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scurvy <- medicaldata::scurvy
# now print the columns for id and treatment
scurvy %>%
select(study_id:treatment) |> #this selects columns
slice_tail(n = 7) #slices last seven rows## # A tibble: 7 × 2
## study_id treatment
## <chr> <fct>
## 1 006 vinegar
## 2 007 sea_water
## 3 008 sea_water
## 4 009 citrus
## 5 010 citrus
## 6 011 purgative_mixture
## 7 012 purgative_mixturemedicaldata::cytomegalovirus %>%
head()url_stem <- "https://raw.githubusercontent.com/higgi13425/rmrwr-book/master/"
url_stem## [1] "https://raw.githubusercontent.com/higgi13425/rmrwr-book/master/"read_csv(glue(url_stem,'data/scurvy.csv'))## Rows: 12 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (8): study_id, treatment, dosing_regimen_for_scurvy, gum_rot_d6, skin_so...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.## # A tibble: 12 × 8
## study_id treatment dosing_regimen_for_s…¹ gum_rot_d6 skin_sores_d6
## <chr> <chr> <chr> <chr> <chr>
## 1 001 cider 1 quart per day 2_moderate 2_moderate
## 2 002 cider 1 quart per day 2_moderate 1_mild
## 3 003 dilute_sulfuric_acid 25 drops of elixir of… 1_mild 3_severe
## 4 004 dilute_sulfuric_acid 25 drops of elixir of… 2_moderate 3_severe
## 5 005 vinegar two spoonfuls, three … 3_severe 3_severe
## 6 006 vinegar two spoonfuls, three … 3_severe 3_severe
## 7 007 sea_water half pint daily 3_severe 3_severe
## 8 008 sea_water half pint daily 3_severe 3_severe
## 9 009 citrus two lemons and an ora… 1_mild 1_mild
## 10 010 citrus two lemons and an ora… 0_none 0_none
## 11 011 purgative_mixture a nutmeg-sized paste … 3_severe 3_severe
## 12 012 purgative_mixture a nutmeg-sized paste … 3_severe 3_severe
## # ℹ abbreviated name: ¹dosing_regimen_for_scurvy
## # ℹ 3 more variables: weakness_of_the_knees_d6 <chr>, lassitude_d6 <chr>,
## # fit_for_duty_d6 <chr>scurvy_data <- read_csv(glue(url_stem, 'data/scurvy.csv'))## Rows: 12 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (8): study_id, treatment, dosing_regimen_for_scurvy, gum_rot_d6, skin_so...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.read_csv(file = glue(url_stem, 'data/scurvy.csv'),
col_names = c("pat_id", "arm", "dose", "gums", "skin", "weak", "lass", "fit"))## Rows: 13 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (8): pat_id, arm, dose, gums, skin, weak, lass, fit
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.## # A tibble: 13 × 8
## pat_id arm dose gums skin weak lass fit
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 study_id treatment dosing_regimen_f… gum_… skin… weak… lass… fit_…
## 2 001 cider 1 quart per day 2_mo… 2_mo… 2_mo… 2_mo… 0_no
## 3 002 cider 1 quart per day 2_mo… 1_mi… 2_mo… 3_se… 0_no
## 4 003 dilute_sulfuric_acid 25 drops of elix… 1_mi… 3_se… 3_se… 3_se… 0_no
## 5 004 dilute_sulfuric_acid 25 drops of elix… 2_mo… 3_se… 3_se… 3_se… 0_no
## 6 005 vinegar two spoonfuls, t… 3_se… 3_se… 3_se… 3_se… 0_no
## 7 006 vinegar two spoonfuls, t… 3_se… 3_se… 3_se… 3_se… 0_no
## 8 007 sea_water half pint daily 3_se… 3_se… 3_se… 3_se… 0_no
## 9 008 sea_water half pint daily 3_se… 3_se… 3_se… 3_se… 0_no
## 10 009 citrus two lemons and a… 1_mi… 1_mi… 0_no… 1_mi… 0_no
## 11 010 citrus two lemons and a… 0_no… 0_no… 0_no… 0_no… 1_yes
## 12 011 purgative_mixture a nutmeg-sized p… 3_se… 3_se… 3_se… 3_se… 0_no
## 13 012 purgative_mixture a nutmeg-sized p… 3_se… 3_se… 3_se… 3_se… 0_noread_csv(file = glue(url_stem, 'data/scurvy.csv'),
col_names = c("pat_id", "arm", "dose", "gums", "skin", "weak", "lass", "fit"),
