tests/testthat/test_lhs_modelsum.R
In eheinzen/arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
context("Testing the modelsum strata and multiple LHS output")
###########################################################################################################
#### Basic modelsum call
###########################################################################################################
test_that("A three-LHS modelsum call", {
expect_identical(
capture.kable(summary(modelsum(list(ht_in, time, Age) ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)),
c(
capture.kable(summary(modelsum(ht_in ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(modelsum(time ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(modelsum(Age ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE))
)
)
})
test_that("A modelsum call with strata", {
expect_identical(
capture.kable(summary(modelsum(Age ~ Sex + dt, adjust = ~ trt, data = mdat, strata = Group), text = TRUE)),
c("|Group | |estimate |std.error |p.value |adj.r.squared |",
"|:-----|:---------------|:--------|:---------|:-------|:-------------|",
"|High |(Intercept) |40.833 |2.062 |< 0.001 |-0.050 |",
"| |Sex Male |0.333 |2.326 |0.887 | |",
"| |Treatment Arm B |-1.812 |2.331 |0.444 | |",
"| |(Intercept) |39.853 |3.948 |< 0.001 |-0.047 |",
"| |dt |-0.000 |0.001 |0.750 | |",
"| |Treatment Arm B |-1.910 |2.347 |0.423 | |",
"|Low |(Intercept) |40.524 |1.304 |< 0.001 |-0.040 |",
"| |Sex Male |-1.192 |1.463 |0.422 | |",
"| |Treatment Arm B |-0.591 |1.505 |0.697 | |",
"| |(Intercept) |45.146 |2.751 |< 0.001 |0.074 |",
"| |dt |0.001 |0.000 |0.054 | |",
"| |Treatment Arm B |-0.363 |1.423 |0.801 | |",
"|Med |(Intercept) |40.300 |2.069 |< 0.001 |-0.056 |",
"| |Sex Male |0.117 |2.095 |0.956 | |",
"| |Treatment Arm B |-1.467 |2.169 |0.505 | |",
"| |(Intercept) |42.941 |4.383 |< 0.001 |-0.040 |",
"| |dt |0.000 |0.001 |0.528 | |",
"| |Treatment Arm B |-1.650 |2.171 |0.454 | |"
)
)
})
test_that("strata levels are maintained", {
tmp <- mdat
tmp$Group[tmp$trt == "A" & tmp$Group == "Low"] <- NA
expect_identical(
capture.kable(summary(set_labels(modelsum(Age ~ Sex + dt, adjust = ~ Group, strata = trt, data = tmp), c(GroupLow = "Low")), text = TRUE)),
c("|Treatment Arm | |estimate |std.error |p.value |adj.r.squared |Nmiss |",
"|:-------------|:-----------|:--------|:---------|:-------|:-------------|:-----|",
"|A |(Intercept) |42.139 |2.047 |< 0.001 |-0.047 |11 |",
"| |Sex Male |-2.277 |2.456 |0.364 | | |",
"| |Group Med |-0.533 |2.472 |0.831 | | |",
"| |(Intercept) |34.850 |3.600 |< 0.001 |0.065 |11 |",
"| |dt |-0.001 |0.000 |0.072 | | |",
"| |Group Med |-1.642 |2.394 |0.500 | | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |0 |",
"| |Sex Male |0.908 |1.407 |0.522 | | |",
"| |Low |0.205 |1.753 |0.907 | | |",
"| |Group Med |-0.317 |1.753 |0.857 | | |",
"| |(Intercept) |47.149 |2.812 |< 0.001 |0.114 |0 |",
"| |dt |0.001 |0.000 |0.003 | | |",
"| |Low |-0.145 |1.613 |0.929 | | |",
"| |Group Med |-0.318 |1.610 |0.844 | | |"
)
)
})
test_that("Multiple adjustments work (#240)", {
tmp.ms <- modelsum(list(age, bmi) ~ fu.time + ast, adjust = list(Unadjusted = ~ 1, "Adjusted for Arm" = ~ arm, "HGB + PS" = ~ hgb + ps),
data = set_labels(mockstudy, list(ast = "AST", ps = "PS")), strata = sex,
gaussian.stats = c("estimate", "std.error", "p.value", "adj.r.squared", "Nmiss", "N"))
tmp.ms2 <- modelsum(list(age, bmi) ~ fu.time + ast, adjust = list(Unadjusted = ~ NULL, "Adjusted for Arm" = ~ arm, "HGB + PS" = ~ hgb + ps),
data = set_labels(mockstudy, list(ast = "AST", ps = "PS")), strata = sex,
gaussian.stats = c("estimate", "std.error", "p.value", "adj.r.squared", "Nmiss", "N"))
expect_identical(
capture.kable(summary(tmp.ms, adjustment.names = TRUE, term.name = TRUE)),
capture.kable(summary(tmp.ms2, adjustment.names = TRUE, term.name = TRUE))
)
expect_identical(
capture.kable(summary(tmp.ms, adjustment.names = TRUE, term.name = TRUE)),
c("|sex |adjustment |Age in Years |estimate |std.error |p.value |adj.r.squared |Nmiss |N |",
"|:------|:----------------|:---------------------------|:--------|:---------|:-------|:-------------|:-----|:---|",
"|Male |Unadjusted |(Intercept) |61.686 |0.654 |< 0.001 |0.005 |0 |916 |",
"| | |**fu.time** |-0.002 |0.001 |0.022 | | | |",
"| |Adjusted for Arm |(Intercept) |61.073 |0.837 |< 0.001 |0.004 |0 |916 |",
"| | |**fu.time** |-0.002 |0.001 |0.016 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.048 |0.889 |0.239 | | | |",
"| | |**Treatment Arm G: IROX** |0.857 |1.015 |0.399 | | | |",
"| |HGB + PS |(Intercept) |57.090 |3.068 |< 0.001 |0.010 |162 |754 |",
"| | |**fu.time** |-0.002 |0.001 |0.008 | | | |",
"| | |**hgb** |0.365 |0.234 |0.118 | | | |",
"| | |**PS** |0.881 |0.746 |0.238 | | | |",
"| |Unadjusted |(Intercept) |61.556 |0.696 |< 0.001 |0.003 |162 |754 |",
"| | |**AST** |-0.028 |0.016 |0.074 | | | |",
