03_LAB_WBC.Rnw

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%%% LABORATORY PARAMETER WBC - BEGIN
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\clearpage
\newpage
\subsection{WBC over Time (no data imputation, LOCF)}

<<03_WBCBOX>>=
df_aval <- ADLB %>% select(PARAM, PARAMCD, AVISIT, AVISITN, AVAL, DTYPE) %>%
  mutate(Xaxis = AVISIT, Yaxis = AVAL) %>%
  filter(PARAMCD == "WBC" & DTYPE == "")

df_LOCF <- ADLB %>% select(PARAM, PARAMCD, AVISIT, AVISITN, AVAL, DTYPE) %>%
  mutate(Xaxis = AVISIT, Yaxis = AVAL) %>%
  filter(PARAMCD == "WBC" & (DTYPE == "" | DTYPE == "LOCF"))
@

<<03_WBCCI, results='asis'>>=
myCaption <- "Summary of WBC over Time, mean +/- 95\\% CIs (no data imputation)"
LbyCI(df_aval$AVAL, df_aval$AVISIT, size = "small")
@

<<03_WBCCI2, results='asis'>>=
myCaption <- "Summary of WBC over Time, mean +/- 95\\% CIs (LOCF)"
LbyCI(df_LOCF$AVAL, df_LOCF$AVISIT, size = "small")
@

<<03_WBCQUART, results='asis'>>=
myCaption <- "Summary of WBC over Time, Q1, Q3 (no data imputation)"
LbyQUART(df_aval$AVAL, df_aval$AVISIT, size = "small")
@

<<03_WBCQUART2, results='asis'>>=
myCaption <- "Summary of WBC over Time, Q1, Q3 (LOCF)"
LbyQUART(df_LOCF$AVAL, df_LOCF$AVISIT, size = "small")
@


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\clearpage
\newpage
\subsection{WBC over Time, boxplots}

<<03_WBCBOX1>>=
df_BOX <- df_aval
xLab <- "Visit"
yLab <- "10^9/L"
cap <- "WBC over Time - Boxplot (no data imputation)"
@

<<WBC_Box_Aval, ref.label="BoxPlot", fig.width=6, fig.height=6, out.width='10cm', fig.cap=cap>>=
@

<<03_WBCBOX2>>=
df_BOX <- df_LOCF
xLab <- "Visit"
yLab <- "10^9/L"
cap <- "WBC over Time - Boxplot (LOCF)"
@

<<WBC_Box_LOCF, ref.label="BoxPlot", fig.width=6, fig.height=6, out.width='10cm', fig.cap=cap>>=
@

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\clearpage
\newpage
\subsection{WBC, Shift Table Baseline vs. Week 24 (no data imputation)}

<<results='asis'>>=
#### Subset WBC at W24
df_W24 <- ADLB %>% select(AGEGR1, AVISIT, PARAMCD, BNRIND, ANRIND, SHIFT1, DTYPE) %>%
  filter(PARAMCD == "WBC" & AVISIT == "Week 24"  & DTYPE == "")
label(df_W24$SHIFT1) <- "Shift BL to Week 24"


s6 <- summary(AGEGR1 ~ SHIFT1, data = df_W24, method = 'reverse', 
              overall = TRUE, test = FALSE, na.include = FALSE, continuous = 8)

latex(s6, npct = "both", landscape = FALSE, long = TRUE, prmsd = TRUE, here = TRUE, 
  prtest = "P", dotchart = FALSE,
  caption = "WBC, Shift Table Baseline to Week 24 (no data imputation)", caption.loc = "top", 
  middle.bold = TRUE, file = "", digits = 2, exclude1 = FALSE, label = "WBC_SH24")
@

<<results='asis'>>=
#print(CrossTable(tab1))
tab1 <- table(df_W24$BNRIND, df_W24$ANRIND)
tab2 <- as.data.frame(tab1)
#tab_sum <- addmargins(tab1)

cap <- "WBC, Shift Table Baseline to Week 24 (no data imputation)"
latex(tab1, file = "", here = TRUE, title = "Baseline/W24", caption = cap, label = runif(1))
mcnemar.test(tab1)
@


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<<fig.width=7, fig.height=5>>=
p1 <- ggplot(tab2, aes(Var1, Var2)) +
  geom_point(aes(size = Freq), colour = "#9999FF") + 
  scale_x_discrete() +
  geom_text(aes(label = Freq)) +
  labs(x ="Baseline", y = "Week 24") +
  scale_size_continuous(range = c(5, 20)) +
  theme_bw()
@

<<shiftWBC, fig.width=7, fig.height=5>>=
# Example: ggsave() function for saving plot;
ggsave("WBC_Shift24.pdf", p1)
@

\begin{figure}[H]
  \centering
  \includegraphics[width=0.7\textwidth]{WBC_Shift24.pdf}
  \caption{WBC, Shift Table Baseline to Week 24 (no data imputation)}
\end{figure}

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%%% LABORATORY PARAMETER WBC - END
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