skip = 1)## Rows: 12 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (8): pat_id, arm, dose, gums, skin, weak, lass, fit
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.## # A tibble: 12 × 8
## pat_id arm dose gums skin weak lass fit
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 001 cider 1 quart per day 2_mo… 2_mo… 2_mo… 2_mo… 0_no
## 2 002 cider 1 quart per day 2_mo… 1_mi… 2_mo… 3_se… 0_no
## 3 003 dilute_sulfuric_acid 25 drops of elixir… 1_mi… 3_se… 3_se… 3_se… 0_no
## 4 004 dilute_sulfuric_acid 25 drops of elixir… 2_mo… 3_se… 3_se… 3_se… 0_no
## 5 005 vinegar two spoonfuls, thr… 3_se… 3_se… 3_se… 3_se… 0_no
## 6 006 vinegar two spoonfuls, thr… 3_se… 3_se… 3_se… 3_se… 0_no
## 7 007 sea_water half pint daily 3_se… 3_se… 3_se… 3_se… 0_no
## 8 008 sea_water half pint daily 3_se… 3_se… 3_se… 3_se… 0_no
## 9 009 citrus two lemons and an … 1_mi… 1_mi… 0_no… 1_mi… 0_no
## 10 010 citrus two lemons and an … 0_no… 0_no… 0_no… 0_no… 1_yes
## 11 011 purgative_mixture a nutmeg-sized pas… 3_se… 3_se… 3_se… 3_se… 0_no
## 12 012 purgative_mixture a nutmeg-sized pas… 3_se… 3_se… 3_se… 3_se… 0_nospec(scurvy_data)## cols(
## study_id = col_character(),
## treatment = col_character(),
## dosing_regimen_for_scurvy = col_character(),
## gum_rot_d6 = col_character(),
## skin_sores_d6 = col_character(),
## weakness_of_the_knees_d6 = col_character(),
## lassitude_d6 = col_character(),
## fit_for_duty_d6 = col_character()
## )scurvy_cols <- read_csv(
file = glue(url_stem, 'data/scurvy.csv'),
col_types = cols(
study_id = col_integer(),
treatment = col_factor(),
dosing_regimen_for_scurvy = col_character(),
gum_rot_d6 = col_character(),
skin_sores_d6 = col_character(),
weakness_of_the_knees_d6 = col_character(),
lassitude_d6 = col_character(),
fit_for_duty_d6 = col_character()
)
)
glimpse(scurvy_cols)## Rows: 12
## Columns: 8
## $ study_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
## $ treatment <fct> cider, cider, dilute_sulfuric_acid, dilute_s…
## $ dosing_regimen_for_scurvy <chr> "1 quart per day", "1 quart per day", "25 dr…
## $ gum_rot_d6 <chr> "2_moderate", "2_moderate", "1_mild", "2_mod…
## $ skin_sores_d6 <chr> "2_moderate", "1_mild", "3_severe", "3_sever…
## $ weakness_of_the_knees_d6 <chr> "2_moderate", "2_moderate", "3_severe", "3_s…
## $ lassitude_d6 <chr> "2_moderate", "3_severe", "3_severe", "3_sev…
## $ fit_for_duty_d6 <chr> "0_no", "0_no", "0_no", "0_no", "0_no", "0_n…scurvy_cols2 <- read_csv(
file = glue(url_stem, 'data/scurvy.csv'),
col_types = "ifcffff")
glimpse(scurvy_cols2)## Rows: 12
## Columns: 8
## $ study_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
## $ treatment <fct> cider, cider, dilute_sulfuric_acid, dilute_s…
## $ dosing_regimen_for_scurvy <chr> "1 quart per day", "1 quart per day", "25 dr…
## $ gum_rot_d6 <fct> 2_moderate, 2_moderate, 1_mild, 2_moderate, …
## $ skin_sores_d6 <fct> 2_moderate, 1_mild, 3_severe, 3_severe, 3_se…
## $ weakness_of_the_knees_d6 <fct> 2_moderate, 2_moderate, 3_severe, 3_severe, …
## $ lassitude_d6 <fct> 2_moderate, 3_severe, 3_severe, 3_severe, 3_…
## $ fit_for_duty_d6 <chr> "0_no", "0_no", "0_no", "0_no", "0_no", "0_n…