"| |Adjusted for Arm |(Intercept) |61.524 |0.947 |< 0.001 |0.001 |162 |754 |",
"| | |**AST** |-0.028 |0.016 |0.075 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.322 |0.977 |0.741 | | | |",
"| | |**Treatment Arm G: IROX** |-0.445 |1.115 |0.690 | | | |",
"| |HGB + PS |(Intercept) |57.707 |3.133 |< 0.001 |0.006 |162 |754 |",
"| | |**AST** |-0.032 |0.016 |0.043 | | | |",
"| | |**hgb** |0.253 |0.232 |0.276 | | | |",
"| | |**PS** |1.529 |0.739 |0.039 | | | |",
"|Female |Unadjusted |(Intercept) |59.385 |0.822 |< 0.001 |-0.002 |0 |583 |",
"| | |**fu.time** |-0.000 |0.001 |0.835 | | | |",
"| |Adjusted for Arm |(Intercept) |59.449 |1.089 |< 0.001 |-0.003 |0 |583 |",
"| | |**fu.time** |-0.000 |0.001 |0.707 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.580 |1.216 |0.634 | | | |",
"| | |**Treatment Arm G: IROX** |-0.856 |1.353 |0.527 | | | |",
"| |HGB + PS |(Intercept) |46.660 |4.632 |< 0.001 |0.015 |104 |479 |",
"| | |**fu.time** |-0.001 |0.001 |0.564 | | | |",
"| | |**hgb** |1.156 |0.378 |0.002 | | | |",
"| | |**PS** |-0.421 |0.902 |0.641 | | | |",
"| |Unadjusted |(Intercept) |61.001 |0.883 |< 0.001 |0.004 |104 |479 |",
"| | |**AST** |-0.033 |0.020 |0.096 | | | |",
"| |Adjusted for Arm |(Intercept) |60.687 |1.266 |< 0.001 |0.006 |104 |479 |",
"| | |**AST** |-0.032 |0.020 |0.102 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.253 |1.297 |0.334 | | | |",
"| | |**Treatment Arm G: IROX** |-1.006 |1.441 |0.486 | | | |",
"| |HGB + PS |(Intercept) |47.825 |4.730 |< 0.001 |0.017 |104 |479 |",
"| | |**AST** |-0.026 |0.020 |0.193 | | | |",
"| | |**hgb** |1.086 |0.376 |0.004 | | | |",
"| | |**PS** |-0.115 |0.873 |0.895 | | | |",
"" ,
"" ,
"|sex |adjustment |Body Mass Index (kg/m^2) |estimate |std.error |p.value |adj.r.squared |Nmiss |N |",
"|:------|:----------------|:---------------------------|:--------|:---------|:-------|:-------------|:-----|:---|",
"|Male |Unadjusted |(Intercept) |26.679 |0.294 |< 0.001 |0.011 |22 |894 |",
"| | |**fu.time** |0.001 |0.000 |< 0.001 | | | |",
"| |Adjusted for Arm |(Intercept) |26.901 |0.376 |< 0.001 |0.012 |22 |894 |",
"| | |**fu.time** |0.001 |0.000 |< 0.001 | | | |",
"| | |**Treatment Arm F: FOLFOX** |-0.594 |0.397 |0.134 | | | |",
"| | |**Treatment Arm G: IROX** |-0.040 |0.451 |0.930 | | | |",
"| |HGB + PS |(Intercept) |23.559 |1.321 |< 0.001 |0.036 |181 |735 |",
"| | |**fu.time** |0.001 |0.000 |0.021 | | | |",
"| | |**hgb** |0.283 |0.101 |0.005 | | | |",
"| | |**PS** |-0.794 |0.322 |0.014 | | | |",
"| |Unadjusted |(Intercept) |27.885 |0.306 |< 0.001 |0.006 |181 |735 |",
"| | |**AST** |-0.016 |0.007 |0.023 | | | |",
"| |Adjusted for Arm |(Intercept) |28.040 |0.412 |< 0.001 |0.004 |181 |735 |",
"| | |**AST** |-0.016 |0.007 |0.023 | | | |",
"| | |**Treatment Arm F: FOLFOX** |-0.354 |0.427 |0.408 | | | |",
"| | |**Treatment Arm G: IROX** |0.015 |0.486 |0.976 | | | |",
"| |HGB + PS |(Intercept) |24.297 |1.350 |< 0.001 |0.032 |181 |735 |",
"| | |**AST** |-0.011 |0.007 |0.123 | | | |",
"| | |**hgb** |0.307 |0.100 |0.002 | | | |",
"| | |**PS** |-0.878 |0.318 |0.006 | | | |",
"|Female |Unadjusted |(Intercept) |26.198 |0.423 |< 0.001 |0.003 |11 |572 |",
"| | |**fu.time** |0.001 |0.001 |0.101 | | | |",
"| |Adjusted for Arm |(Intercept) |26.198 |0.560 |< 0.001 |0.002 |11 |572 |",
"| | |**fu.time** |0.001 |0.001 |0.164 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.366 |0.625 |0.558 | | | |",
"| | |**Treatment Arm G: IROX** |-0.386 |0.692 |0.577 | | | |",
"| |HGB + PS |(Intercept) |27.620 |2.409 |< 0.001 |-0.000 |113 |470 |",
"| | |**fu.time** |0.001 |0.001 |0.099 | | | |",
"| | |**hgb** |-0.121 |0.196 |0.539 | | | |",
"| | |**PS** |0.184 |0.467 |0.694 | | | |",
"| |Unadjusted |(Intercept) |26.500 |0.456 |< 0.001 |0.001 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.247 | | | |",
"| |Adjusted for Arm |(Intercept) |26.062 |0.649 |< 0.001 |0.008 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.225 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.102 |0.669 |0.100 | | | |",
"| | |**Treatment Arm G: IROX** |-0.276 |0.741 |0.710 | | | |",
"| |HGB + PS |(Intercept) |27.324 |2.462 |< 0.001 |-0.003 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.255 | | | |",
"| | |**hgb** |-0.064 |0.196 |0.743 | | | |",
"| | |**PS** |-0.103 |0.454 |0.821 | | | |"
)
)
expect_identical(
capture.kable(summary(modelsum(Age ~ Sex + time, data = mdat), text = TRUE, adjustment.names = TRUE)),
c("|adjustment | |estimate |std.error |p.value |adj.r.squared |",
"|:----------|:-----------|:--------|:---------|:-------|:-------------|",
"|unadjusted |(Intercept) |39.826 |0.779 |< 0.001 |-0.011 |",
"| |Sex Male |-0.258 |1.115 |0.818 | |",
"|unadjusted |(Intercept) |41.130 |1.197 |< 0.001 |0.009 |",
"| |time |-0.371 |0.275 |0.182 | |"
)
)
})
###########################################################################################################
