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Remove str() from mcs reshape
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@ljwright
ljwright committed Sep 19, 2024
1 parent ff83b36 commit 7dc9dc8
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76 changes: 17 additions & 59 deletions docs/mcs-reshape_long_wide.md
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Original file line number Diff line number Diff line change
Expand Up @@ -55,68 +55,26 @@ df_wide <- map(3:7, load_height_wide) %>%
reduce(~ full_join(.x, .y, by = c("MCSID", "CNUM00"))) %>%
rename(ECHTCM00 = ECHTCMA0, ECWTCMA00 = ECWTCMA0)

str(df_wide)
df_wide
```

``` text
tibble [16,618 × 12] (S3: tbl_df/tbl/data.frame)
$ MCSID : chr [1:16618] "M10001N" "M10002P" "M10007U" "M10011Q" ...
..- attr(*, "label")= chr "MCS Research ID - Anonymised Family/Household Identifier"
..- attr(*, "format.stata")= chr "%7s"
$ CNUM00 : dbl+lbl [1:16618] 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1...
..@ labels: Named num [1:3] 1 2 3
.. ..- attr(*, "names")= chr [1:3] "1st Cohort Member of the family" "2nd Cohort Member of the family" "3rd Cohort Member of the family"
..@ label : chr "Cohort Member number within an MCS family"
$ CCHTCM00 : dbl+lbl [1:16618] 114, 110, 118, 121, 110, 118, 110, 113, 112, 108, 11...
..@ label : chr "PHYS: Height in cms"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:5] -9 -8 -1 99998 99999
.. ..- attr(*, "names")= chr [1:5] "Refusal" "Don't Know" "Not applicable" "Refusal" ...
$ CCWTCM00 : dbl+lbl [1:16618] 21.2, 19.2, 25.3, 32.9, 19.7, 23.0, 18.9, 19.4, 20.6...
..@ label : chr "PHYS: Weight in Kilograms"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:3] -9 -8 -1
.. ..- attr(*, "names")= chr [1:3] "Refusal" "Don't Know" "Not applicable"
$ DCHTCM00 : dbl+lbl [1:16618] 128, 123, 129, 137, 122, 130, 121, 128, 123, 121, N...
..@ label : chr "Height in cms"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:3] -9 -8 -1
.. ..- attr(*, "names")= chr [1:3] "Refusal" "Don''t Know" "Not applicable"
$ DCWTCM00 : dbl+lbl [1:16618] 25.5, 26.2, 26.5, 51.2, 24.1, 29.0, 21.7, 22.0, 24.6...
..@ label : chr "Weight in Kilos"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:3] -9 -8 -1
.. ..- attr(*, "names")= chr [1:3] "Refusal" "Don''t Know" "Not applicable"
$ ECHTCM00 : dbl+lbl [1:16618] NA, 144, 154, 168, 143, 152, NA, 150, 141, 147, 15...
..@ label : chr "Height in cms"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -7 -1
.. ..- attr(*, "names")= chr [1:2] "No answer" "Not applicable"
$ ECWTCMA00: dbl+lbl [1:16618] NA, 41.8, 40.6, 74.0, 38.2, 41.5, NA, 37.3, 33.8...
..@ label : chr "Weight in kilos"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -7 -1
.. ..- attr(*, "names")= chr [1:2] "No answer" "Not applicable"
$ FCHTCM00 : dbl+lbl [1:16618] NA, 163, 174, NA, 164, 167, NA, 164, 161, 157, 16...
..@ label : chr "Height in centimeters"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -5 -1
.. ..- attr(*, "names")= chr [1:2] "UNABLE TO OBTAIN HEIGHT MEASUREMENT" "Not applicable"
$ FCWTCM00 : dbl+lbl [1:16618] NA, 52.3, 57.1, NA, 56.2, 51.5, NA, 56.9, 46.8...
..@ label : chr "Weight in kilos"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -5 -1
