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---
title: "Personalized Monitoring of HIV Viral Load Through Prognostic Healthcare (#179)"
author: "IeDEA | FIMP"
---
```{r setup, include=FALSE}
options(java.parameters = "-Xmx15g")
knitr::opts_chunk$set(warning=FALSE,
message=FALSE,
echo=FALSE,
#dpi=96,
# fig.width=7,# fig.height=4, # Default figure widths
# dev="png", #dev.args=list(type="cairo"), # The png device
# Change to dev="postscript" if you want the EPS-files
# for submitting. Also remove the dev.args() as the postscript
# doesn't accept the type="cairo" argument.
error=FALSE)
# Evaluate the figure caption after the plot
#knitr::opts_knit$set(eval.after='fig.cap')
# Use the table counter that the htmlTable() provides
options(table_counter = TRUE)
# Use the figCapNo() with roman letters
#options(fig_caption_no_roman = TRUE)
#options(kableExtra.latex.load_packages = F)
# Then install the Grmd-package by running below code:
#devtools::install_github("gforge/Grmd")
# function to install missing packages
ipak <- function(pkg){
new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
if (length(new.pkg))
install.packages(new.pkg, dependencies = TRUE, repos='http://cran.rstudio.com/')
sapply(pkg, require, character.only = TRUE)
}
#install.packages('package_name', dependencies=TRUE, repos='http://cran.rstudio.com/')
packages =c( "dplyr", "readxl","Hmisc","Gmisc", "magrittr", "flextable", "MASS", "tidyverse", "caret", "knitr", "kableExtra","xtable", "stargazer", "ggpubr", "haven", "PerformanceAnalytics", "naniar", "gridExtra", "ggthemes", "TSstudio")
ipak(packages)
# packages not pubished
#devtools::install_github("kassambara/easyGgplot2")
library(easyGgplot2)
# packages not pubished
#devtools::install_github('cttobin/ggthemr')
#library(ggthemr)
select = dplyr::select; summarize = dplyr::summarize; rename = dplyr::rename; mutate = dplyr::mutate;
#ggthemr("flat")
#source("unbalanced_functions.R")
source("table1_utils.R")
```
```{r warning=FALSE}
rural.cb <- tibble::tribble(
~code, ~label,
1,'Urban', 2,'Mostly urban', 3,'Mostly rural', 4,'Rural', 9,'Unknown'
)
level.cb <- tibble::tribble(
~code, ~label,
1,'Health centre',2,'District hospital',3,'Regional, provincial or university hospital',9,'Unknown'
)
civstfmt.cb <- tibble::tribble(
~code, ~label,
1,'Never Married and Not Living w/Partner',2,'Legally Married',3,'Living w/Partner',4,'Separated',5,'Divorced',6,'Widowed'
)
entptfmt.cb <- tibble::tribble(
~code, ~label,
1,'outpatient care',2,'inpatient care',3,'pmtct care',4,'TB ward care',
5,'community-based org',6,'private care',7,'self-referral',8,'other',
9,'RTC (routine testing and counseling)',10,'VCT',11,'HCT(home-based)',
12,'MCH (mother child health)',13,'TB clinic',14,'Research Institute',15,'Family Member',
16,'Transfer-In',17,'STI Clinic',18,'Unknown',19,'Exposed infant',20,'Under 5 yrs',
21,'IDU outreach',22,'YYC(Young Child Clinic)'
)
pillfmt.cb <- tibble::tribble(
~code, ~label,
1,'none',2,'very few',3,'about half',4,'most',5,'all'
)
adhfmt.cb <- tibble::tribble(
~code, ~label,
1,'Good: 3 or fewer missed doses since last visit',
2,'Poor: 4 or more missed doses since last visit',3,'Good: fewer than 2 missed days',
4,'Poor: 2 or more missed days'
)
arvadfmt.cb <- tibble::tribble(
~code, ~label,
1,'GOOD (>, 95%)',2,'FAIR (85-94%)',3,'POOR (< 85%)'
)
ynfmt.cb <- tibble::tribble(
~code, ~label,
1,'Yes',2,'No'
)
zeroonefmt.cb <- tibble::tribble(
~code, ~label,
1,'Yes',0,'No'
)
```
```{r warning=F}
getFirstXnonNA=function(data,n=3,var){
#first = dplyr::first(na.omit(value))
return(data %>%
arrange(ptidno, `apptdate`) %>%
group_by(ptidno) %>%
filter(visit_num <= n) %>%
mutate(
var_new=dplyr::first(na.omit(!!as.symbol(var)))
)%>%
ungroup())%>%
filter(visit_num == 1)
#filter(apptdate == min(apptdate)) %>%
}
getFirstNonNAInXMonths=function(data,m=3,var){
#first = dplyr::first(na.omit(value))
days=m*30
return(data %>%
arrange(ptidno, `apptdate`) %>%
group_by(ptidno) %>%
filter(apptdate <= min(apptdate)+days) %>%
mutate(
var_new=dplyr::first(na.omit(!!as.symbol(var)))
)%>%
ungroup())%>%
filter(visit_num == 1)
#filter(apptdate == min(apptdate)) %>%
}
getBaselineOnArvStartWithinXMonths=function(data,m=3,var, refdate){
#first = dplyr::first(na.omit(value))
days=m*30
return(data %>%
arrange(ptidno, `apptdate`) %>%
group_by(ptidno) %>%
filter(apptdate <= !!as.symbol(refdate)) %>%
mutate(
var_new=dplyr::first(na.omit(!!as.symbol(var)))
)%>%
ungroup())%>%
filter(visit_num == 1)
#filter(apptdate == min(apptdate)) %>%
}
binarize <- function(x) {
case_when(
x=='1'~ "Yes",
x=='0'~ "No",
is.na(x) ~ "No",
TRUE ~ x)
}
```
```{r warning=F,cache=T}
load("main.dataset.Rda")
#merge master dataset
dataset=dataset.cx.arv
#Replace numerical codes with strings from codebook
dataset$civilstatusENROL <- factor(civstfmt.cb[match(dataset$civilstatusENROL, civstfmt.cb$code), ]$label)
#dataset$male <- factor(zeroonefmt.cb[match(dataset$male, zeroonefmt.cb$code), ]$label)
dataset$transfer <- factor(zeroonefmt.cb[match(dataset$transfer, zeroonefmt.cb$code), ]$label)
dataset$Death <- factor(zeroonefmt.cb[match(dataset$Death, zeroonefmt.cb$code), ]$label)
