From a7b8eaaa39b3f10f43db6056bd0fcd725a83ca29 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Wed, 9 Oct 2024 09:34:24 -0400 Subject: [PATCH 01/24] Pass additional modifying functions in arguments of `merge_meta_with_data()` --- R/fct_appdata.R | 8 ++++++-- man/merge_meta_with_data.Rd | 7 ++++++- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index f0ab2b9a..303026da 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -57,6 +57,9 @@ get_raw_csv_data <- function( #' @param expected_columns A character vector with the columns that should be #' expected in the data frame. If missing, these columns will be added with #' missing data (thus, will be made explicitly missing). +#' @param .add_fns A list of additional functions to be applied to the data. The +#' functions should take the merged data object as argument and return the +#' modified merged data object. #' #' @return A data frame. #' @export @@ -66,7 +69,8 @@ merge_meta_with_data <- function( meta, expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", "LBREASND", "unit", - "lower_limit", "upper_limit", "LBCLSIG") + "lower_limit", "upper_limit", "LBCLSIG"), + .add_fns = list(fn1 = apply_study_specific_fixes) ){ stopifnot(is.data.frame(data)) stopifnot(inherits(meta, "list")) @@ -112,7 +116,7 @@ merge_meta_with_data <- function( "item_value" = VAL, "reason_notdone" = LBREASND ) |> - apply_study_specific_fixes() + purrr::reduce(.add_fns, \(x1, x2) {x1 |> x2()}, .init = _) attr(merged_data, "synch_time") <- synch_time merged_data } diff --git a/man/merge_meta_with_data.Rd b/man/merge_meta_with_data.Rd index de890352..145ac05c 100644 --- a/man/merge_meta_with_data.Rd +++ b/man/merge_meta_with_data.Rd @@ -8,7 +8,8 @@ merge_meta_with_data( data, meta, expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", - "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG") + "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG"), + .add_fns = list(fn1 = apply_study_specific_fixes) ) } \arguments{ @@ -19,6 +20,10 @@ merge_meta_with_data( \item{expected_columns}{A character vector with the columns that should be expected in the data frame. If missing, these columns will be added with missing data (thus, will be made explicitly missing).} + +\item{.add_fns}{A list of additional functions to be applied to the data. The +functions should take the merged data object as argument and return the +modified merged data object.} } \value{ A data frame. From f091000349ec6c9944d82f79589429148a6633fe Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Wed, 9 Oct 2024 14:42:22 -0400 Subject: [PATCH 02/24] Recode to use base R and character values --- R/fct_appdata.R | 10 +++++----- man/merge_meta_with_data.Rd | 8 ++++---- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 303026da..f5f016b4 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -57,9 +57,9 @@ get_raw_csv_data <- function( #' @param expected_columns A character vector with the columns that should be #' expected in the data frame. If missing, these columns will be added with #' missing data (thus, will be made explicitly missing). -#' @param .add_fns A list of additional functions to be applied to the data. The -#' functions should take the merged data object as argument and return the -#' modified merged data object. +#' @param .add_fns A character vector of additional functions to be applied to +#' the data. The functions should take the merged data object as argument and +#' return the modified merged data object. #' #' @return A data frame. #' @export @@ -70,7 +70,7 @@ merge_meta_with_data <- function( expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG"), - .add_fns = list(fn1 = apply_study_specific_fixes) + .add_fns = "apply_study_specific_fixes" ){ stopifnot(is.data.frame(data)) stopifnot(inherits(meta, "list")) @@ -116,7 +116,7 @@ merge_meta_with_data <- function( "item_value" = VAL, "reason_notdone" = LBREASND ) |> - purrr::reduce(.add_fns, \(x1, x2) {x1 |> x2()}, .init = _) + Reduce(\(x1, x2) do.call(x2, list(x1)), .add_fns, init = _) attr(merged_data, "synch_time") <- synch_time merged_data } diff --git a/man/merge_meta_with_data.Rd b/man/merge_meta_with_data.Rd index 145ac05c..8eb41b80 100644 --- a/man/merge_meta_with_data.Rd +++ b/man/merge_meta_with_data.Rd @@ -9,7 +9,7 @@ merge_meta_with_data( meta, expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG"), - .add_fns = list(fn1 = apply_study_specific_fixes) + .add_fns = "apply_study_specific_fixes" ) } \arguments{ @@ -21,9 +21,9 @@ merge_meta_with_data( expected in the data frame. If missing, these columns will be added with missing data (thus, will be made explicitly missing).} -\item{.add_fns}{A list of additional functions to be applied to the data. The -functions should take the merged data object as argument and return the -modified merged data object.} +\item{.add_fns}{A character vector of additional functions to be applied to +the data. The functions should take the merged data object as argument and +return the modified merged data object.