# from dput(output_str) output_str <- c( "", "", "", "", "", "", "", "", "", "", "", "", "", "", "Test", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "
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Test

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MG

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Sunday, July 13, 2014

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All analyses were performed using R (ver. 3.1.1)[R Core Team, 2013] and packages rms (ver. 4.2-0) [F. Harrell, 2014] for analysis, Gmisc for plot and table output (ver. 0.6.6), and knitr (ver ) [Xie, 2013] for reproducible research.

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Results

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We found 205 patients with malignant melanoma between the years 1962 and 1977. Patients were followed until the end of 1977, the median follow-up time was 5.5 years (range 0.0 to 15.2 years). Males were more common than females and had also a higher mortality rate.

", "", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", "
", " ", "Table 1: Baseline characteristics", "
", " ", "", " ", "", "Death", "
", " ", "", "Total", "", "Alive", "", " ", "", "Melanoma", "", "Non-melanoma", "
", "Sex", "
", " Male", "", "126 (61%)", "", "91 (72%)", "", " ", "", "28 (22%)", "", "7 (6%)", "
", " Female", "", "79 (39%)", "", "43 (54%)", "", " ", "", "29 (37%)", "", "7 (9%)", "
", "Age", "
", " Mean (SD)", "", "52 (± 17)", "", "50 (± 16)", "", " ", "", "55 (± 18)", "", "65 (± 11)", "
", "Ulceration", "
", " Absent", "", "115 (56%)", "", "92 (80%)", "", " ", "", "16 (14%)", "", "7 (6%)", "
", " Present", "", "90 (44%)", "", "42 (47%)", "", " ", "", "41 (46%)", "", "7 (8%)", "
", "Thickness", "
", " Mean (SD)", "", "2.9 (±3.0)", "", "2.2 (±2.3)", "", " ", "", "4.3 (±3.6)", "", "3.7 (±3.6)", "
", " ", " Age at the time of surgery.
Tumour thicknes, also known as Breslow thickness, measured in mm.", "
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Main results

", "", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", "
", " ", "Table 2: Adjusted and unadjusted estimates for melanoma specific death.", "
", " ", "", " ", "", "Crude", "", " ", "", "Adjusted", "
", "Variable", "", "Total", "", "Event", "", " ", "", "HR", "", "2.5 % to 97.5 %", "", " ", "", "HR", "", "2.5 % to 97.5 %", "
", "Sex", "
", " Male", "", "126", "", "28 (22%)", "", " ", "", "1", "", "ref", "", " ", "", "1", "", "ref", "
", " Female", "", "79", "", "29 (37%)", "", " ", "", "1.94", "", "1.15 to 3.26", "", " ", "", "1.54", "", "0.91 to 2.60", "
", "Age", "", "52 (± 17)", "", "55 (± 18)", "", " ", "", "1.02", "", "1.00 to 1.04", "", " ", "", "1.01", "", "1.00 to 1.03", "
", "Ulceration", "
", " Absent", "", "115", "", "16 (14%)", "", " ", "", "1", "", "ref", "", " ", "", "1", "", "ref", "
", " Present", "", "90", "", "41 (46%)", "", " ", "", "4.36", "", "2.44 to 7.77", "", " ", "", "3.20", "", "1.75 to 5.88", "
", "Breslow thickness", "", "3 (± 3)", "", "4 (± 4)", "", " ", "", "1.17", "", "1.10 to 1.25", "", " ", "", "1.12", "", "1.04 to 1.20", "
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After adjusting for the three variables, age, sex, tumor thickness and ulceration, only the latter two remained significant (p-value < 0.001 and 0.004), see table 1 and figure I.

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", "Figure I: A forest plot comparing the regression coefficients.", "
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There was no strong indication for non-linearity for any of the continuous variables although the impact of thickness did seem to lessen above 4 mm, see figure II.

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", "Figure II: The adjusted and unadjusted restricted cubic spline for tumor thickness. Solid line and confidence interval indicate the adjusted line while the dashed is the unadjusted line. The grey area at the bottom indicates the density.", "
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", "", "", "
", "", "", "", "", "", "", "", "" ) test_that("Proper script removal", { expect_false(all(grepl("--s", prFtpOtherRemoval(output_str)))) expect_false(all(grepl("Content-Style-Type", prFtpOtherRemoval(output_str)))) expect_false(all(grepl("