dataset$nhif <- factor(zeroonefmt.cb[match(dataset$nhif, zeroonefmt.cb$code), ]$label)
dataset$entrypoint = factor(entptfmt.cb[match(dataset$entrypoint, entptfmt.cb$code), ]$label)
dataset= dataset %>%
mutate(across(c('Death','male', 'entrypoint', "civilstatusENROL", "transfer", "nhif"), as.factor))
```
```{r fig.align='center',warning=FALSE, cache=T}
x=c('male','Death','civilstatusENROL', 'transfer','Height','Weight', 'entrypoint', 'nhif', 'bmi','program', 'ageatarvstart' )
y=c('vl_count1','vl_count2','vl_count3')
```
## Potential Variables
```{r fig.align='center',warning=FALSE, cache=F}
# binarize response
binary.var =c(
'Cough','KSdiag','NephroCardiomyopathy','TBsignNone','cervicalcadiag','chronicisosporiasisdiag',
'coughTB','cryptococcdiag','cryptospordiag','cytomegdiag','encephaldiag','esocandiddiag','ethambutol',
'ethambutolinh','herpessvdiag','WeightLoss','inh','inhtbtx','lymphomadiag',
'mdrTbTx','mycobacdiag','mycosisdiag','nightsweats','nightsweatsTB','lymphomadiag','oiProph','on_ARV','otherTbTx',
'pcpdiag','pmldiag','pyrazinamide','rifabutin','rifafour','rifampicin','rifater','rifinah','rsbPneumoniaDiag','salmonelladiag',
'streptomycin','tbextrapulmdiag','tbpulmdiag','tbtx','three_FDC','wastingsyndiag','toxoplasdiag','weightlossTB'
)
```
### Clinical Profile Prior to ART Initiation | Viral Load Failure 1
```{r fig.align='center',warning=FALSE, cache=T}
na.rm.var=F;stats=T;dataset.cx=dataset.cx.arv;outcome="vl_failure1";
# Getting descriptive statistics
mergeDesc(
# vitals
#"current ARV status" = getTable1Stats("on_ARV",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"age at first exposure to ARV" = getTable1Stats("ageatarvstart",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"male gender" = getTable1Stats("male",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"civil status at enrollment" = getTable1Stats("civilstatusENROL",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"weight" = getTable1Stats("weight",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Weight Loss" = getTable1Stats("WeightLoss",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"BMI" = getTable1Stats("BMI",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"hemoglobin" = getTable1Stats("hgb",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"CD4" = getTable1Stats("cd4",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Cough" = getTable1Stats("Cough",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Night Sweats" = getTable1Stats("nightsweats",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# staging
"WHO stage" = getTable1Stats("WHOstage",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Staging: Symptomatic HIV-associated Nephropathy/Cardiomyopathy" = getTable1Stats("NephroCardiomyopathy",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB symptoms
"TB sign: none" = getTable1Stats("TBsignNone",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: cough" = getTable1Stats("coughTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: weight loss" = getTable1Stats("weightlossTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# Diagnosis
"Diagnosis: recurrent severe bacterial pneumonia" = getTable1Stats("rsbPneumoniaDiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Recurrent Septicemia including non-typhoidal Salmonella" = getTable1Stats("salmonelladiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Wasting Syndrome" = getTable1Stats("wastingsyndiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Toxoplasmosis, CNS" = getTable1Stats("toxoplasdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary TB" = getTable1Stats("tbextrapulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pulmonary TB" = getTable1Stats("tbpulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Lymphoma (cerebral or B-cell non-Hodgkin)" = getTable1Stats("lymphomadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Kaposi's Sarcoma" = getTable1Stats("KSdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cervical Cancer" = getTable1Stats("cervicalcadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Chronic Isosporiasis" = getTable1Stats("chronicisosporiasisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated non-TB Mycobacterial Infection" = getTable1Stats("mycobacdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated Mycosis" = getTable1Stats("mycosisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary Cryptococcosis/Meningitis" = getTable1Stats("cryptococcdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cryptosporidiosis" = getTable1Stats("cryptospordiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cytomegalovirus Disease" = getTable1Stats("cytomegdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Encephalopathy" = getTable1Stats("encephaldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Candidiasis (Oesophageal, Bronchi, Trachea, or Lungs)" = getTable1Stats("esocandiddiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Chronic Herpes Simplex" = getTable1Stats("herpessvdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pneumocystis Pneumonia" = getTable1Stats("pcpdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Progressive Multifocal Leukoencephalopathy" = getTable1Stats("pmldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB Prophylaxis
