Merge pull request #22 from yannsay-impact/fix_cleaningtools9002

Fix cleaningtools9002

R/create_analysis.R

@@ -22,7 +22,7 @@
 #' @param loa list of analysis: Default is NULL. If provided it will be used to create the analysis.
 #' @param group_var Default is NULL. If provided, it will first create a list of analysis and then
 #' will run the analysis. It should be a vector.
-#' @param sm_seperator Separator for choice multiple questions. The default is "."
+#' @param sm_separator Separator for choice multiple questions. The default is "."
 #'
 #' @return A list with 3 items:
 #'  - The results table in a long format with the analysis key
@@ -63,7 +63,7 @@
 create_analysis <- function(.design,
                             loa = NULL,
                             group_var = NULL,
-                            sm_seperator = ".") {
+                            sm_separator = ".") {
   if (!"tbl_svy" %in% attributes(.design)$class) {
     stop("It seems object design is not a design, did you use srvyr::as_survey ?")
   }
@@ -77,7 +77,7 @@ create_analysis <- function(.design,
   }
 
   if (is.null(loa)) {
-    loa <- create_loa(.design = .design, group_var = group_var, sm_seperator = sm_seperator)
+    loa <- create_loa(.design = .design, group_var = group_var, sm_separator = sm_separator)
   }
 
 
@@ -110,7 +110,7 @@ create_analysis <- function(.design,
           group_var = loa[["group_var"]],
           analysis_var = loa[["analysis_var"]],
           level = loa[["level"]],
-          sm_separator = sm_seperator
+          sm_separator = sm_separator
         ))
       }
       if (loa[["analysis_type"]] == "ratio") {
@@ -147,7 +147,7 @@ create_analysis <- function(.design,
 #'  and "admin1, population" are different:
 #'    - c("admin1", "population") : will perform the analysis grouping once by admin1, and once by population
 #'    - "admin1, population" : will perform the analysis grouping once by admin1 and admin 2
-#' @param sm_seperator Separator for choice multiple questions. The default is "."
+#' @param sm_separator Separator for choice multiple questions. The default is "."
 #'
 #' @return a list of analysis.
 #' @export
@@ -165,16 +165,16 @@ create_analysis <- function(.design,
 #' )
 create_loa <- function(.design,
                        group_var = NULL,
-                       sm_seperator = ".") {
+                       sm_separator = ".") {
   loa_dictionary <- data.frame(
     type = c("character", "double", "double", "logical", "integer", "integer"),
     analysis_type = c("prop_select_one", "mean", "median", "prop_select_multiple", "mean", "median")
   )
   cols_to_remove <- c("start", "end", "today", "uuid")
 
-  select_multiple_parents_columns <- .design %>% cleaningtools::auto_detect_sm_parents(sm_seperator = sm_seperator)
+  select_multiple_parents_columns <- .design %>% cleaningtools::auto_detect_sm_parents(sm_separator = sm_separator)
   select_multiple_children_columns <- .design %>%
-    cleaningtools::auto_sm_parent_children(sm_seperator = sm_seperator) %>%
+    cleaningtools::auto_sm_parent_children(sm_separator = sm_separator) %>%
     dplyr::pull(sm_child)
 
   loa <- .design$variables %>%

R/create_analysis_prop_select_multiple.R

@@ -24,7 +24,7 @@
 #'   smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = TRUE, prob = c(.8, .2)),
 #'   uuid = 1:100 %>% as.character()
 #' ) %>%
-#'   cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+#'   cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 #'
 #' somedata <- somedata$data_with_fix_concat
 #'

README.Rmd

@@ -199,7 +199,7 @@ somedata <- data.frame(
   smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = T, prob = c(.8, .2)),
   uuid = 1:100 %>% as.character()
 ) %>%
-  cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+  cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
 somedata <- somedata$data_with_fix_concat
 create_analysis_prop_select_multiple(srvyr::as_survey(somedata),