#### Other warnings and tests and things...
###########################################################################################################
test_that("Reordering variables and subsetting", {
tmp.tab <- modelsum(list(Age, time) ~ Sex + dt + ethan, adjust = ~ Group, strata = trt, data = mdat)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2), 2:1], text = TRUE)),
capture.kable(summary(modelsum(list(time, Age) ~ ethan + Sex + dt, adjust = ~ Group, strata = trt, data = mdat), text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2)], text = TRUE)),
capture.kable(summary(tmp.tab[c("ethan", "Sex", "dt")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2:1], text = TRUE)),
capture.kable(summary(tmp.tab[, c("time", "Age")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[1:2], text = TRUE)),
capture.kable(summary(tmp.tab[c(TRUE, TRUE, FALSE)], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2], text = TRUE)),
capture.kable(summary(tmp.tab[, c(FALSE, TRUE)], text = TRUE))
)
expect_warning(tmp.tab[1:4], "Some indices not found")
expect_warning(tmp.tab[, 1:3], "Some indices not found")
expect_error(tmp.tab[TRUE], "Logical vector")
expect_error(tmp.tab[, TRUE], "Logical vector")
})
test_that("Merging modelsum objects", {
tb1 <- modelsum(list(Age, time) ~ Sex + Phase, strata = trt, data = mdat)
tb2 <- modelsum(list(as.numeric(dt), ht_in) ~ Group, strata = trt, data = mdat)
tb3 <- modelsum(list(Age, ht_in, time) ~ Group + ethan, strata = trt, data = mdat)
tb4 <- modelsum(list(Age, time) ~ Sex + Phase + Group + ethan, strata = trt, data = mdat)
expect_error(merge(tb1, tb2), "No terms in common")
expect_identical(
capture.kable(summary(merge(tb1, tb2, all = TRUE))),
c(capture.kable(summary(tb1)), "", "", capture.kable(summary(tb2)))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all.x = TRUE), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all = TRUE), text = TRUE)),
c(
capture.kable(summary(tb4, text = TRUE)), "", "",
capture.kable(summary(modelsum(ht_in ~ Group + ethan, data = mdat, strata = trt), text = TRUE))
)
)
})
test_that("Changing labels", {
mdat.tmp <- set_labels(mdat, NULL)
mdat.tmp$`1x` <- 1:nrow(mdat.tmp)
mdat.tmp$`2x` <- rep(c("A", "B"), each = nrow(mdat.tmp)/2)
tab <- modelsum(list(Age, time) ~ Sex + `1x` + `2x`, adjust = ~ Group, strata = trt, data = mdat.tmp)
tmp <- capture.kable(summary(tab, text = TRUE, term.name = TRUE))
expect_warning(labels(tab) <- c(hi = "hi", SexMale = "Male", Age = "Age 1", time = "Time", trt = "Trt Arm",
GroupLow = "Low", "`1x`" = "onex", "`2x`B" = "B"), NA)
expect_identical(
capture.kable(summary(tab, text = TRUE, term.name = TRUE)),
c("|Trt Arm |Age 1 |estimate |std.error |p.value |adj.r.squared |",
"|:-------|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |42.000 |1.795 |< 0.001 |-0.052 |",
"| |Male |-2.000 |1.918 |0.305 | |",
"| |Low |-1.182 |2.303 |0.611 | |",
"| |Group Med |-0.545 |2.290 |0.813 | |",
"| |(Intercept) |41.277 |2.281 |< 0.001 |-0.087 |",
"| |onex |-0.019 |0.113 |0.870 | |",
"| |Low |0.237 |7.336 |0.974 | |",
"| |Group Med |-0.083 |4.085 |0.984 | |",
"| |(Intercept) |41.000 |1.543 |< 0.001 |-0.087 |",
"| |B |-0.667 |3.495 |0.850 | |",
"| |Low |-0.242 |4.198 |0.954 | |",
"| |Group Med |-0.333 |2.817 |0.907 | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |",
"| |Male |0.908 |1.407 |0.522 | |",
"| |Low |0.205 |1.753 |0.907 | |",
"| |Group Med |-0.317 |1.753 |0.857 | |",
"| |(Intercept) |38.753 |1.835 |< 0.001 |-0.056 |",
"| |onex |0.027 |0.081 |0.739 | |",
"| |Low |-1.414 |5.083 |0.782 | |",
"| |Group Med |-1.105 |2.996 |0.714 | |",
"| |(Intercept) |39.187 |1.296 |< 0.001 |-0.058 |",
"| |B |0.011 |2.383 |0.996 | |",
"| |Low |0.170 |2.962 |0.955 | |",
"| |Group Med |-0.299 |2.161 |0.891 | |",
"" ,
"" ,
"|Trt Arm |Time |estimate |std.error |p.value |adj.r.squared |",
"|:-------|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |4.469 |0.568 |< 0.001 |-0.016 |",
"| |Male |-0.223 |0.606 |0.716 | |",
"| |Low |-1.115 |0.728 |0.136 | |",
"| |Group Med |-0.620 |0.724 |0.398 | |",
"| |(Intercept) |5.331 |0.671 |< 0.001 |0.090 |",
"| |onex |-0.066 |0.033 |0.058 | |",
"| |Low |2.947 |2.159 |0.182 | |",
"| |Group Med |1.316 |1.202 |0.282 | |",
"| |(Intercept) |4.357 |0.475 |< 0.001 |0.004 |",
"| |B |-0.967 |1.076 |0.376 | |",
"| |Low |-0.118 |1.292 |0.928 | |",
"| |Group Med |-0.190 |0.867 |0.828 | |",
"|B |(Intercept) |4.301 |0.591 |< 0.001 |0.086 |",
"| |Male |0.898 |0.566 |0.119 | |",
"| |Low |-1.621 |0.705 |0.026 | |",
"| |Group Med |-0.879 |0.705 |0.218 | |",
"| |(Intercept) |3.710 |0.725 |< 0.001 |0.112 |",
"| |onex |0.065 |0.032 |0.048 | |",
"| |Low |-5.461 |2.008 |0.009 | |",