} } \value{ A data frame. From 1ff5c2d9ffe0321f6225528563944495aa9a75ad Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Wed, 9 Oct 2024 15:39:22 -0400 Subject: [PATCH 03/24] Move additional merging functions to metadata --- R/fct_appdata.R | 10 ++++------ R/fct_data_helpers.R | 6 ++++++ data-raw/metadata.xlsx | Bin 56106 -> 56939 bytes data/metadata.rda | Bin 3383 -> 3445 bytes man/merge_meta_with_data.Rd | 7 +------ 5 files changed, 11 insertions(+), 12 deletions(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index f5f016b4..29a2c937 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -57,9 +57,6 @@ get_raw_csv_data <- function( #' @param expected_columns A character vector with the columns that should be #' expected in the data frame. If missing, these columns will be added with #' missing data (thus, will be made explicitly missing). -#' @param .add_fns A character vector of additional functions to be applied to -#' the data. The functions should take the merged data object as argument and -#' return the modified merged data object. #' #' @return A data frame. #' @export @@ -69,8 +66,7 @@ merge_meta_with_data <- function( meta, expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", "LBREASND", "unit", - "lower_limit", "upper_limit", "LBCLSIG"), - .add_fns = "apply_study_specific_fixes" + "lower_limit", "upper_limit", "LBCLSIG") ){ stopifnot(is.data.frame(data)) stopifnot(inherits(meta, "list")) @@ -116,7 +112,9 @@ merge_meta_with_data <- function( "item_value" = VAL, "reason_notdone" = LBREASND ) |> - Reduce(\(x1, x2) do.call(x2, list(x1)), .add_fns, init = _) + Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous + meta$settings$add_fns %||% "identity", # Return merged data if no additional functions + init = _) # Initiate with the merged data attr(merged_data, "synch_time") <- synch_time merged_data } diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R index 09cb6e54..2336249e 100644 --- a/R/fct_data_helpers.R +++ b/R/fct_data_helpers.R @@ -29,6 +29,12 @@ get_metadata <- function( meta <- lapply(sheets, function(x){ readxl::read_excel(filepath, sheet = x, col_types = "text") }) + if ("settings" %in% names(meta)) + meta$settings <- + meta$settings |> + as.list() |> + lapply(\(x) as.character(na.omit(x))) + if(length(expand_tab_items[nchar(expand_tab_items) > 0 ] ) == 0) return(meta) if("items_expanded" %in% names(meta)) warning({ "Table 'items_expanded' already present. 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zb5Nr2>4UBkZBJG(j7MA7#t!%WFj$ed$u}BGf?}R&pDQn*^xAJ)ox|W z6+%%6!3~27F4cm`SS=-%S{S1}TXKZcn1lX5RsVT1f|) zAmwLa%yQTZ0x1*@HW3AkATXqxVJ!s6ZcJq=A+ITwMUO_46BiiYEbjBaiTbMyg}UIK zlVCoy*G)aBlYzmANaRk2*6Jzjg9WK1MN^6Q**?BOtF6M^!`doBUIiNA6*XzH)umSv z@s@aWTbfAeZc>`PW6gN#n1<*luTcBqjGRH^6C%G4%id diff --git a/man/merge_meta_with_data.Rd b/man/merge_meta_with_data.Rd index 8eb41b80..de890352 100644 --- a/man/merge_meta_with_data.Rd +++ b/man/merge_meta_with_data.Rd @@ -8,8 +8,7 @@ merge_meta_with_data( data, meta, expected_columns = c("LBORNR_Lower", "LBORNR_Upper", "LBORRESU", "LBORRESUOTH", - "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG"), - .add_fns = "apply_study_specific_fixes" + "LBREASND", "unit", "lower_limit", "upper_limit", "LBCLSIG") ) } \arguments{ @@ -20,10 +19,6 @@ merge_meta_with_data( \item{expected_columns}{A character vector with the columns that should be expected in the data frame. If missing, these columns will be added with missing data (thus, will be made explicitly missing).} - -\item{.add_fns}{A character vector of additional functions to be applied to -the data. The functions should take the merged data object as argument and -return the modified merged data object.} } \value{ A data frame. From 5d4a44449045d521bb5b6d64ff39940b40b53aa7 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Thu, 10 Oct 2024 10:01:55 -0400 Subject: [PATCH 04/24] Adjust `%||%` to check for empty values, not just `NULL` --- R/golem_utils_server.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index 69be451b..7f6e6177 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -21,7 +21,7 @@ drop_nulls <- function(x) { x[!sapply(x, is.null)] } -#' If x is `NULL`, return y, otherwise return x +#' If x is empty (`NULL` or 0 length), return y, otherwise return x #' #' @param x,y Two elements to test, one potentially `NULL` #' @@ -30,7 +30,7 @@ drop_nulls <- function(x) { #' @examples #' NULL %||% 1 "%||%" <- function(x, y) { - if (is.null(x)) { + if (length(x) == 0) { y } else { x From 64514052a7df7e16435a76400b8cc24ac041809d Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Thu, 10 Oct 2024 10:02:38 -0400 Subject: [PATCH 05/24] Specify `add_fns` as `post_merge_fns` --- R/fct_appdata.R | 2 +- data-raw/metadata.xlsx | Bin 56939 -> 56973 bytes data/metadata.rda | Bin 3445 -> 3459 bytes 3 files changed, 1 insertion(+), 1 deletion(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 29a2c937..2e8d9870 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -113,7 +113,7 @@ merge_meta_with_data <- function( "reason_notdone" = LBREASND ) |> Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous - meta$settings$add_fns %||% "identity", # Return merged data if no additional functions + meta$settings$post_merge_fns %||% "identity", # Return merged data if no additional functions init = _) # Initiate with the merged data attr(merged_data, "synch_time") <- synch_time merged_data diff --git a/data-raw/metadata.xlsx b/data-raw/metadata.xlsx index e6cfc5eb7b8f7acf857d85ee8acc9690dab52248..698d7fe0cffe0fb67083a9e81466f10578011cdb 100644 GIT binary patch delta 4532 zcmY+IS3I0ix5j5imk`l=7s=?o3(*H5qxTlQ6QaL*7m1hXLN4*B!bEQ%hjNU8dVDpqweqvuIUZ4Vuju?eAxD{*O3Zb~ih@)4M8YOBjA2$}#nGXF z&I&*qzCA`XzxlxYYhwr{hIHgDKRQsqme)*Cn2GN7d!cCvzPeJ4zOuhqXPIH>vwEG} z?qvOjnxp-t4^vLr05Q@A@cueo8VgdbP`$2M{a$A58|nLmjQu^Tfp1uXN6R(Tk!>~e zhxL1^5%uo6GWNzfx~0-y^2MacY8A(-A$}nvn=90Zlw<=}!P-);49}`37Vqo!ezrI; z3TS!-C&{`GFKzbRF%kTM)%JSkZ=fPFifcB=Bj~=PPf^`^?>UK+(O^~8M|8XL zYJ77clASw0YRzM?0;0B?t-HLoBQCJIkKfdUTP^Y=OWxW?