README.md

@@ -149,12 +149,15 @@ ex2_results[["loa"]]
 ``` r
 ex3_results <- create_analysis(.design = srvyr::as_survey(shorter_df), group_var = c("admin1", "admin2"))
 #> Joining with `by = join_by(type)`
-#> ■■■■■■■■■■■■■■ 42% | ETA: 1s
-#> ■■■■■■■■■■■■■■■ 47% | ETA: 1s
-#> ■■■■■■■■■■■■■■■■■■■■■■ 68% | ETA: 1s
-#> ■■■■■■■■■■■■■■■■■■■■■■■ 74% | ETA: 1s
-#> ■■■■■■■■■■■■■■■■■■■■■■■■■ 79% | ETA: 1s
-#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 95% | ETA: 0s
+#> ■■■■■■■■■■■■ 37% | ETA: 3s
+#> ■■■■■■■■■■■■■■ 42% | ETA: 3s
+#> ■■■■■■■■■■■■■■■ 47% | ETA: 3s
+#> ■■■■■■■■■■■■■■■■■ 53% | ETA: 2s
+#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2s
+#> ■■■■■■■■■■■■■■■■■■■■■■ 68% | ETA: 2s
+#> ■■■■■■■■■■■■■■■■■■■■■■■ 74% | ETA: 2s
+#> ■■■■■■■■■■■■■■■■■■■■■■■■■■ 84% | ETA: 1s
+#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 89% | ETA: 1s
 ex3_results[["loa"]]
 #>      analysis_type             analysis_var group_var level
 #> 1  prop_select_one                   admin1      <NA>  0.95
@@ -183,6 +186,7 @@ ex3_results[["loa"]]
 ``` r
 ex4_results <- create_analysis(.design = srvyr::as_survey(shorter_df), group_var = "admin1, admin2")
 #> Joining with `by = join_by(type)`
+#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 92% | ETA: 0s
 ex4_results[["loa"]]
 #>      analysis_type             analysis_var      group_var level
 #> 1  prop_select_one                   admin1           <NA>  0.95
@@ -337,9 +341,9 @@ create_analysis_prop_select_one(srvyr::as_survey(somedata, strata = groups),
 #> # A tibble: 3 × 13
 #>   analysis_type  analysis_var analysis_var_value group_var group_var_value  stat
 #>   <chr>          <chr>        <chr>              <chr>     <chr>           <dbl>
-#> 1 prop_select_o… value        a                  <NA>      <NA>             0.55
-#> 2 prop_select_o… value        b                  <NA>      <NA>             0.35
-#> 3 prop_select_o… value        c                  <NA>      <NA>             0.1 
+#> 1 prop_select_o… value        a                  <NA>      <NA>             0.51
+#> 2 prop_select_o… value        b                  <NA>      <NA>             0.36
+#> 3 prop_select_o… value        c                  <NA>      <NA>             0.13
 #> # ℹ 7 more variables: stat_low <dbl>, stat_upp <dbl>, n <int>, n_total <int>,
 #> #   n_w <dbl>, n_w_total <dbl>, analysis_key <chr>
 create_analysis_prop_select_one(srvyr::as_survey(somedata, strata = groups),
@@ -350,12 +354,12 @@ create_analysis_prop_select_one(srvyr::as_survey(somedata, strata = groups),
 #> # A tibble: 6 × 13
 #>   analysis_type  analysis_var analysis_var_value group_var group_var_value  stat
 #>   <chr>          <chr>        <chr>              <chr>     <chr>           <dbl>
-#> 1 prop_select_o… value        a                  groups    group_a          0.6 
-#> 2 prop_select_o… value        b                  groups    group_a          0.28
-#> 3 prop_select_o… value        c                  groups    group_a          0.12
-#> 4 prop_select_o… value        a                  groups    group_b          0.5 
-#> 5 prop_select_o… value        b                  groups    group_b          0.42
-#> 6 prop_select_o… value        c                  groups    group_b          0.08
+#> 1 prop_select_o… value        a                  groups    group_a         0.516
+#> 2 prop_select_o… value        b                  groups    group_a         0.359
+#> 3 prop_select_o… value        c                  groups    group_a         0.125
+#> 4 prop_select_o… value        a                  groups    group_b         0.5  
+#> 5 prop_select_o… value        b                  groups    group_b         0.361