"anti-TB med: Rifabutin" = getTable1Stats("rifabutin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifafour(RHZE)" = getTable1Stats("rifafour",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifampicin(R)" = getTable1Stats("rifampicin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifater(RHZ)" = getTable1Stats("rifater",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifinah(RH)" = getTable1Stats("rifinah",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Streptomycin" = getTable1Stats("streptomycin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: 3-FDC(RHE)" = getTable1Stats("three_FDC",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutol",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutolinh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: INH" = getTable1Stats("inhtbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Other" = getTable1Stats("otherTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"anti-TB med: Multi-Drug Resistant Tx" = getTable1Stats("mdrTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Pyrazinamide(Z)" = getTable1Stats("pyrazinamide",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB Prophylaxis: INH" = getTable1Stats("inh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"OI Prophylaxis" = getTable1Stats("oiProph",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB treatment" = getTable1Stats("tbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# ARVS
"# current ARVs" = getTable1Stats("numARVs",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARVs taken last 7 days" = getTable1Stats("PillsTakenLast7Days",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ART adherence: percent taken since last visit" = getTable1Stats("art_adherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV Adherence- combines formats from both the old and the new CTC 2" = getTable1Stats("art_adherence2",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV adherence since last visit" = getTable1Stats("arvadherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
#"ART regimen" = getTable1Stats("regimen",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
)%>%
htmlTable( caption = "<b> Clinical Profile Prior to ART Initiation | Viral Load Failure 2 </b>",useViewer=T,ctable = TRUE, align = 'lcccc',
n.cgroup = c(1,2,1 ), cgroup = c('', 'Second Virologic Failure', '') ,tfoot="<sup>‡</sup>"
)%>% htmlTable::addHtmlTableStyle(col.rgroup = c("#FFF", "#EEF"))
```
### Clinical Profile Prior to ART Initiation | Viral Load Failure 2
```{r fig.align='center',warning=FALSE, cache=T}
na.rm.var=F;stats=T;dataset.cx=dataset.cx.arv;outcome="vl_failure2";
# Getting descriptive statistics
mergeDesc(
# vitals
#"current ARV status" = getTable1Stats("on_ARV",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"age at first exposure to ARV" = getTable1Stats("ageatarvstart",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"male gender" = getTable1Stats("male",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"civil status at enrollment" = getTable1Stats("civilstatusENROL",outcome,desc_both,statistics=stats,na.rm=na.rm.var),
"weight" = getTable1Stats("weight",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Weight Loss" = getTable1Stats("WeightLoss",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"BMI" = getTable1Stats("BMI",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"hemoglobin" = getTable1Stats("hgb",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"CD4" = getTable1Stats("cd4",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Cough" = getTable1Stats("Cough",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Night Sweats" = getTable1Stats("nightsweats",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# staging
"WHO stage" = getTable1Stats("WHOstage",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Staging: Symptomatic HIV-associated Nephropathy/Cardiomyopathy" = getTable1Stats("NephroCardiomyopathy",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB symptoms
"TB sign: none" = getTable1Stats("TBsignNone",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: cough" = getTable1Stats("coughTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: weight loss" = getTable1Stats("weightlossTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# Diagnosis