&e@qbkqD>-F^+cL@&c}u zs1>Zg{0=mtwY_?S^*xSyiu_ieHXSKX<5OUlK=MN3fcg1;V9^D^@v;`)ciF}H%ZDj< zy4G#_$ASmNP62T4(d&*SqX9ZWj)lxa5>7m+Bqf@U&4!uXTIfoZ= z!7GoIKFB-mG~$RNZz(KGXl}q(hrm9lwDskAeThul_T!gS;-c5#`ySg5V{>$3cecuX zjKwGk}ehQg--ePBkB?t5q42#o>=@pA;un<74Dp2ShGaKT+h6fvOQtQ2|nVE zV_HWVon;elED-rbUF~nH2nkB`PpBRFSG}GT>_EKRcM;iz7fb*d-d!KlXoowtvp!H4 z8CO5EdvrXxm6q@D4!<3jlE_6T$Nh$ffgEctRtaq|bZT!f>bOF*p(AnX))6k_FG)GB zb$yM2dw|T0cd+zM#i&RHQNQj9i${RmSyRWk$9?4_av<*kO(px^pm*i#h4UO!W?sy~ zPGH9MXEMroIXL`7P$+546vQMj*xGGjibjfwv4{<*D07ru~?1E=FsV6_eAP@;W(3+YK zkmL_=cgq6@J!S>TVt4WWlH%@?HwIGh5;QWgwNP1n7Zs}`Oe#j87!o^zRgqh`dqt`c zJ`Vnc>r@9xK(Zo-vCFt3H#s&;fk^ZbO&!|da6NS{7ir7nNo=`^FC2ug$wFQDa3mG8 z<%YLNNKT(SKGY&^|1FW2@>7RL(U)uh$?%maEQhbY3Tk*qbc;&VBb@eKi_&#dT2=d4dNV*Rq} zGb?wLQS|eWSHJo_)6*$c%`Bu@2Ho~Ta<7s{Xlaa4?pM!kx})hN2dcw8-)-0due--H zsM^0Q-|6l%GCpb5`kbkvdX2w%zfiWCL!jU>x23QN*St?tV!KmYGB|!Jl$v?=@N*Uo zInSKE%I$QzOY*Ye_`0ucyMrLCM`a-*EUW ztwIfTXXrwS$MY{IlAZ}6YToyq+nyF@p732xy@Vk;K4K+8LtrgcjKthmgnHXSTzsRh zHLzUDua^On-Z9m8BXx?OKF8Dyo;ug?+%mGEJg>KAWV6GWUaM0=vL8=7AD#OR@;E72 zX9VGPr1pfQUwDday0<|PGV-u8vTRqMXvjwpvldqV1yMb8L` z9xR9M8xcYvso)D)7GS0CZb$jhZum0VGST(pb}8p)RtUQZn>sC|ag%}=S9P%$65E&h zbgkmg?ZCPa9Ir;w&vBz{aRwTfBG?J+1n^_FFzh2@(?qmN{|M{0zvJMLAg$N(A*mJ3 z7IylxKYPmGIlugE6OdGyRc3IKc$F53|Ha`nPfGg$0a4?+Ad*E2JLyt{w4m*dcXnlgrG zJ+do4gMJ_X9{bPpd9Kq-+xFJKYc1V*U*c5O9BeXF_HZaDG2W}SBj*v$)LZvq);zrm z`s`alVXwv241jVbMJeZOA?`EhC$|i7KSVJM<>Wn8+t;sd=X#^mbDz!d&Qkg(87I#T67PIP4c8|>pR>MhKiiN>vbFJJ3_h6V_&L$bT3C_oAe_q<{rIi;8XfJbO;m& zr(2ksR`I%!^LA3}HNFrGmig!u&)BH+_;#hqyf`$h;kp4Rm>|F7Ae1ZMDH20gD;@pN zascAYOjgf96sgF}Q1Pn(g?RmuxoU<8|%d zEc5yXRS895d_SkoD~=FH>^Y_B8JrR0g-aedm1V25GrvQSXjks|3IF0|RZ>N`rNS1WTeh8&3qFOE+@c?P?xIh(A5}? 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zy|aTw9BV9JHJ4KgS$A=BB8pwzX2E$OMl)o$ykMVQFQTcU%l95u)h6R>zF`J45B-fG znPbAy7Xy7GDc1QR9QnGZDO^r&1v?g6DoM3MH68Uw zo0_Fmhɍt8eK z@V&ler;>F~Z4k`Svqw9TC{ z!uLSwcB9!oY2I~IkifNsD#u%%3AHds)G{6RrKtI!mc(b=ObbRsyfr6a@~|6bjdQ^e z9oGOpcbs+HiwF>c-3;?d0zj&hQjED(MT|XK)1bV3>73V~(_N?3Hm#E~qLP(RDn$rV zl9eV`gye?Tqn_-cHBE?K*~LqzEb9j7bkF!CffGIP|WbNxL}3U4y#5tPJGwc*&1 z&EMRarxhU$b%jWkDN;zJg!L&A&NCLB?-oNyXzxz&(K))E(=jzOS?xzGw#l_*qq_*C*(`RlHpLQVhaKCJl8!V~+fcPCB}tR$yRlWAho4uK>T1zA zwJTpmR_0u>R3#9M5aSq8cB~dk!AnIg3{jrV*+Ogar77AKZ(u=^fEDa$0W03 zrTovXu*h3{6T3Ep>P?i_ Date: Thu, 10 Oct 2024 10:07:32 -0400 Subject: [PATCH 06/24] Add `pre_merge_fns` setting --- R/fct_appdata.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 2e8d9870..b04a1b1e 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -75,7 +75,10 @@ merge_meta_with_data <- function( synch_time <- attr(data, "synch_time") %||% "" merged_data <- data |> rename_raw_data(column_names = meta$column_names) |> - readr::type_convert(clinsight_col_specs) |> + readr::type_convert(clinsight_col_specs) |> + Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous + meta$settings$pre_merge_fns %||% "identity", # Return renamed data if no additional functions + init = _) |> # Initiate with the renamed data add_timevars_to_data() |> # fix MC values before merging: fix_multiple_choice_vars(expected_vars = meta$items_expanded$var) |> From 7cf9ee48eca4a7ca5979f8e89511e00682831cbd Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Thu, 10 Oct 2024 12:54:31 -0400 Subject: [PATCH 07/24] Add inline function to check existence of an object for `dplyr` mutations --- R/fct_data_helpers.R | 2 +- R/golem_utils_server.R | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R index 2336249e..f53a0911 100644 --- a/R/fct_data_helpers.R +++ b/R/fct_data_helpers.R @@ -150,7 +150,7 @@ add_timevars_to_data <- function( dplyr::mutate( edit_date_time = as.POSIXct(edit_date_time, tz = "UTC"), event_date = as.Date(event_date), - day = event_date - min(event_date, na.rm = TRUE), + day = day %|_|% event_date - min(event_date, na.rm = TRUE), vis_day = ifelse(event_id %in% c("SCR", "VIS", "VISEXT", "VISVAR", "FU1", "FU2"), day, NA), vis_num = as.numeric(factor(vis_day))-1, event_name = dplyr::case_when( diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index 7f6e6177..6502381d 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -52,3 +52,19 @@ drop_nulls <- function(x) { x } } + +#' If x does not exist, return y, otherwise return x +#' +#' @param x,y Two elements to test, one potentially not existent +#' +#' @noRd +#' +#' @examples +#' mtcars2 %|_|% mtcars +"%|_|%" <- function(x, y) { + if (exists(deparse(substitute(x)))) { + x + } else { + y + } +} From ba6c086731f3e116167613ec9db3f05ea6dc8d8f Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Thu, 10 Oct 2024 13:25:48 -0400 Subject: [PATCH 08/24] Impute `event_name` from `event` instead of `event_name` --- R/fct_data_helpers.R | 8 ++++---- R/sysdata.rda | Bin 798 -> 788 bytes data-raw/internal_data.R | 2 +- data-raw/metadata.xlsx | Bin 56973 -> 56973 bytes data/metadata.rda | Bin 3459 -> 3459 bytes 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R index f53a0911..ee66f6d7 100644 --- a/R/fct_data_helpers.R +++ b/R/fct_data_helpers.R @@ -151,9 +151,9 @@ add_timevars_to_data <- function( edit_date_time = as.POSIXct(edit_date_time, tz = "UTC"), event_date = as.Date(event_date), day = day %|_|% event_date - min(event_date, na.rm = TRUE), - vis_day = ifelse(event_id %in% c("SCR", "VIS", "VISEXT", "VISVAR", "FU1", "FU2"), day, NA), + vis_day = ifelse(grepl("^SCR|^VIS|^FU", event_id), day, NA), vis_num = as.numeric(factor(vis_day))-1, - event_name = dplyr::case_when( + event_name = event_name %|_|% dplyr::case_when( event_id == "SCR" ~ "Screening", event_id %in% c("VIS", "VISEXT", "VISVAR") ~ paste0("Visit ", vis_num), grepl("^FU[[:digit:]]+", event_id) ~ paste0("Visit ", vis_num, "(FU)"), @@ -161,9 +161,9 @@ add_timevars_to_data <- function( event_id == "EOT" ~ "EoT", event_id == "EXIT" ~ "Exit", form_id %in% c("AE", "CM", "CP", "MH", "MH", "MHTR", "PR", "ST", "CMTR", "CMHMA") ~ "Any visit", - TRUE ~ paste0("Other (", event_name, ")") + TRUE ~ paste0("Other (", event, ")") ), - event_label = dplyr::case_when( + event_label = event_label %|_|% dplyr::case_when( !is.na(vis_num) ~ paste0("V", vis_num), event_id == "UN" ~ paste0("UV", event_repeat), TRUE ~ event_name diff --git a/R/sysdata.rda b/R/sysdata.rda index 0e2f6218e3017d3128b79ff35a00ec33fc31bee1..1c5599e04272b6071c08721c6c458328d8251a72 100644 GIT binary patch delta 774 zcmV+h1Nr=(29yR4LRx4!F+o`-Q(3K`LJN@&9De|y00I=#Q1of2Xk^4>4GkFvCKE#@ 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zE5dAs$ETj`p)^fslR?TUvlrH6Fhp|-XK>1U(^(T~kr$FINNtcbX31*dDwkbrBN|d6MSxKY9F@wO^Dolit zz?