+#> 6 prop_select_o… value        c                  groups    group_b         0.139
 #> # ℹ 7 more variables: stat_low <dbl>, stat_upp <dbl>, n <int>, n_total <int>,
 #> #   n_w <dbl>, n_w_total <dbl>, analysis_key <chr>
 ```
@@ -372,7 +376,7 @@ somedata <- data.frame(
   smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = T, prob = c(.8, .2)),
   uuid = 1:100 %>% as.character()
 ) %>%
-  cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+  cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 #> groups
 #> smvar
 #> smvar.option1
@@ -398,12 +402,12 @@ create_analysis_prop_select_multiple(srvyr::as_survey(somedata),
   level = 0.95
 )
 #> # A tibble: 4 × 13
-#>   analysis_type  analysis_var analysis_var_value group_var group_var_value  stat
-#>   <chr>          <chr>        <chr>              <chr>     <chr>           <dbl>
-#> 1 prop_select_m… smvar        option1            <NA>      <NA>             0.7 
-#> 2 prop_select_m… smvar        option2            <NA>      <NA>             0.71
-#> 3 prop_select_m… smvar        option3            <NA>      <NA>             0.15
-#> 4 prop_select_m… smvar        option4            <NA>      <NA>             0.81
+#>   analysis_type analysis_var analysis_var_value group_var group_var_value   stat
+#>   <chr>         <chr>        <chr>              <chr>     <chr>            <dbl>
+#> 1 prop_select_… smvar        option1            <NA>      <NA>            0.698 
+#> 2 prop_select_… smvar        option2            <NA>      <NA>            0.635 
+#> 3 prop_select_… smvar        option3            <NA>      <NA>            0.0312
+#> 4 prop_select_… smvar        option4            <NA>      <NA>            0.854 
 #> # ℹ 7 more variables: stat_low <dbl>, stat_upp <dbl>, n <dbl>, n_total <dbl>,
 #> #   n_w <dbl>, n_w_total <dbl>, analysis_key <chr>
 
@@ -415,14 +419,14 @@ create_analysis_prop_select_multiple(srvyr::as_survey(somedata),
 #> # A tibble: 8 × 13
 #>   analysis_type  analysis_var analysis_var_value group_var group_var_value  stat
 #>   <chr>          <chr>        <chr>              <chr>     <chr>           <dbl>
-#> 1 prop_select_m… smvar        option1            groups    group_a          0.72
-#> 2 prop_select_m… smvar        option2            groups    group_a          0.66
-#> 3 prop_select_m… smvar        option3            groups    group_a          0.14
-#> 4 prop_select_m… smvar        option4            groups    group_a          0.82
-#> 5 prop_select_m… smvar        option1            groups    group_b          0.68
-#> 6 prop_select_m… smvar        option2            groups    group_b          0.76
-#> 7 prop_select_m… smvar        option3            groups    group_b          0.16
-#> 8 prop_select_m… smvar        option4            groups    group_b          0.8 
+#> 1 prop_select_m… smvar        option1            groups    group_a         0.66 
+#> 2 prop_select_m… smvar        option2            groups    group_a         0.66 
+#> 3 prop_select_m… smvar        option3            groups    group_a         0.06 
+#> 4 prop_select_m… smvar        option4            groups    group_a         0.84 
+#> 5 prop_select_m… smvar        option1            groups    group_b         0.739
+#> 6 prop_select_m… smvar        option2            groups    group_b         0.609
+#> 7 prop_select_m… smvar        option3            groups    group_b         0    
+#> 8 prop_select_m… smvar        option4            groups    group_b         0.870
 #> # ℹ 7 more variables: stat_low <dbl>, stat_upp <dbl>, n <dbl>, n_total <dbl>,
 #> #   n_w <dbl>, n_w_total <dbl>, analysis_key <chr>
 ```