"| |Group Med |-2.797 |1.184 |0.022 | |",
"| |(Intercept) |4.750 |0.516 |< 0.001 |0.098 |",
"| |B |1.700 |0.948 |0.079 | |",
"| |Low |-3.345 |1.179 |0.007 | |",
"| |Group Med |-1.750 |0.860 |0.047 | |"
)
)
labels(tab) <- NULL
expect_identical(
capture.kable(summary(tab, text = TRUE, term.name = TRUE)),
tmp
)
expect_identical(
tmp,
c("|trt |Age |estimate |std.error |p.value |adj.r.squared |",
"|:---|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |42.000 |1.795 |< 0.001 |-0.052 |",
"| |Sex Male |-2.000 |1.918 |0.305 | |",
"| |Group Low |-1.182 |2.303 |0.611 | |",
"| |Group Med |-0.545 |2.290 |0.813 | |",
"| |(Intercept) |41.277 |2.281 |< 0.001 |-0.087 |",
"| |1x |-0.019 |0.113 |0.870 | |",
"| |Group Low |0.237 |7.336 |0.974 | |",
"| |Group Med |-0.083 |4.085 |0.984 | |",
"| |(Intercept) |41.000 |1.543 |< 0.001 |-0.087 |",
"| |2x B |-0.667 |3.495 |0.850 | |",
"| |Group Low |-0.242 |4.198 |0.954 | |",
"| |Group Med |-0.333 |2.817 |0.907 | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |",
"| |Sex Male |0.908 |1.407 |0.522 | |",
"| |Group Low |0.205 |1.753 |0.907 | |",
"| |Group Med |-0.317 |1.753 |0.857 | |",
"| |(Intercept) |38.753 |1.835 |< 0.001 |-0.056 |",
"| |1x |0.027 |0.081 |0.739 | |",
"| |Group Low |-1.414 |5.083 |0.782 | |",
"| |Group Med |-1.105 |2.996 |0.714 | |",
"| |(Intercept) |39.187 |1.296 |< 0.001 |-0.058 |",
"| |2x B |0.011 |2.383 |0.996 | |",
"| |Group Low |0.170 |2.962 |0.955 | |",
"| |Group Med |-0.299 |2.161 |0.891 | |",
"" ,
"" ,
"|trt |time |estimate |std.error |p.value |adj.r.squared |",
"|:---|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |4.469 |0.568 |< 0.001 |-0.016 |",
"| |Sex Male |-0.223 |0.606 |0.716 | |",
"| |Group Low |-1.115 |0.728 |0.136 | |",
"| |Group Med |-0.620 |0.724 |0.398 | |",
"| |(Intercept) |5.331 |0.671 |< 0.001 |0.090 |",
"| |1x |-0.066 |0.033 |0.058 | |",
"| |Group Low |2.947 |2.159 |0.182 | |",
"| |Group Med |1.316 |1.202 |0.282 | |",
"| |(Intercept) |4.357 |0.475 |< 0.001 |0.004 |",
"| |2x B |-0.967 |1.076 |0.376 | |",
"| |Group Low |-0.118 |1.292 |0.928 | |",
"| |Group Med |-0.190 |0.867 |0.828 | |",
"|B |(Intercept) |4.301 |0.591 |< 0.001 |0.086 |",
"| |Sex Male |0.898 |0.566 |0.119 | |",
"| |Group Low |-1.621 |0.705 |0.026 | |",
"| |Group Med |-0.879 |0.705 |0.218 | |",
"| |(Intercept) |3.710 |0.725 |< 0.001 |0.112 |",
"| |1x |0.065 |0.032 |0.048 | |",
"| |Group Low |-5.461 |2.008 |0.009 | |",
"| |Group Med |-2.797 |1.184 |0.022 | |",
"| |(Intercept) |4.750 |0.516 |< 0.001 |0.098 |",
"| |2x B |1.700 |0.948 |0.079 | |",
"| |Group Low |-3.345 |1.179 |0.007 | |",
"| |Group Med |-1.750 |0.860 |0.047 | |"
)
)
})
###########################################################################################################
#### Reported bugs for modelsum
###########################################################################################################
test_that("02/23/2018: wrapping long labels (#59)", {
labs <- list(
Group = "This is a really long label for the Group variable",
time = "Another really long label. Can you believe how long this is",
dt = "ThisLabelHasNoSpacesSoLetsSeeHowItBehaves",
trt = NULL
)
expect_identical(
capture.kable(print(summary(modelsum(Age ~ Group + time + dt, strata = trt, data = set_labels(mdat, labs)), text = TRUE, digits = 4), width = 30)),
c("|trt | |estimate |std.error |p.value |adj.r.squared |",
"|:---|:------------------------------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |41.0000 |1.5200 |< 0.001 |-0.0552 |",
"| |This is a really long label |-0.9091 |2.2915 |0.694 | |",
"| |for the Group variable Low | | | | |",
"| |This is a really long label |-0.6364 |2.2915 |0.783 | |",
"| |for the Group variable Med | | | | |",
"| |(Intercept) |43.2848 |2.1872 |< 0.001 |0.0257 |",
"| |Another really long label. |-0.7192 |0.5187 |0.175 | |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |(Intercept) |36.3141 |2.9357 |< 0.001 |0.0352 |",
"| |ThisLabelHasNoSpacesSoLetsSeeH |-0.0006 |0.0004 |0.141 | |",
"| |owItBehaves | | | | |",
"|B |(Intercept) |39.1875 |1.2837 |< 0.001 |-0.0375 |",
"| |This is a really long label |0.1809 |1.7423 |0.918 | |",
"| |for the Group variable Low | | | | |",
"| |This is a really long label |-0.2928 |1.7423 |0.867 | |",
"| |for the Group variable Med | | | | |",
"| |(Intercept) |39.9678 |1.4192 |< 0.001 |-0.0107 |",
"| |Another really long label. |-0.2118 |0.3205 |0.512 | |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |(Intercept) |46.9878 |2.5356 |< 0.001 |0.1478 |",
"| |ThisLabelHasNoSpacesSoLetsSeeH |0.0011 |0.0003 |0.002 | |",
"| |owItBehaves | | | | |"
)
)
})
eheinzen/arsenal documentation built on Sept. 11, 2022, 10:59 a.m.