=<3g5&khRQk>S1tI7rzal%~4QbF4INYzO!?_{8$2V^APPm>r%CWLQ~0KN($ogWpq)m`gI*9*v^aa3hs%L-atph$#;Q3&r= zjbcoi9}@*ujy)R@%Pp>KSt#(rDK*O+c^e{$Ged^$sYyo)Dr~4)l@gOxXnlA*3av68 zto-j=Mt`*6(5*YIZdq6^wUK2iQXDBuFqXM^wkt_xmYGsyjP>o&3745EP61Z>P2-WO zNK%57XsV=-I?!g~fWa*!gV3r>uQs^cy%-D#krWLKA`2KmVFk#8LKf2^^`?-fz)QWEd?;A}X9u+hq6h zja_aA`wwWT33wE1gjCh0%T|?KM~Jh@p>BC2yx&rqn?6zT;T=;T#tHcT%1&q0EkF8l k&-S=MibPRTi*R{lV$=ixZUc=`RR6`?kxmpOBC+07Knqb Date: Thu, 10 Oct 2024 14:23:13 -0400 Subject: [PATCH 09/24] Fix broken tests --- tests/testthat/_snaps/fct_appdata.md | 64 +++++++++--------- .../testapp-raw/altered_metadata.xlsx | Bin 54515 -> 54533 bytes 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/tests/testthat/_snaps/fct_appdata.md b/tests/testthat/_snaps/fct_appdata.md index ec24ab51..f07a5a64 100644 --- a/tests/testthat/_snaps/fct_appdata.md +++ b/tests/testthat/_snaps/fct_appdata.md @@ -30,45 +30,45 @@ Code df[c(1, 1000, 2000, 3000, 4000, 5000), ] Output - # A tibble: 6 x 23 - site_code subject_id event_id event_date event_name event_repeat form_id - - 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 2 NA NA - 3 NA NA - 4 NA NA - 5 NA NA - 6 NA NA - # i 16 more variables: form_repeat , edit_date_time , day , - # vis_day , vis_num , event_label , item_name , - # item_type , item_group , item_value , item_unit , - # lower_lim , upper_lim , significance , reason_notdone , - # region + # A tibble: 6 x 24 + site_code subject_id event_id event_date event event_repeat form_id + + 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM + 2 NA NA + 3 NA NA + 4 NA NA + 5 NA NA + 6 NA NA + # i 17 more variables: form_repeat , edit_date_time , day , + # vis_day , vis_num , event_name , event_label , + # item_name , item_type , item_group , item_value , + # item_unit , lower_lim , upper_lim , significance , + # reason_notdone , region --- Code df Output - # A tibble: 543 x 23 - site_code subject_id event_id event_date event_name event_repeat form_id - - 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 2 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 3 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 4 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 5 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 6 9600 9600-002 SCR 2022-01-01 Screening 1 STE - 7 9600 9600-002 SCR 2022-01-01 Screening 1 STE - 8 9600 9600-002 SCR 2022-01-01 Screening 1 VS - 9 9600 9600-002 SCR 2022-01-01 Screening 1 VS - 10 9600 9600-002 SCR 2022-01-01 Screening 1 VS + # A tibble: 543 x 24 + site_code subject_id event_id event_date event event_repeat form_id + + 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM + 2 9600 9600-001 SCR 2022-11-09 Screening 1 DM + 3 9600 9600-002 SCR 2022-01-01 Screening 1 DM + 4 9600 9600-002 SCR 2022-01-01 Screening 1 DM + 5 9600 9600-002 SCR 2022-01-01 Screening 1 DM + 6 9600 9600-002 SCR 2022-01-01 Screening 1 STE + 7 9600 9600-002 SCR 2022-01-01 Screening 1 STE + 8 9600 9600-002 SCR 2022-01-01 Screening 1 VS + 9 9600 9600-002 SCR 2022-01-01 Screening 1 VS + 10 9600 9600-002 SCR 2022-01-01 Screening 1 VS # i 533 more rows - # i 16 more variables: form_repeat , edit_date_time , day , - # vis_day , vis_num , event_label , item_name , - # item_type , item_group , item_value , item_unit , - # lower_lim , upper_lim , significance , reason_notdone , - # region + # i 17 more variables: form_repeat , edit_date_time , day , + # vis_day , vis_num , event_name , event_label , + # item_name , item_type , item_group , item_value , + # item_unit , lower_lim , upper_lim , significance , + # reason_notdone , region # get_appdata works: produces the expected output diff --git a/tests/testthat/fixtures/testapp-raw/altered_metadata.xlsx b/tests/testthat/fixtures/testapp-raw/altered_metadata.xlsx index ad8313e478731c2e2619cac987700691ee3ac304..ea325c99efdf79f9f391da9ae70e0749ecdc1634 100644 GIT binary patch delta 8841 zcmZ8nbx<5%)@5)B1b270;32^w3~s??aQ6gfaQDH2Yj6wh5`w$C4H^g%+&_}t+TVWL 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z2&uIyr2>F8oVqApY@#oR;#g}2Rr*EwbLQM)HZ|sk4Tmuu+UX$cK$XYqJna@XHnA?j z>+KBUnp;WjpTuR%FpH6||Mn;jhGkyDuJ|*l>Aq`?_j* zd3BA0rGxTGaWBzMS}R{ssvb%>6Cg%lZ1w5(`U`-USc{u(b_^(x3*P5;xDJZaqjQu9 zQ;AU*{EWZ+Qm!9}2hXJbwT(K&OCq3+tjy&ZqfTkOSP5JvUF5nVX7CBJ(1clW7=8aJ zwuZS(NckMtTB*bCF#Bz0v;uxZ1QLvlxngA^5kv@$La}LFdkvE2Z~VZtkXRM{!9mJpUMwN{@1?