tests/testthat/test-create_analysis.R

@@ -4,23 +4,23 @@ test_that("Gives corrects results", {
   no_loa_expected_output <- readRDS(testthat::test_path("fixtures", "results_create_analysis_no_loa_v2.RDS"))
 
   no_loa_test_design <- srvyr::as_survey(no_loa_expected_output$dataset)
-  actual_output <- create_analysis(no_loa_test_design, group_var = "admin1", sm_seperator = "/")
+  actual_output <- create_analysis(no_loa_test_design, group_var = "admin1", sm_separator = "/")
 
   expect_equal(actual_output, no_loa_expected_output, ignore_attr = T)
 
   # with a loa #add ratios
   with_loa_expected_output <- readRDS(testthat::test_path("fixtures", "results_create_analysis_with_loa_v2.RDS"))
 
   with_loa_test_design <- srvyr::as_survey(with_loa_expected_output$dataset)
-  with_loa_actual_output <- create_analysis(with_loa_test_design, loa = with_loa_expected_output$loa, sm_seperator = "/")
+  with_loa_actual_output <- create_analysis(with_loa_test_design, loa = with_loa_expected_output$loa, sm_separator = "/")
 
   expect_equal(with_loa_actual_output, with_loa_expected_output, ignore_attr = T)
 
   # with loa and no ratio
   no_ratio_loa <- with_loa_expected_output$loa %>%
     dplyr::filter(analysis_type != "ratio")
 
-  no_ratio_loa_actual_output <- create_analysis(with_loa_test_design, no_ratio_loa, sm_seperator = "/")
+  no_ratio_loa_actual_output <- create_analysis(with_loa_test_design, no_ratio_loa, sm_separator = "/")
 
   no_ratio_loa_expected_results_table <- with_loa_expected_output$results_table %>%
     dplyr::filter(analysis_type != "ratio")
@@ -142,7 +142,7 @@ test_that("If loa and group variable are provided, group_var will be ignored", {
       .design = srvyr::as_survey(expected_output$dataset),
       loa = expected_output$loa,
       group_var = "admin1",
-      sm_seperator = "/"
+      sm_separator = "/"
     ),
     "You have provided a list of analysis and group variable, group variable will be ignored"
   )

tests/testthat/test-create_analysis_prop_select_multiple.R

@@ -8,7 +8,7 @@ test_that("create_analysis_prop_select_multiple returns correct output, no weigh
     smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = T, prob = c(.8, .2)),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -104,7 +104,7 @@ test_that("create_analysis_prop_select_multiple handles NA", {
     smvar.option4 = rep(NA_character_, 100),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -221,7 +221,7 @@ test_that("create_analysis_prop_select_multiple returns correct output, with wei
     smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = T, prob = c(.8, .2)),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -319,7 +319,7 @@ test_that("create_analysis_prop_select_multiple handles when only 1 value", {
     smvar.option4 = c(rep(NA_integer_, 99), T),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
   somedata <- somedata$data_with_fix_concat
   one_value_expected_output <- data.frame(
     analysis_type = rep("prop_select_multiple", 4),
@@ -415,7 +415,7 @@ test_that("create_analysis_prop_select_multiple handles lonely PSU", {
     smvar.option4 = sample(c(TRUE, FALSE), size = 51, replace = T, prob = c(.8, .2)),
     uuid = 1:51 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -478,7 +478,7 @@ test_that("create_analysis_prop_select_multiple returns correct output with 3 gr
     smvar.option4 = sample(c(TRUE, FALSE), size = 300, replace = T, prob = c(.8, .2)),
     uuid = 1:300 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -564,7 +564,7 @@ test_that("create_analysis_prop_select_multiple returns correct output with 2 gr
     smvar.option4 = sample(c(TRUE, FALSE), size = 300, replace = T, prob = c(.8, .2)),
     uuid = 1:300 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -678,7 +678,7 @@ test_that("create_analysis_prop_select_multiple handles NA in the dummy variable
     smvar.option4 = sample(c(TRUE, FALSE), size = 100, replace = T, prob = c(.8, .2)),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat
 
@@ -782,7 +782,7 @@ test_that("create_analysis_prop_select_multiple works with 0/1's instead of TRUE
     smvar.option4 = sample(c(1, 0), size = 100, replace = T, prob = c(.8, .2)),
     uuid = 1:100 %>% as.character()
   ) %>%
-    cleaningtools::recreate_parent_column(uuid = "uuid", sm_seperator = ".")
+    cleaningtools::recreate_parent_column(uuid = "uuid", sm_separator = ".")
 
   somedata <- somedata$data_with_fix_concat