"Diagnosis: recurrent severe bacterial pneumonia" = getTable1Stats("rsbPneumoniaDiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Recurrent Septicemia including non-typhoidal Salmonella" = getTable1Stats("salmonelladiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Wasting Syndrome" = getTable1Stats("wastingsyndiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Toxoplasmosis, CNS" = getTable1Stats("toxoplasdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary TB" = getTable1Stats("tbextrapulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pulmonary TB" = getTable1Stats("tbpulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Lymphoma (cerebral or B-cell non-Hodgkin)" = getTable1Stats("lymphomadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Kaposi's Sarcoma" = getTable1Stats("KSdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cervical Cancer" = getTable1Stats("cervicalcadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Chronic Isosporiasis" = getTable1Stats("chronicisosporiasisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated non-TB Mycobacterial Infection" = getTable1Stats("mycobacdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated Mycosis" = getTable1Stats("mycosisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary Cryptococcosis/Meningitis" = getTable1Stats("cryptococcdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cryptosporidiosis" = getTable1Stats("cryptospordiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cytomegalovirus Disease" = getTable1Stats("cytomegdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Encephalopathy" = getTable1Stats("encephaldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Candidiasis (Oesophageal, Bronchi, Trachea, or Lungs)" = getTable1Stats("esocandiddiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Chronic Herpes Simplex" = getTable1Stats("herpessvdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pneumocystis Pneumonia" = getTable1Stats("pcpdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Progressive Multifocal Leukoencephalopathy" = getTable1Stats("pmldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB Prophylaxis
"anti-TB med: Rifabutin" = getTable1Stats("rifabutin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifafour(RHZE)" = getTable1Stats("rifafour",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifampicin(R)" = getTable1Stats("rifampicin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifater(RHZ)" = getTable1Stats("rifater",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifinah(RH)" = getTable1Stats("rifinah",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Streptomycin" = getTable1Stats("streptomycin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: 3-FDC(RHE)" = getTable1Stats("three_FDC",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutol",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutolinh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: INH" = getTable1Stats("inhtbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Other" = getTable1Stats("otherTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"anti-TB med: Multi-Drug Resistant Tx" = getTable1Stats("mdrTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Pyrazinamide(Z)" = getTable1Stats("pyrazinamide",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB Prophylaxis: INH" = getTable1Stats("inh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"OI Prophylaxis" = getTable1Stats("oiProph",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB treatment" = getTable1Stats("tbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# ARVS
"# current ARVs" = getTable1Stats("numARVs",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARVs taken last 7 days" = getTable1Stats("PillsTakenLast7Days",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ART adherence: percent taken since last visit" = getTable1Stats("art_adherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV Adherence- combines formats from both the old and the new CTC 2" = getTable1Stats("art_adherence2",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV adherence since last visit" = getTable1Stats("arvadherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
#"ART regimen" = getTable1Stats("regimen",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
)%>%
htmlTable( caption = "<b> Clinical Profile Prior to ART Initiation | Viral Load Failure 2 </b>",useViewer=T,ctable = TRUE, align = 'lcccc',
n.cgroup = c(1,2,1 ), cgroup = c('', 'Second Virologic Failure', '') ,tfoot="<sup>‡</sup>"
)%>% htmlTable::addHtmlTableStyle(col.rgroup = c("#FFF", "#EEF"))
```
### Clinical Profile Prior to ART Initiation | Viral Load Failure 3
```{r fig.align='center',warning=FALSE, cache=T}
na.rm.var=F;stats=T;dataset.cx=dataset.cx.arv;outcome="vl_failure3";
# Getting descriptive statistics
mergeDesc(
# vitals
#"current ARV status" = getTable1Stats("on_ARV",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"weight" = getTable1Stats("weight",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Weight Loss" = getTable1Stats("WeightLoss",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"BMI" = getTable1Stats("BMI",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"hemoglobin" = getTable1Stats("hgb",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"CD4" = getTable1Stats("cd4",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Cough" = getTable1Stats("Cough",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Night Sweats" = getTable1Stats("nightsweats",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# staging
"WHO stage" = getTable1Stats("WHOstage",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Staging: Symptomatic HIV-associated Nephropathy/Cardiomyopathy" = getTable1Stats("NephroCardiomyopathy",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB symptoms