<&WBV1E)dCK zR+4|Gg)gSai#z}Cb&C#}7zVw}4?)ELj8{7B$P`A6vfe~--0^fys@ zlpSykaUG>2{zpL&z`)@B`~6=cUr61kBwz<}H7W!!gK&=>|b&{F*pVt8v1_t~8c^nOh>!cW94N@~H3Rs1lPD%pkAY4 Date: Thu, 10 Oct 2024 14:31:44 -0400 Subject: [PATCH 10/24] Further generalize `add_timevars_to_data()` --- R/fct_data_helpers.R | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R index ee66f6d7..d14bc984 100644 --- a/R/fct_data_helpers.R +++ b/R/fct_data_helpers.R @@ -151,22 +151,22 @@ add_timevars_to_data <- function( edit_date_time = as.POSIXct(edit_date_time, tz = "UTC"), event_date = as.Date(event_date), day = day %|_|% event_date - min(event_date, na.rm = TRUE), - vis_day = ifelse(grepl("^SCR|^VIS|^FU", event_id), day, NA), + vis_day = ifelse(grepl("^SCR|^VIS|^FU", event_id, ignore.case = TRUE), day, NA), vis_num = as.numeric(factor(vis_day))-1, event_name = event_name %|_|% dplyr::case_when( - event_id == "SCR" ~ "Screening", - event_id %in% c("VIS", "VISEXT", "VISVAR") ~ paste0("Visit ", vis_num), - grepl("^FU[[:digit:]]+", event_id) ~ paste0("Visit ", vis_num, "(FU)"), - event_id == "UN" ~ paste0("Unscheduled visit ", event_repeat), - event_id == "EOT" ~ "EoT", - event_id == "EXIT" ~ "Exit", - form_id %in% c("AE", "CM", "CP", "MH", "MH", "MHTR", "PR", "ST", "CMTR", "CMHMA") ~ "Any visit", - TRUE ~ paste0("Other (", event, ")") + grepl("^SCR", event_id, ignore.case = TRUE) ~ "Screening", + grepl("^VIS", event_id, ignore.case = TRUE) ~ paste0("Visit ", vis_num), + grepl("^FU[[:digit:]]+", event_id, ignore.case = TRUE) ~ paste0("Visit ", vis_num, "(FU)"), + grepl("^UN", event_id, ignore.case = TRUE) ~ paste0("Unscheduled visit ", event_repeat), + toupper(event_id) == "EOT" ~ "EoT", + toupper(event_id) == "EXIT" ~ "Exit", + grepl("^AE|^CM|^CP|^MH|^PR|^ST", form_id) ~ "Any visit", + .default = paste0("Other (", event, ")") ), event_label = event_label %|_|% dplyr::case_when( !is.na(vis_num) ~ paste0("V", vis_num), - event_id == "UN" ~ paste0("UV", event_repeat), - TRUE ~ event_name + grepl("^UN", event_id, ignore.case = TRUE) ~ paste0("UV", event_repeat), + .default = event_name ), .by = subject_id ) |> @@ -174,7 +174,7 @@ add_timevars_to_data <- function( factor(site_code, levels = order_string(site_code)), factor(subject_id, levels = order_string(subject_id)) ) - if(any(grepl("^Other ", df$event_name))) warning( + if(any(is.na(df$event_name) | grepl("^Other ", df$event_name))) warning( "Undefined Events detected. Please verify data before proceeding." ) df From 325c27df2d58a574a6bf8691003e49e50a54a42b Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:00:12 -0400 Subject: [PATCH 11/24] Initialize region field --- R/fct_appdata.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index b04a1b1e..40f3d36f 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -115,6 +115,7 @@ merge_meta_with_data <- function( "item_value" = VAL, "reason_notdone" = LBREASND ) |> + dplyr::mutate(region = region %|_|% "Missing") |> Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous meta$settings$post_merge_fns %||% "identity", # Return merged data if no additional functions init = _) # Initiate with the merged data From 25065001f9b2b3e74d70f5501474cb1dc1eb7118 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Fri, 11 Oct 2024 09:31:59 -0400 Subject: [PATCH 12/24] Add mid-merging functions --- R/fct_appdata.R | 36 +++++++++++++++++++++++++++--------- data-raw/metadata.xlsx | Bin 56973 -> 56987 bytes data/metadata.rda | Bin 3459 -> 3484 bytes 3 files changed, 27 insertions(+), 9 deletions(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 40f3d36f..55efdda0 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -83,21 +83,20 @@ merge_meta_with_data <- function( # fix MC values before merging: fix_multiple_choice_vars(expected_vars = meta$items_expanded$var) |> dplyr::right_join(meta$items_expanded, by = "var") |> - dplyr::filter(!is.na(item_value)) |> + dplyr::filter(!is.na(item_value)) |> + readr::type_convert(clinsight_col_specs) |> + Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous + meta$settings$mid_merge_fns %||% "identity", # Return renamed data if no additional functions + init = _) |> # Initiate with the renamed data dplyr::mutate( - suffix = ifelse(item_name == "ECG interpretation", "LBCLSIG", suffix), - suffix = ifelse(is.na(suffix), "VAL", suffix), - # TODO: improve code below to handle exceptions in a more general manner - suffix = ifelse(suffix %in% c("LBORRES", "VSORRES", "EGORRES") | - item_group %in% c("Cytogenetics", "General"), - "VAL", suffix) + suffix_names = suffix_names %|_|% ifelse(is.na(suffix) | grepl("ORRES$", suffix) | item_group == "General", "VAL", suffix) ) |> - dplyr::select(-var) |> + dplyr::select(-var, -suffix) |> dplyr::mutate( edit_date_time = max(edit_date_time, na.rm = TRUE), .by = c(subject_id, item_name, event_name, event_repeat) ) |> - tidyr::pivot_wider(names_from = suffix, values_from = item_value) |> + tidyr::pivot_wider(names_from = suffix_names, values_from = item_value) |> add_missing_columns(expected_columns) |> dplyr::mutate( LBORNR_Lower = as.numeric(ifelse(!is.na(lower_limit), lower_limit, LBORNR_Lower)), @@ -124,6 +123,25 @@ merge_meta_with_data <- function( } +#' Apply study-specific suffix fixes +#' +#' These changes are study/EDC-specific and part of the legacy code for ClinSight. +#' +#' @param data A data frame +#' +#' @return A data frame. +apply_study_specific_suffix_fixes <- function(data) { + dplyr::mutate(data, + suffix = ifelse(item_name == "ECG interpretation", "LBCLSIG", suffix), + suffix = ifelse(is.na(suffix), "VAL", suffix), + # TODO: improve code below to handle exceptions in a more general manner + suffix_names = ifelse(suffix %in% c("LBORRES", "VSORRES", "EGORRES") | + item_group %in% c("Cytogenetics", "General"), + "VAL", suffix) + ) +} + + #' Apply study-specific fixes #' #' These changes are probably study-specific and need to be changed accordingly. diff --git a/data-raw/metadata.xlsx b/data-raw/metadata.xlsx index 352e0713fe37c947509b55298dce9bb820eff6fd..de630fc117416f78e47565bc018a32dfb2c46387 100644 GIT binary patch delta 5037 zcmZ9QRan$*x5j4%aA>845v03I5E#0KMnDM(kxmI|Mv#7i0sfRUC?Fj}H%gDvQbQvp 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zzR?