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context("Testing the modelsum strata and multiple LHS output")
###########################################################################################################
#### Basic modelsum call
###########################################################################################################
test_that("A three-LHS modelsum call", {
expect_identical(
capture.kable(summary(modelsum(list(ht_in, time, Age) ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)),
c(
capture.kable(summary(modelsum(ht_in ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(modelsum(time ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE)), "", "",
capture.kable(summary(modelsum(Age ~ Sex + dt, adjust = ~ trt + Phase, data = mdat), text = TRUE))
)
)
})
test_that("A modelsum call with strata", {
expect_identical(
capture.kable(summary(modelsum(Age ~ Sex + dt, adjust = ~ trt, data = mdat, strata = Group), text = TRUE)),
c("|Group | |estimate |std.error |p.value |adj.r.squared |",
"|:-----|:---------------|:--------|:---------|:-------|:-------------|",
"|High |(Intercept) |40.833 |2.062 |< 0.001 |-0.050 |",
"| |Sex Male |0.333 |2.326 |0.887 | |",
"| |Treatment Arm B |-1.812 |2.331 |0.444 | |",
"| |(Intercept) |39.853 |3.948 |< 0.001 |-0.047 |",
"| |dt |-0.000 |0.001 |0.750 | |",
"| |Treatment Arm B |-1.910 |2.347 |0.423 | |",
"|Low |(Intercept) |40.524 |1.304 |< 0.001 |-0.040 |",
"| |Sex Male |-1.192 |1.463 |0.422 | |",
"| |Treatment Arm B |-0.591 |1.505 |0.697 | |",
"| |(Intercept) |45.146 |2.751 |< 0.001 |0.074 |",
"| |dt |0.001 |0.000 |0.054 | |",
"| |Treatment Arm B |-0.363 |1.423 |0.801 | |",
"|Med |(Intercept) |40.300 |2.069 |< 0.001 |-0.056 |",
"| |Sex Male |0.117 |2.095 |0.956 | |",
"| |Treatment Arm B |-1.467 |2.169 |0.505 | |",
"| |(Intercept) |42.941 |4.383 |< 0.001 |-0.040 |",
"| |dt |0.000 |0.001 |0.528 | |",
"| |Treatment Arm B |-1.650 |2.171 |0.454 | |"
)
)
})
test_that("strata levels are maintained", {
tmp <- mdat
tmp$Group[tmp$trt == "A" & tmp$Group == "Low"] <- NA
expect_identical(
capture.kable(summary(set_labels(modelsum(Age ~ Sex + dt, adjust = ~ Group, strata = trt, data = tmp), c(GroupLow = "Low")), text = TRUE)),
c("|Treatment Arm | |estimate |std.error |p.value |adj.r.squared |Nmiss |",
"|:-------------|:-----------|:--------|:---------|:-------|:-------------|:-----|",
"|A |(Intercept) |42.139 |2.047 |< 0.001 |-0.047 |11 |",
"| |Sex Male |-2.277 |2.456 |0.364 | | |",
"| |Group Med |-0.533 |2.472 |0.831 | | |",
"| |(Intercept) |34.850 |3.600 |< 0.001 |0.065 |11 |",
"| |dt |-0.001 |0.000 |0.072 | | |",
"| |Group Med |-1.642 |2.394 |0.500 | | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |0 |",
"| |Sex Male |0.908 |1.407 |0.522 | | |",
"| |Low |0.205 |1.753 |0.907 | | |",
"| |Group Med |-0.317 |1.753 |0.857 | | |",
"| |(Intercept) |47.149 |2.812 |< 0.001 |0.114 |0 |",
"| |dt |0.001 |0.000 |0.003 | | |",
"| |Low |-0.145 |1.613 |0.929 | | |",
"| |Group Med |-0.318 |1.610 |0.844 | | |"
)
)
})
test_that("Multiple adjustments work (#240)", {
tmp.ms <- modelsum(list(age, bmi) ~ fu.time + ast, adjust = list(Unadjusted = ~ 1, "Adjusted for Arm" = ~ arm, "HGB + PS" = ~ hgb + ps),
data = set_labels(mockstudy, list(ast = "AST", ps = "PS")), strata = sex,
gaussian.stats = c("estimate", "std.error", "p.value", "adj.r.squared", "Nmiss", "N"))
tmp.ms2 <- modelsum(list(age, bmi) ~ fu.time + ast, adjust = list(Unadjusted = ~ NULL, "Adjusted for Arm" = ~ arm, "HGB + PS" = ~ hgb + ps),
data = set_labels(mockstudy, list(ast = "AST", ps = "PS")), strata = sex,
gaussian.stats = c("estimate", "std.error", "p.value", "adj.r.squared", "Nmiss", "N"))
expect_identical(
capture.kable(summary(tmp.ms, adjustment.names = TRUE, term.name = TRUE)),
capture.kable(summary(tmp.ms2, adjustment.names = TRUE, term.name = TRUE))
)
expect_identical(
capture.kable(summary(tmp.ms, adjustment.names = TRUE, term.name = TRUE)),
c("|sex |adjustment |Age in Years |estimate |std.error |p.value |adj.r.squared |Nmiss |N |",
"|:------|:----------------|:---------------------------|:--------|:---------|:-------|:-------------|:-----|:---|",
"|Male |Unadjusted |(Intercept) |61.686 |0.654 |< 0.001 |0.005 |0 |916 |",
"| | |**fu.time** |-0.002 |0.001 |0.022 | | | |",
"| |Adjusted for Arm |(Intercept) |61.073 |0.837 |< 0.001 |0.004 |0 |916 |",
"| | |**fu.time** |-0.002 |0.001 |0.016 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.048 |0.889 |0.239 | | | |",
"| | |**Treatment Arm G: IROX** |0.857 |1.015 |0.399 | | | |",
"| |HGB + PS |(Intercept) |57.090 |3.068 |< 0.001 |0.010 |162 |754 |",
"| | |**fu.time** |-0.002 |0.001 |0.008 | | | |",
"| | |**hgb** |0.365 |0.234 |0.118 | | | |",
"| | |**PS** |0.881 |0.746 |0.238 | | | |",
"| |Unadjusted |(Intercept) |61.556 |0.696 |< 0.001 |0.003 |162 |754 |",
"| | |**AST** |-0.028 |0.016 |0.074 | | | |",
