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removing helper temp #209

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Jul 1, 2024
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removing helper temp #209

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78 changes: 38 additions & 40 deletions vignettes/Data_Requirements.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,10 @@ require(devtools, quietly = TRUE)
require(tinytable, quietly = TRUE)

devtools::install_github("istallworthy/devMSMs", quiet = TRUE)

devtools::install_github("istallworthy/devMSMsHelpers", quiet = TRUE)
library(devMSMsHelpers)

```

```{r, echo = FALSE, message = FALSE, warning = FALSE}
Expand Down Expand Up @@ -180,7 +184,7 @@ tinytable::tt(helper_functions, theme = "striped") |>
We first install the *devMSMs* and *devMSMsHelpers* packages.

```{r, eval = FALSE}
# install.packages("devtools")
install.packages("devtools")
require(devtools, quietly = TRUE)
devtools::install_github("istallworthy/devMSMs", quiet = TRUE)
devtools::install_github("istallworthy/devMSMsHelpers", quiet = TRUE)
Expand All @@ -206,12 +210,7 @@ Please see the <a href="https://istallworthy.github.io/devMSMs/articles/Specify_
```{r}
set.seed(1234)

# required

exposure = c("ESETA1.6", "ESETA1.15", "ESETA1.24", "ESETA1.35", "ESETA1.58") # wide format


# required
exposure = c("ESETA1.6", "ESETA1.15", "ESETA1.24", "ESETA1.35", "ESETA1.58")

ti_conf = c("state", "BioDadInHH2", "PmAge2", "PmBlac2", "TcBlac2", "PmMrSt2", "PmEd2", "KFASTScr",
"RMomAgeU", "RHealth", "HomeOwnd", "SWghtLB", "SurpPreg", "SmokTotl", "DrnkFreq",
Expand All @@ -232,12 +231,10 @@ tv_conf = c("SAAmylase.6","SAAmylase.15", "SAAmylase.24",
"StrDif_Tot.35",
"fscore.35", "fscore.58")

home_dir = NA
# home_dir = NA

# required
outcome <- "StrDif_Tot.58"


```

Some helper functions have optional arguments to suppress saving output locally (`save.out` = FALSE) and printing it to the console ( `verbose` = FALSE). The defaults to both arguments are TRUE. Users must supply a path to a home directory if `save.out` = TRUE.
Expand Down Expand Up @@ -293,21 +290,22 @@ factor_confounders <- c("state", "TcBlac2", "BioDadInHH2", "HomeOwnd", "PmBlac2"
integer_confounders <- c("KFASTScr", "PmEd2", "RMomAgeU", "SWghtLB", "peri_health",
"caregiv_health", "gov_assist", "B18Raw", "EARS_TJo", "MDI")

data_long_f <- formatLongData(
data = data_long,
exposure = exposure,
outcome = outcome,
sep = "\\.",
time_var = "WAVE",
id_var = "ID",
missing = NA,
factor_confounders = factor_confounders,
integer_confounders = integer_confounders,
home_dir = home_dir,
save.out = save.out
)
# data_long_f <- formatLongData(
# data = data_long,
# exposure = exposure,
# outcome = outcome,
# sep = "\\.",
# time_var = "WAVE",
# id_var = "ID",
# missing = NA,
# factor_confounders = factor_confounders,
# integer_confounders = integer_confounders,
# home_dir = home_dir,
# save.out = save.out
# )

# head(data_long_f, n = c(5, 10))

head(data_long_f, n = c(5, 10))
```

We get a descriptive statistics summary of the exposure, ESETA1, and the outcome, StrDif_Tot.58, for our visual inspections.
Expand All @@ -323,22 +321,22 @@ We then transform our newly formatted long data into wide format, specifying `id
```{r}
require("stats", quietly = TRUE)

sep <- "\\."
v <- sapply(strsplit(tv_conf[!grepl("\\:", tv_conf)], sep), head, 1)
v <- c(v[!duplicated(v)], sapply(strsplit(exposure[1], sep), head, 1))

data_wide_f <- stats::reshape(
data = data_long_f,
idvar = "ID",
v.names = v,
timevar = "WAVE",
times = c(6, 15, 24, 35, 58),
direction = "wide"
)

data_wide_f <- data_wide_f[, colSums(is.na(data_wide_f)) < nrow(data_wide_f)]

head(data_wide_f, n = c(5, 10))
# sep <- "\\."
# v <- sapply(strsplit(tv_conf[!grepl("\\:", tv_conf)], sep), head, 1)
# v <- c(v[!duplicated(v)], sapply(strsplit(exposure[1], sep), head, 1))
#
# data_wide_f <- stats::reshape(
# data = data_long_f,
# idvar = "ID",
# v.names = v,
# timevar = "WAVE",
# times = c(6, 15, 24, 35, 58),
# direction = "wide"
# )
#
# data_wide_f <- data_wide_f[, colSums(is.na(data_wide_f)) < nrow(data_wide_f)]
#
# head(data_wide_f, n = c(5, 10))
```

<br> <br>
Expand Down