(V5iopQFj&P=$wUcId_z<>XwR0wL&!=^+%h2 zGAMz!P|)E}l!a6wLZB6qk&u^afpy(Ti%lBX#EvE3#)`k-j?x zp)pSqo06>r?x&hikoLYoLWPdRr>a=*r#C!@=@yoVP}*>dyluVMx^7Kn;X4`%9*xyZ zW5)9ep;Bs`aye3?b5xQcPK?JIKSCW+8ZsHIrifF3UII9+$Va3K4{I6&1b8H7EDB2k zn$F}0JB~fG(L2tHk{A}Sg;?o!;G0tfd&Wb))U_X?32a7v#K5#*+OcY5hkOMQ*JM)$Y6-&6wcw4_$Euk5v}!_#oanWRyaw3Qk1Ba zM2ZoSr38;4;e(WTofMTOY3J_!DdQh8&Nx#<%fj0Pvs$j*6rxC_N>NHIq}AUT!QO2Z zCPGNyP6mU5fNgu_3<6+o?+J{ap_Vbs2An%3>&5 z@bh(~HJp9z1CV!Mf*X?YMlgz`6dut8T;o`@@Od&DA-iM2JOg5Lbi3wK6I)@{R>(H( zPomqLBQ=@|FAk_W;U@BYxWX|tBYby-@KF@!`7OSx?pj93UMeRQMpg{CrR9_f5Rj@N z9+ha;l4R8R7%H`K>e`M;ZIf!rM}84WvRLED+Z0Kf95-%CN;pwdZ9>$jl$utj)q}jM z*CFc9&h@oyP7O-e&1-T>!F8;QN>rpcQkG#Ya`9|dlFKbJsL2`Z-KrBWDpH&Rt@Inm zX{3;)1t`^3Ngj2e&BXzNT1f|?RGD6Gak)A07!e^94b~9_j36+A=0TzZgbf3EN{DUB zUnQdFt3x9fXmLw6Ip4_m))@&X)C+@O* zIR>3h2Kx_ksVNC~6l{c4(_NOWYPgR9XNywZxg)sWQkpjW!_9B&FZph1d6QBsRw^2o)g2msg)MMYEp7ji{7P>=^BAOIEOQ*{6U From c9755b7d2c47ac616becdf3502f582dc26ed2273 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Fri, 11 Oct 2024 09:36:22 -0400 Subject: [PATCH 13/24] Update version and NEWS --- DESCRIPTION | 2 +- NEWS.md | 2 ++ inst/golem-config.yml | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4eccaca8..979e2598 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: clinsight Title: ClinSight -Version: 0.1.0.9000 +Version: 0.1.0.9001 Authors@R: c( person("Leonard Daniël", "Samson", , "lsamson@gcp-service.com", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-6252-7639")), diff --git a/NEWS.md b/NEWS.md index a2c68eb2..930d9445 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # clinsight (development version) +- Generalized `merge_meta_with_data()` to allow user-defined processing functions. + # clinsight 0.1.0 ## Changed diff --git a/inst/golem-config.yml b/inst/golem-config.yml index d489d7c7..c4db010d 100644 --- a/inst/golem-config.yml +++ b/inst/golem-config.yml @@ -1,6 +1,6 @@ default: golem_name: clinsight - golem_version: 0.1.0 + golem_version: 0.1.0.9001 app_prod: no user_identification: test_user study_data: !expr clinsight::clinsightful_data From f48ebac7bd44a45eff2b549657156add31cbabc1 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 10:13:31 -0400 Subject: [PATCH 14/24] Remove duplicate type conversion --- R/fct_appdata.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 55efdda0..a7bad4ad 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -84,7 +84,6 @@ merge_meta_with_data <- function( fix_multiple_choice_vars(expected_vars = meta$items_expanded$var) |> dplyr::right_join(meta$items_expanded, by = "var") |> dplyr::filter(!is.na(item_value)) |> - readr::type_convert(clinsight_col_specs) |> Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous meta$settings$mid_merge_fns %||% "identity", # Return renamed data if no additional functions init = _) |> # Initiate with the renamed data From 6087b0e41502e954aa0635ee9cfa13106055ec12 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 10:34:09 -0400 Subject: [PATCH 15/24] Create `apply_custom_functions()` to handle --- R/fct_appdata.R | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index a7bad4ad..25b66173 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -76,17 +76,13 @@ merge_meta_with_data <- function( merged_data <- data |> rename_raw_data(column_names = meta$column_names) |> readr::type_convert(clinsight_col_specs) |> - Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous - meta$settings$pre_merge_fns %||% "identity", # Return renamed data if no additional functions - init = _) |> # Initiate with the renamed data + apply_custom_functions(meta$settings$pre_merge_fns) |> add_timevars_to_data() |> # fix MC values before merging: fix_multiple_choice_vars(expected_vars = meta$items_expanded$var) |> dplyr::right_join(meta$items_expanded, by = "var") |> dplyr::filter(!is.na(item_value)) |> - Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous - meta$settings$mid_merge_fns %||% "identity", # Return renamed data if no additional functions - init = _) |> # Initiate with the renamed data + apply_custom_functions(meta$settings$mid_merge_fns) |> dplyr::mutate( suffix_names = suffix_names %|_|% ifelse(is.na(suffix) | grepl("ORRES$", suffix) | item_group == "General", "VAL", suffix) ) |> @@ -114,9 +110,7 @@ merge_meta_with_data <- function( "reason_notdone" = LBREASND ) |> dplyr::mutate(region = region %|_|% "Missing") |> - Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous - meta$settings$post_merge_fns %||% "identity", # Return merged data if no additional functions - init = _) # Initiate with the merged data + apply_custom_functions(meta$settings$post_merge_fns) |> attr(merged_data, "synch_time") <- synch_time merged_data } @@ -209,6 +203,19 @@ apply_study_specific_fixes <- function( ) } +#' Apply custom modification functions +#' +#' @param data A data frame (for example, raw data merged). +#' @param functions A character vector containing the names of the functions to +#' apply to the data. Default is NULL. +#' @param .default A character vector containing the names of the functions to +#' apply if none are provided. Default is "identity". +apply_custom_functions <- function(data, functions = NULL, .default = "identity") { + Reduce(\(x1, x2) do.call(x2, list(x1)), # Apply next function to output of previous + functions %||% .default, # Apply default functions if no additional functions