"| |Adjusted for Arm |(Intercept) |61.524 |0.947 |< 0.001 |0.001 |162 |754 |",
"| | |**AST** |-0.028 |0.016 |0.075 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.322 |0.977 |0.741 | | | |",
"| | |**Treatment Arm G: IROX** |-0.445 |1.115 |0.690 | | | |",
"| |HGB + PS |(Intercept) |57.707 |3.133 |< 0.001 |0.006 |162 |754 |",
"| | |**AST** |-0.032 |0.016 |0.043 | | | |",
"| | |**hgb** |0.253 |0.232 |0.276 | | | |",
"| | |**PS** |1.529 |0.739 |0.039 | | | |",
"|Female |Unadjusted |(Intercept) |59.385 |0.822 |< 0.001 |-0.002 |0 |583 |",
"| | |**fu.time** |-0.000 |0.001 |0.835 | | | |",
"| |Adjusted for Arm |(Intercept) |59.449 |1.089 |< 0.001 |-0.003 |0 |583 |",
"| | |**fu.time** |-0.000 |0.001 |0.707 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.580 |1.216 |0.634 | | | |",
"| | |**Treatment Arm G: IROX** |-0.856 |1.353 |0.527 | | | |",
"| |HGB + PS |(Intercept) |46.660 |4.632 |< 0.001 |0.015 |104 |479 |",
"| | |**fu.time** |-0.001 |0.001 |0.564 | | | |",
"| | |**hgb** |1.156 |0.378 |0.002 | | | |",
"| | |**PS** |-0.421 |0.902 |0.641 | | | |",
"| |Unadjusted |(Intercept) |61.001 |0.883 |< 0.001 |0.004 |104 |479 |",
"| | |**AST** |-0.033 |0.020 |0.096 | | | |",
"| |Adjusted for Arm |(Intercept) |60.687 |1.266 |< 0.001 |0.006 |104 |479 |",
"| | |**AST** |-0.032 |0.020 |0.102 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.253 |1.297 |0.334 | | | |",
"| | |**Treatment Arm G: IROX** |-1.006 |1.441 |0.486 | | | |",
"| |HGB + PS |(Intercept) |47.825 |4.730 |< 0.001 |0.017 |104 |479 |",
"| | |**AST** |-0.026 |0.020 |0.193 | | | |",
"| | |**hgb** |1.086 |0.376 |0.004 | | | |",
"| | |**PS** |-0.115 |0.873 |0.895 | | | |",
"" ,
"" ,
"|sex |adjustment |Body Mass Index (kg/m^2) |estimate |std.error |p.value |adj.r.squared |Nmiss |N |",
"|:------|:----------------|:---------------------------|:--------|:---------|:-------|:-------------|:-----|:---|",
"|Male |Unadjusted |(Intercept) |26.679 |0.294 |< 0.001 |0.011 |22 |894 |",
"| | |**fu.time** |0.001 |0.000 |< 0.001 | | | |",
"| |Adjusted for Arm |(Intercept) |26.901 |0.376 |< 0.001 |0.012 |22 |894 |",
"| | |**fu.time** |0.001 |0.000 |< 0.001 | | | |",
"| | |**Treatment Arm F: FOLFOX** |-0.594 |0.397 |0.134 | | | |",
"| | |**Treatment Arm G: IROX** |-0.040 |0.451 |0.930 | | | |",
"| |HGB + PS |(Intercept) |23.559 |1.321 |< 0.001 |0.036 |181 |735 |",
"| | |**fu.time** |0.001 |0.000 |0.021 | | | |",
"| | |**hgb** |0.283 |0.101 |0.005 | | | |",
"| | |**PS** |-0.794 |0.322 |0.014 | | | |",
"| |Unadjusted |(Intercept) |27.885 |0.306 |< 0.001 |0.006 |181 |735 |",
"| | |**AST** |-0.016 |0.007 |0.023 | | | |",
"| |Adjusted for Arm |(Intercept) |28.040 |0.412 |< 0.001 |0.004 |181 |735 |",
"| | |**AST** |-0.016 |0.007 |0.023 | | | |",
"| | |**Treatment Arm F: FOLFOX** |-0.354 |0.427 |0.408 | | | |",
"| | |**Treatment Arm G: IROX** |0.015 |0.486 |0.976 | | | |",
"| |HGB + PS |(Intercept) |24.297 |1.350 |< 0.001 |0.032 |181 |735 |",
"| | |**AST** |-0.011 |0.007 |0.123 | | | |",
"| | |**hgb** |0.307 |0.100 |0.002 | | | |",
"| | |**PS** |-0.878 |0.318 |0.006 | | | |",
"|Female |Unadjusted |(Intercept) |26.198 |0.423 |< 0.001 |0.003 |11 |572 |",
"| | |**fu.time** |0.001 |0.001 |0.101 | | | |",
"| |Adjusted for Arm |(Intercept) |26.198 |0.560 |< 0.001 |0.002 |11 |572 |",
"| | |**fu.time** |0.001 |0.001 |0.164 | | | |",
"| | |**Treatment Arm F: FOLFOX** |0.366 |0.625 |0.558 | | | |",
"| | |**Treatment Arm G: IROX** |-0.386 |0.692 |0.577 | | | |",
"| |HGB + PS |(Intercept) |27.620 |2.409 |< 0.001 |-0.000 |113 |470 |",
"| | |**fu.time** |0.001 |0.001 |0.099 | | | |",
"| | |**hgb** |-0.121 |0.196 |0.539 | | | |",
"| | |**PS** |0.184 |0.467 |0.694 | | | |",
"| |Unadjusted |(Intercept) |26.500 |0.456 |< 0.001 |0.001 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.247 | | | |",
"| |Adjusted for Arm |(Intercept) |26.062 |0.649 |< 0.001 |0.008 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.225 | | | |",
"| | |**Treatment Arm F: FOLFOX** |1.102 |0.669 |0.100 | | | |",
"| | |**Treatment Arm G: IROX** |-0.276 |0.741 |0.710 | | | |",
"| |HGB + PS |(Intercept) |27.324 |2.462 |< 0.001 |-0.003 |113 |470 |",
"| | |**AST** |0.012 |0.010 |0.255 | | | |",
"| | |**hgb** |-0.064 |0.196 |0.743 | | | |",
"| | |**PS** |-0.103 |0.454 |0.821 | | | |"
)
)
expect_identical(
capture.kable(summary(modelsum(Age ~ Sex + time, data = mdat), text = TRUE, adjustment.names = TRUE)),
c("|adjustment | |estimate |std.error |p.value |adj.r.squared |",
"|:----------|:-----------|:--------|:---------|:-------|:-------------|",
"|unadjusted |(Intercept) |39.826 |0.779 |< 0.001 |-0.011 |",
"| |Sex Male |-0.258 |1.115 |0.818 | |",
"|unadjusted |(Intercept) |41.130 |1.197 |< 0.001 |0.009 |",
"| |time |-0.371 |0.275 |0.182 | |"
)
)
})
###########################################################################################################