.. ..- attr(*, "names")= chr [1:2] "UNABLE TO OBTAIN HEIGHT MEASUREMENT" "Not applicable"
$ GCHTCM00 : dbl+lbl [1:16618] NA, 174, 181, NA, 169, 185, NA, 166, NA, 157, 18...
..@ label : chr "Height in cms"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -5 -1
.. ..- attr(*, "names")= chr [1:2] "Unable to obtain height measurement" "Not applicable"
$ GCWTCM00 : dbl+lbl [1:16618] NA, 59.4, 71.4, NA, 75.7, 74.1, NA, 56...
..@ label : chr "Weight in kilos"
..@ format.stata: chr "%12.0g"
..@ labels : Named num [1:2] -5 -1
.. ..- attr(*, "names")= chr [1:2] "Unable to obtain weight measurement" "Not applicable"
# A tibble: 16,618 × 12
MCSID CNUM00 CCHTCM00 CCWTCM00 DCHTCM00 DCWTCM00 ECHTCM00 ECWTCMA00 FCHTCM00
<chr> <dbl+l> <dbl+lb> <dbl+lb> <dbl+lb> <dbl+lb> <dbl+lb> <dbl+lbl> <dbl+lb>
1 M100… 1 [1st… 114. 21.2 128. 25.5 NA NA NA
2 M100… 1 [1st… 110. 19.2 123 26.2 144. 41.8 163.
3 M100… 1 [1st… 118 25.3 129 26.5 154. 40.6 174.
4 M100… 1 [1st… 121 32.9 137 51.2 168. 74 NA
5 M100… 1 [1st… 110. 19.7 122. 24.1 143 38.2 164.
6 M100… 1 [1st… 118. 23 130 29 152. 41.5 167
7 M100… 1 [1st… 110. 18.9 121. 21.7 NA NA NA
8 M100… 1 [1st… 113. 19.4 128. 22 150. 37.3 164.
9 M100… 1 [1st… 112. 20.6 123 24.6 141. 33.8 161
10 M100… 1 [1st… 108 18.4 121 24.2 147 40.3 157
# ℹ 16,608 more rows
# ℹ 3 more variables: FCWTCM00 <dbl+lbl>, GCHTCM00 <dbl+lbl>,
# GCWTCM00 <dbl+lbl>
```

`df_wide` has 12 columns. Besides, the identifiers, `MCSID` and `cnum`,
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2 changes: 1 addition & 1 deletion quarto/mcs-reshape_long_wide.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ df_wide <- map(3:7, load_height_wide) %>%
reduce(~ full_join(.x, .y, by = c("MCSID", "CNUM00"))) %>%
rename(ECHTCM00 = ECHTCMA0, ECWTCMA00 = ECWTCMA0)
str(df_wide)
df_wide
```

`df_wide` has 12 columns. Besides, the identifiers, `MCSID` and `cnum`, there are 10 columns for height and weight measurements at each sweep. Each of these 10 columns is prefixed by a single letter indicating the sweep. We can reshape the dataset into long format (one row per person x sweep combination) using the `pivot_longer()` function so that the resulting data frame has five columns: two person identifiers, a variable for sweep, and variables for height and weight. We specify the columns to be reshaped using the `cols` argument, provide the new variable names in the `names_to` argument, and the pattern the existing column names take using the `names_pattern` argument. For `names_pattern` we specify `"(.)(.*)"`, which breaks the column name into two pieces: the first character (`"(.)"`) and the rest of the name (`"(.*)"`). `names_pattern` uses regular expressions. `.` matches single characters, and `.*` modifies this to make zero or more characters. As noted, the first character holds information on sweep; in the reshaped data frame the character is stored as a value in a new column `sweep`. `.value` is a placeholder for the new columns in the reshaped data frame that store the values from the columns selected by `cols`; these new columns are named using the second piece from `names_pattern` - in this case `CHTCM00` (height) and `CWTCM00` (weight).
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