age and sex |
| dp.inputs.kos.data | Get input numbers of people living with HIV who know their... |
| dp.inputs.kos.source | Get the source indicated for number who know their HIV+... |
| dp.inputs.life.table | Get the input life table selection |
| dp.inputs.migr.plhiv | Get inputs numbers of in-migrants living with HIV |
| dp.inputs.nosocomial.infections | Nosocomial infections among children |
| dp.inputs.pmtct | Get PMTCT inputs |
| dp.inputs.pop.country | Get the national population entered in a subnational... |
| dp.inputs.pop.percent | Get the percentage of the national population living in a... |
| dp.inputs.shiny90.program | Get inputs used to estimate knowledge of HIV status |
| dp.inputs.survey.art.coverage | Get ART coverage data entered from household surveys |
| dp.inputs.survey.hiv.prevalence | Get HIV prevalence data entered from household surveys |
| dp.inputs.tfr | Spectrum demographic inputs |
| dp.inputs.use.external.pop | Check whether an external population was specified |
| dp.inputs.viral.suppression | Get viral suppression inputs |
| dp.output.art.50plus | Get inputs saved for EPP |
| dp.output.art.initiations | Get the number of people initiating ART |
| dp.output.art.need | Get Spectrum's calculated number in need of ART |
| dp.output.artpop | Get Spectrum's calculated HIV-positive population on ART |
| dp.output.bigpop | Get Spectrum's calculated population |
| dp.output.births | Get Spectrum's calculated number of births |
| dp.output.cd4.15_up | Get Spectrum's estimate of adult PLHIV by CD4 category |
| dp.output.child.hiv.14 | Get numbers of 14-year-olds living with HIV |
| dp.output.csavr.deaths.hiv | CSAVR estimates |
| dp.output.deaths.art | Get Spectrum's calculated HIV-related deaths among PLHIV on... |
| dp.output.deaths.hiv | Get Spectrum's calculated HIV-related deaths |
| dp.output.deaths.nonaids.excess | Get estimates of non-AIDS excess deaths |
| dp.output.deaths.nonhiv | Get Spectrum's calculated HIV-unrelated deaths |
| dp.output.hivpop | Get Spectrum's calculated HIV-positive population |
| dp.output.imr | Get Spectrum's calculated infant mortality rate |
| dp.output.incident.hiv | Get Spectrum's calculated new HIV infections |
| dp.output.pmtct | Get Spectrum PMTCT outputs |
| dp.output.ua.data | Extract uncertainty analysis data |
| dp.status.projection.valid | Check whether the projection was valid when last saved |
| extract.geo.info | Read Spectrum geographic metadata |
| extract.proj.name | Read the projection name |
| extract.raw.tag | Extract specific Spectrum data |
| ha.inputs.condom.use | HIV program coverage inputs |
| ha.inputs.configuration | Extract inputs listed in the Goals ASM "Configure" form |
| ha.inputs.final.year | Get the final year of a Spectrum projection |
| ha.inputs.first.year | Get the first year of a Spectrum projection |
| ha.inputs.fitdata.trend | Data for model calibration |
| ha.inputs.keypop.size | Get input key population sizes |
| ha.inputs.lifetime.partners | Extract Goals ASM behavioral inputs |
| ha.inputs.transmission | Extract inputs listed in the Goals ASM "Epidemiology" form |
| ha.output.population.reached | Get the number of people reached by HIV interventions |
| ha.output.transmitted | Get the number of infections transmitted |
| read.module.data | Load Spectrum module data |
| read.raw.dp | Load Spectrum DemProj module data |
| read.raw.ha | Load Spectrum Goal ASM module data |
| read.raw.pjn | Read Spectrum projection parameters |
| read.raw.spu | Read HIV uncertainty data |
| spu.indicator.data | Reformat SPU data as a data frame |