#### Other warnings and tests and things...
###########################################################################################################
test_that("Reordering variables and subsetting", {
tmp.tab <- modelsum(list(Age, time) ~ Sex + dt + ethan, adjust = ~ Group, strata = trt, data = mdat)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2), 2:1], text = TRUE)),
capture.kable(summary(modelsum(list(time, Age) ~ ethan + Sex + dt, adjust = ~ Group, strata = trt, data = mdat), text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[c(3,1,2)], text = TRUE)),
capture.kable(summary(tmp.tab[c("ethan", "Sex", "dt")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2:1], text = TRUE)),
capture.kable(summary(tmp.tab[, c("time", "Age")], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[1:2], text = TRUE)),
capture.kable(summary(tmp.tab[c(TRUE, TRUE, FALSE)], text = TRUE))
)
expect_identical(
capture.kable(summary(tmp.tab[, 2], text = TRUE)),
capture.kable(summary(tmp.tab[, c(FALSE, TRUE)], text = TRUE))
)
expect_warning(tmp.tab[1:4], "Some indices not found")
expect_warning(tmp.tab[, 1:3], "Some indices not found")
expect_error(tmp.tab[TRUE], "Logical vector")
expect_error(tmp.tab[, TRUE], "Logical vector")
})
test_that("Merging modelsum objects", {
tb1 <- modelsum(list(Age, time) ~ Sex + Phase, strata = trt, data = mdat)
tb2 <- modelsum(list(as.numeric(dt), ht_in) ~ Group, strata = trt, data = mdat)
tb3 <- modelsum(list(Age, ht_in, time) ~ Group + ethan, strata = trt, data = mdat)
tb4 <- modelsum(list(Age, time) ~ Sex + Phase + Group + ethan, strata = trt, data = mdat)
expect_error(merge(tb1, tb2), "No terms in common")
expect_identical(
capture.kable(summary(merge(tb1, tb2, all = TRUE))),
c(capture.kable(summary(tb1)), "", "", capture.kable(summary(tb2)))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all.x = TRUE), text = TRUE)),
capture.kable(summary(tb4, text = TRUE))
)
expect_identical(
capture.kable(summary(merge(tb1, tb3, all = TRUE), text = TRUE)),
c(
capture.kable(summary(tb4, text = TRUE)), "", "",
capture.kable(summary(modelsum(ht_in ~ Group + ethan, data = mdat, strata = trt), text = TRUE))
)
)
})
test_that("Changing labels", {
mdat.tmp <- set_labels(mdat, NULL)
mdat.tmp$`1x` <- 1:nrow(mdat.tmp)
mdat.tmp$`2x` <- rep(c("A", "B"), each = nrow(mdat.tmp)/2)
tab <- modelsum(list(Age, time) ~ Sex + `1x` + `2x`, adjust = ~ Group, strata = trt, data = mdat.tmp)
tmp <- capture.kable(summary(tab, text = TRUE, term.name = TRUE))
expect_warning(labels(tab) <- c(hi = "hi", SexMale = "Male", Age = "Age 1", time = "Time", trt = "Trt Arm",
GroupLow = "Low", "`1x`" = "onex", "`2x`B" = "B"), NA)
expect_identical(
capture.kable(summary(tab, text = TRUE, term.name = TRUE)),
c("|Trt Arm |Age 1 |estimate |std.error |p.value |adj.r.squared |",
"|:-------|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |42.000 |1.795 |< 0.001 |-0.052 |",
"| |Male |-2.000 |1.918 |0.305 | |",
"| |Low |-1.182 |2.303 |0.611 | |",
"| |Group Med |-0.545 |2.290 |0.813 | |",
"| |(Intercept) |41.277 |2.281 |< 0.001 |-0.087 |",
"| |onex |-0.019 |0.113 |0.870 | |",
"| |Low |0.237 |7.336 |0.974 | |",
"| |Group Med |-0.083 |4.085 |0.984 | |",
"| |(Intercept) |41.000 |1.543 |< 0.001 |-0.087 |",
"| |B |-0.667 |3.495 |0.850 | |",
"| |Low |-0.242 |4.198 |0.954 | |",
"| |Group Med |-0.333 |2.817 |0.907 | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |",
"| |Male |0.908 |1.407 |0.522 | |",
"| |Low |0.205 |1.753 |0.907 | |",
"| |Group Med |-0.317 |1.753 |0.857 | |",
"| |(Intercept) |38.753 |1.835 |< 0.001 |-0.056 |",
"| |onex |0.027 |0.081 |0.739 | |",
"| |Low |-1.414 |5.083 |0.782 | |",
"| |Group Med |-1.105 |2.996 |0.714 | |",
"| |(Intercept) |39.187 |1.296 |< 0.001 |-0.058 |",
"| |B |0.011 |2.383 |0.996 | |",
"| |Low |0.170 |2.962 |0.955 | |",
"| |Group Med |-0.299 |2.161 |0.891 | |",
"" ,
"" ,
"|Trt Arm |Time |estimate |std.error |p.value |adj.r.squared |",
"|:-------|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |4.469 |0.568 |< 0.001 |-0.016 |",
"| |Male |-0.223 |0.606 |0.716 | |",
"| |Low |-1.115 |0.728 |0.136 | |",
"| |Group Med |-0.620 |0.724 |0.398 | |",
"| |(Intercept) |5.331 |0.671 |< 0.001 |0.090 |",
"| |onex |-0.066 |0.033 |0.058 | |",
"| |Low |2.947 |2.159 |0.182 | |",
"| |Group Med |1.316 |1.202 |0.282 | |",
"| |(Intercept) |4.357 |0.475 |< 0.001 |0.004 |",
"| |B |-0.967 |1.076 |0.376 | |",
"| |Low |-0.118 |1.292 |0.928 | |",
"| |Group Med |-0.190 |0.867 |0.828 | |",
"|B |(Intercept) |4.301 |0.591 |< 0.001 |0.086 |",
"| |Male |0.898 |0.566 |0.119 | |",
"| |Low |-1.621 |0.705 |0.026 | |",
"| |Group Med |-0.879 |0.705 |0.218 | |",
"| |(Intercept) |3.710 |0.725 |< 0.001 |0.112 |",
"| |onex |0.065 |0.032 |0.048 | |",