"TB sign: none" = getTable1Stats("TBsignNone",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: cough" = getTable1Stats("coughTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB sign: weight loss" = getTable1Stats("weightlossTB",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# Diagnosis
"Diagnosis: recurrent severe bacterial pneumonia" = getTable1Stats("rsbPneumoniaDiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Recurrent Septicemia including non-typhoidal Salmonella" = getTable1Stats("salmonelladiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Wasting Syndrome" = getTable1Stats("wastingsyndiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Toxoplasmosis, CNS" = getTable1Stats("toxoplasdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary TB" = getTable1Stats("tbextrapulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pulmonary TB" = getTable1Stats("tbpulmdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Lymphoma (cerebral or B-cell non-Hodgkin)" = getTable1Stats("lymphomadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Kaposi's Sarcoma" = getTable1Stats("KSdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cervical Cancer" = getTable1Stats("cervicalcadiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Chronic Isosporiasis" = getTable1Stats("chronicisosporiasisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated non-TB Mycobacterial Infection" = getTable1Stats("mycobacdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"Diagnosis: Disseminated Mycosis" = getTable1Stats("mycosisdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Extrapulmonary Cryptococcosis/Meningitis" = getTable1Stats("cryptococcdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cryptosporidiosis" = getTable1Stats("cryptospordiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Cytomegalovirus Disease" = getTable1Stats("cytomegdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: HIV Encephalopathy" = getTable1Stats("encephaldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Candidiasis (Oesophageal, Bronchi, Trachea, or Lungs)" = getTable1Stats("esocandiddiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Chronic Herpes Simplex" = getTable1Stats("herpessvdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Pneumocystis Pneumonia" = getTable1Stats("pcpdiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"Diagnosis: Progressive Multifocal Leukoencephalopathy" = getTable1Stats("pmldiag",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# TB Prophylaxis
"anti-TB med: Rifabutin" = getTable1Stats("rifabutin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifafour(RHZE)" = getTable1Stats("rifafour",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifampicin(R)" = getTable1Stats("rifampicin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifater(RHZ)" = getTable1Stats("rifater",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Rifinah(RH)" = getTable1Stats("rifinah",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Streptomycin" = getTable1Stats("streptomycin",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: 3-FDC(RHE)" = getTable1Stats("three_FDC",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutol",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Ethambutol(E)" = getTable1Stats("ethambutolinh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: INH" = getTable1Stats("inhtbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Other" = getTable1Stats("otherTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
#"anti-TB med: Multi-Drug Resistant Tx" = getTable1Stats("mdrTbTx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"anti-TB med: Pyrazinamide(Z)" = getTable1Stats("pyrazinamide",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB Prophylaxis: INH" = getTable1Stats("inh",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"OI Prophylaxis" = getTable1Stats("oiProph",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"TB treatment" = getTable1Stats("tbtx",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
# ARVS
"# current ARVs" = getTable1Stats("numARVs",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARVs taken last 7 days" = getTable1Stats("PillsTakenLast7Days",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ART adherence: percent taken since last visit" = getTable1Stats("art_adherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV Adherence- combines formats from both the old and the new CTC 2" = getTable1Stats("art_adherence2",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var),
"ARV adherence since last visit" = getTable1Stats("arvadherence",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
#"ART regimen" = getTable1Stats("regimen",outcome,desc_both,dataset.cx,statistics=stats,na.rm=na.rm.var)
)%>%
htmlTable( caption = "<b> Clinical Profile Prior to ART Initiation | Viral Load Failure 3 </b>",useViewer=T,ctable = TRUE, align = 'lcccc',
n.cgroup = c(1,2,1 ), cgroup = c('', 'Third Virologic Failure', '') ,tfoot="<sup>‡</sup>"
)%>% htmlTable::addHtmlTableStyle(col.rgroup = c("#FFF", "#EEF"))
```