"| |Low |-5.461 |2.008 |0.009 | |",
"| |Group Med |-2.797 |1.184 |0.022 | |",
"| |(Intercept) |4.750 |0.516 |< 0.001 |0.098 |",
"| |B |1.700 |0.948 |0.079 | |",
"| |Low |-3.345 |1.179 |0.007 | |",
"| |Group Med |-1.750 |0.860 |0.047 | |"
)
)
labels(tab) <- NULL
expect_identical(
capture.kable(summary(tab, text = TRUE, term.name = TRUE)),
tmp
)
expect_identical(
tmp,
c("|trt |Age |estimate |std.error |p.value |adj.r.squared |",
"|:---|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |42.000 |1.795 |< 0.001 |-0.052 |",
"| |Sex Male |-2.000 |1.918 |0.305 | |",
"| |Group Low |-1.182 |2.303 |0.611 | |",
"| |Group Med |-0.545 |2.290 |0.813 | |",
"| |(Intercept) |41.277 |2.281 |< 0.001 |-0.087 |",
"| |1x |-0.019 |0.113 |0.870 | |",
"| |Group Low |0.237 |7.336 |0.974 | |",
"| |Group Med |-0.083 |4.085 |0.984 | |",
"| |(Intercept) |41.000 |1.543 |< 0.001 |-0.087 |",
"| |2x B |-0.667 |3.495 |0.850 | |",
"| |Group Low |-0.242 |4.198 |0.954 | |",
"| |Group Med |-0.333 |2.817 |0.907 | |",
"|B |(Intercept) |38.733 |1.470 |< 0.001 |-0.050 |",
"| |Sex Male |0.908 |1.407 |0.522 | |",
"| |Group Low |0.205 |1.753 |0.907 | |",
"| |Group Med |-0.317 |1.753 |0.857 | |",
"| |(Intercept) |38.753 |1.835 |< 0.001 |-0.056 |",
"| |1x |0.027 |0.081 |0.739 | |",
"| |Group Low |-1.414 |5.083 |0.782 | |",
"| |Group Med |-1.105 |2.996 |0.714 | |",
"| |(Intercept) |39.187 |1.296 |< 0.001 |-0.058 |",
"| |2x B |0.011 |2.383 |0.996 | |",
"| |Group Low |0.170 |2.962 |0.955 | |",
"| |Group Med |-0.299 |2.161 |0.891 | |",
"" ,
"" ,
"|trt |time |estimate |std.error |p.value |adj.r.squared |",
"|:---|:-----------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |4.469 |0.568 |< 0.001 |-0.016 |",
"| |Sex Male |-0.223 |0.606 |0.716 | |",
"| |Group Low |-1.115 |0.728 |0.136 | |",
"| |Group Med |-0.620 |0.724 |0.398 | |",
"| |(Intercept) |5.331 |0.671 |< 0.001 |0.090 |",
"| |1x |-0.066 |0.033 |0.058 | |",
"| |Group Low |2.947 |2.159 |0.182 | |",
"| |Group Med |1.316 |1.202 |0.282 | |",
"| |(Intercept) |4.357 |0.475 |< 0.001 |0.004 |",
"| |2x B |-0.967 |1.076 |0.376 | |",
"| |Group Low |-0.118 |1.292 |0.928 | |",
"| |Group Med |-0.190 |0.867 |0.828 | |",
"|B |(Intercept) |4.301 |0.591 |< 0.001 |0.086 |",
"| |Sex Male |0.898 |0.566 |0.119 | |",
"| |Group Low |-1.621 |0.705 |0.026 | |",
"| |Group Med |-0.879 |0.705 |0.218 | |",
"| |(Intercept) |3.710 |0.725 |< 0.001 |0.112 |",
"| |1x |0.065 |0.032 |0.048 | |",
"| |Group Low |-5.461 |2.008 |0.009 | |",
"| |Group Med |-2.797 |1.184 |0.022 | |",
"| |(Intercept) |4.750 |0.516 |< 0.001 |0.098 |",
"| |2x B |1.700 |0.948 |0.079 | |",
"| |Group Low |-3.345 |1.179 |0.007 | |",
"| |Group Med |-1.750 |0.860 |0.047 | |"
)
)
})
###########################################################################################################
#### Reported bugs for modelsum
###########################################################################################################
test_that("02/23/2018: wrapping long labels (#59)", {
labs <- list(
Group = "This is a really long label for the Group variable",
time = "Another really long label. Can you believe how long this is",
dt = "ThisLabelHasNoSpacesSoLetsSeeHowItBehaves",
trt = NULL
)
expect_identical(
capture.kable(print(summary(modelsum(Age ~ Group + time + dt, strata = trt, data = set_labels(mdat, labs)), text = TRUE, digits = 4), width = 30)),
c("|trt | |estimate |std.error |p.value |adj.r.squared |",
"|:---|:------------------------------|:--------|:---------|:-------|:-------------|",
"|A |(Intercept) |41.0000 |1.5200 |< 0.001 |-0.0552 |",
"| |This is a really long label |-0.9091 |2.2915 |0.694 | |",
"| |for the Group variable Low | | | | |",
"| |This is a really long label |-0.6364 |2.2915 |0.783 | |",
"| |for the Group variable Med | | | | |",
"| |(Intercept) |43.2848 |2.1872 |< 0.001 |0.0257 |",
"| |Another really long label. |-0.7192 |0.5187 |0.175 | |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |(Intercept) |36.3141 |2.9357 |< 0.001 |0.0352 |",
"| |ThisLabelHasNoSpacesSoLetsSeeH |-0.0006 |0.0004 |0.141 | |",
"| |owItBehaves | | | | |",
"|B |(Intercept) |39.1875 |1.2837 |< 0.001 |-0.0375 |",
"| |This is a really long label |0.1809 |1.7423 |0.918 | |",
"| |for the Group variable Low | | | | |",
"| |This is a really long label |-0.2928 |1.7423 |0.867 | |",
"| |for the Group variable Med | | | | |",
"| |(Intercept) |39.9678 |1.4192 |< 0.001 |-0.0107 |",
"| |Another really long label. |-0.2118 |0.3205 |0.512 | |",
"| |Can you believe how long this | | | | |",
"| |is | | | | |",
"| |(Intercept) |46.9878 |2.5356 |< 0.001 |0.1478 |",
"| |ThisLabelHasNoSpacesSoLetsSeeH |0.0011 |0.0003 |0.002 | |",
"| |owItBehaves | | | | |"
)
)
})
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