provided + init = data) # Initialize with the data object +} + #' Get appdata #' #' Converts data to a list of data frames in the expected format to be used by the From a98092059e5ca05171fc99bb8eed5937d557faee Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 11:07:41 -0400 Subject: [PATCH 16/24] Clean up metadata settings element generation --- R/fct_data_helpers.R | 9 ++++----- data/metadata.rda | Bin 3484 -> 3473 bytes 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R index d14bc984..835aadc3 100644 --- a/R/fct_data_helpers.R +++ b/R/fct_data_helpers.R @@ -29,11 +29,10 @@ get_metadata <- function( meta <- lapply(sheets, function(x){ readxl::read_excel(filepath, sheet = x, col_types = "text") }) - if ("settings" %in% names(meta)) - meta$settings <- - meta$settings |> - as.list() |> - lapply(\(x) as.character(na.omit(x))) + + meta$settings <- meta$settings |> + lapply(\(x) as.character(na.omit(x))) |> + Filter(f = length) if(length(expand_tab_items[nchar(expand_tab_items) > 0 ] ) == 0) return(meta) if("items_expanded" %in% names(meta)) warning({ diff --git a/data/metadata.rda b/data/metadata.rda index a41a511259d1b058897e8f90b4651d1162b91959..4ebf6b99ea0e293c4f4a097307bc5d63a00ec8ca 100644 GIT binary patch literal 3473 zcmV;C4Q}#6T4*^jL0KkKSrPI!CIBjB|Ih#b|N3YF|KLCG|KPv>|KLCXKmZT{00IaG zA_3qLem;!mXJ}sw13u2H>(jM~tyEH%o9_6&_CQcj001bWln`Y#2{ipeH1e4BA?hBZ zdZ(lVKm#G500000$)M1RXSGvF=@ayT01=}BFaQ9ILjf2@0Wc#(dZSSqdYT4+0QEEg z02*ij000004Lw9Bs-CIn)M#il(a**z*ErCK4X7!EPirq-Su&D0%WVZz?xEv><%x(GMEEQp1zLIYJuDe?EZGEq?U z1XWYoiHuNUAR|zf?WkInOH=R7AU5ijkVTXtY){6h6bq05ptlsFK`Z6kRj=A7m+aJH 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--- R/fct_appdata.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/fct_appdata.R b/R/fct_appdata.R index 25b66173..bd7a6938 100644 --- a/R/fct_appdata.R +++ b/R/fct_appdata.R @@ -110,7 +110,7 @@ merge_meta_with_data <- function( "reason_notdone" = LBREASND ) |> dplyr::mutate(region = region %|_|% "Missing") |> - apply_custom_functions(meta$settings$post_merge_fns) |> + apply_custom_functions(meta$settings$post_merge_fns) attr(merged_data, "synch_time") <- synch_time merged_data } From 4d7fd4524cd3ae3388fec1dd161d5a1265b630c4 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 11:45:17 -0400 Subject: [PATCH 18/24] Reset `%||%` to standard evaluation --- R/golem_utils_server.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index 6502381d..6016c7c6 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -21,7 +21,7 @@ drop_nulls <- function(x) { x[!sapply(x, is.null)] } -#' If x is empty (`NULL` or 0 length), return y, otherwise return x +#' If x is `NULL`, return y, otherwise return x #' #' @param x,y Two elements to test, one potentially `NULL` #' @@ -30,7 +30,7 @@ drop_nulls <- function(x) { #' @examples #' NULL %||% 1 "%||%" <- function(x, y) { - if (length(x) == 0) { + if (is.null(x)) { y } else { x From 6adeceabf46f549fc1b6cabb7ab3cb4b0f2e2e69 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:03:37 -0400 Subject: [PATCH 19/24] Display message if using user supplied data. --- R/golem_utils_server.R | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index 6016c7c6..e9051da5 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -55,14 +55,16 @@ drop_nulls <- function(x) { #' If x does not exist, return y, otherwise return x #' -#' @param x,y Two elements to test, one potentially not existent +#' @param x,y two elements to test, one potentially not existent +#' @param verbose logical, indicating whether warning message should be displayed. #' #' @noRd #' #' @examples #' mtcars2 %|_|% mtcars -"%|_|%" <- function(x, y) { - if (exists(deparse(substitute(x)))) { +"%|_|%" <- function(x, y, verbose = TRUE) { + if (exists(deparse1(substitute(x)))) { + if (verbose) warning(paste("Using user supplied", deparse(deparse1(substitute(x))), "instead of deriving."), call. = FALSE) x } else { y From b001c9b6560558423e8f8ffab694fe0e889c8fb6 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:11:50 -0400 Subject: [PATCH 20/24] Remove `event_name` from required columns --- R/fct_data_helpers.R | 2 +- R/sysdata.rda | Bin 788 -> 783 bytes data-raw/internal_data.R | 1 - data-raw/metadata.xlsx | Bin 56987 -> 56926 bytes data/metadata.rda | Bin 3473 -> 3456 bytes 5 files 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z8edVQUDc`*vBFFOl%+(XBv6cvR1!N!1RSHt@6uG6r=zpyPvjoMoNy+j%f{IRvr4Yp z6rxC_N>NHIq|xFS!QpHbCPGNxP4=O`ar&a7@85db_?L5DsydoeNG+$b8=vJO6+%-8!3|>yF4cm`SSe_toT6ln zI`-&<%e5&@@mBX6PV-cdr3EO_RY@LYpv}Vpf?7!jom81#ZE&{sE(O69iU%7Ag2oUS zL3+qF1kg9r8A^z3%3mpHx#`qoV($(aX1UJ(2iI6K7V3g_O@Q~Nx@ql1n_F=S9BI(r zZla$Y7%fR6Dx5F6$?xMDx|{9HJ*uRnCE!u65mQ#1Em~D^9wN^kg50u4eYr|%n;pZ= zgmlb<7$@QVaCuK~3Vklu{MZOFNQx>_+&>u@wgCVefxS^w|KjdQrwS4RK1RgAD&J%M From 568a05f7f86511b827e38a28ab74b162a482fed7 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:31:01 -0400 Subject: [PATCH 21/24] Resolve test errors --- tests/testthat/_snaps/fct_appdata.md | 64 +++++++++++++-------------- tests/testthat/test-rename_raw_data.R | 4 +- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/tests/testthat/_snaps/fct_appdata.md b/tests/testthat/_snaps/fct_appdata.md index f07a5a64..6b4ec7b9 100644 --- a/tests/testthat/_snaps/fct_appdata.md +++ b/tests/testthat/_snaps/fct_appdata.md @@ -30,45 +30,45 @@ Code df[c(1, 1000, 2000, 3000, 4000, 5000), ] Output - # A tibble: 6 x 24 - site_code subject_id event_id event_date event event_repeat form_id - - 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 2 NA NA - 3 NA NA - 4 NA NA - 5 NA NA - 6 NA NA - # i 17 more variables: form_repeat , edit_date_time , day , - # vis_day , vis_num , event_name , event_label , - # item_name , item_type , item_group , item_value , - # item_unit , lower_lim , upper_lim , significance , - # reason_notdone , region + # A tibble: 6 x 23 + site_code subject_id event_id event_date event_repeat form_id form_repeat + + 1 9600 9600-001 SCR 2022-11-09 1 DM 1 + 2 NA NA NA + 3 NA NA NA + 4 NA NA NA + 5 NA NA NA + 6 NA NA NA + # i 16 more variables: edit_date_time , day , vis_day , + # vis_num , event_name , event_label , item_name , + # item_type , item_group , item_value , item_unit , + # lower_lim , upper_lim , significance , reason_notdone , + # region --- Code df Output - # A tibble: 543 x 24 - site_code subject_id event_id event_date event event_repeat form_id - - 1 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 2 9600 9600-001 SCR 2022-11-09 Screening 1 DM - 3 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 4 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 5 9600 9600-002 SCR 2022-01-01 Screening 1 DM - 6 9600 9600-002 SCR 2022-01-01 Screening 1 STE - 7 9600 9600-002 SCR 2022-01-01 Screening 1 STE - 8 9600 9600-002 SCR 2022-01-01 Screening 1 VS - 9 9600 9600-002 SCR 2022-01-01 Screening 1 VS - 10 9600 9600-002 SCR 2022-01-01 Screening 1 VS + # A tibble: 543 x 23 + site_code subject_id event_id event_date event_repeat form_id form_repeat + + 1 9600 9600-001 SCR 2022-11-09 1 DM 1 + 2 9600 9600-001 SCR 2022-11-09 1 DM 1 + 3 9600 9600-002 SCR 2022-01-01 1 DM 1 + 4 9600 9600-002 SCR 2022-01-01 1 DM 1 + 5 9600 9600-002 SCR 2022-01-01 1 DM 1 + 6 9600 9600-002 SCR 2022-01-01 1 STE 1 + 7 9600 9600-002 SCR 2022-01-01 1 STE 1 + 8 9600 9600-002 SCR 2022-01-01 1 VS 1 + 9 9600 9600-002 SCR 2022-01-01 1 VS 1 + 10 9600 9600-002 SCR 2022-01-01 1 VS 1 # i 533 more rows - # i 17 more variables: form_repeat , edit_date_time , day , - # vis_day , vis_num , event_name , event_label , - # item_name , item_type , item_group , item_value , - # item_unit , lower_lim , upper_lim , significance , - # reason_notdone , region + # i 16 more variables: edit_date_time , day , vis_day , + # vis_num , event_name , event_label , item_name , + # item_type , item_group , item_value , item_unit , + # lower_lim , upper_lim , significance , reason_notdone , + # region # get_appdata works: produces the expected output diff --git a/tests/testthat/test-rename_raw_data.R b/tests/testthat/test-rename_raw_data.R index 94e0b232..fd7db26e 100644 --- a/tests/testthat/test-rename_raw_data.R +++ b/tests/testthat/test-rename_raw_data.R @@ -1,7 +1,7 @@ describe("rename_raw_data() renames raw study data and throws informative errors if needed.", { it("renames a data frame as expected", { - col_names <- metadata$column_names + col_names <- rbind(metadata$column_names, list("Placeholder", "pl")) testdata <- lapply(mtcars, as.character) |> as.data.frame() col_names$name_raw <- names(testdata) @@ -11,7 +11,7 @@ describe("rename_raw_data() renames raw study data and throws informative errors }) it("errors with incorrect input", { - col_names <- metadata$column_names + col_names <- rbind(metadata$column_names, list("Placeholder", "pl")) col_names$name_raw <- names(mtcars) expect_error( rename_raw_data(mtcars, column_names = "incorrect input"), From 12b28f180a6e01221e1198f6d80a744658673bd5 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Tue, 15 Oct 2024 08:37:02 -0400 Subject: [PATCH 22/24] Specify the `parent.frame()` as the environment to check existence within --- R/golem_utils_server.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index e9051da5..33492d03 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -63,7 +63,7 @@ drop_nulls <- function(x) { #' @examples #' mtcars2 %|_|% mtcars "%|_|%" <- function(x, y, verbose = TRUE) { - if (exists(deparse1(substitute(x)))) { + if (exists(deparse1(substitute(x)), envir = parent.frame())) { if (verbose) warning(paste("Using user supplied", deparse(deparse1(substitute(x))), "instead of deriving."), call. = FALSE) x } else { From ea4714ab12883b93b60d3529647b08cec3c3c8d7 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Tue, 15 Oct 2024 08:58:48 -0400 Subject: [PATCH 23/24] Add tests for `%|_|%` --- tests/testthat/test-golem_utils_server.R | 27 ++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/tests/testthat/test-golem_utils_server.R b/tests/testthat/test-golem_utils_server.R index 08376179..b1bbe06e 100644 --- a/tests/testthat/test-golem_utils_server.R +++ b/tests/testthat/test-golem_utils_server.R @@ -44,3 +44,30 @@ test_that("%|NA|% works", { ) }) +test_that("%|_|% works", { + expect_equal( + mtcarrs %|_|% iris, + iris + ) + expect_warning( + test_wrn <- mtcars %|_|% iris, + 'Using user supplied "mtcars" instead of deriving.' + ) + expect_equal( + test_wrn, + mtcars + ) + expect_warning( + test_wrn <- dplyr::mutate(mtcars, test = mpg %|_|% "RHS"), + 'Using user supplied "mpg" instead of deriving.' + ) + expect_equal( + test_wrn, + cbind(mtcars, list(test = mtcars$mpg)) + ) + expect_equal( + dplyr::mutate(mtcars, test = mpg2 %|_|% "RHS"), + cbind(mtcars, list(test = "RHS")) + ) +}) + From 3e9dc7b21e04efa3ce988b9785cff238bde3f3b6 Mon Sep 17 00:00:00 2001 From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com> Date: Tue, 15 Oct 2024 11:03:13 -0400 Subject: [PATCH 24/24] Change `warning()` to `cat()` --- R/golem_utils_server.R | 2 +- tests/testthat/test-golem_utils_server.R | 18 ++++++++++++------ 2 files changed, 13 insertions(+), 7 deletions(-) diff --git a/R/golem_utils_server.R b/R/golem_utils_server.R index 33492d03..907d64cd 100644 --- a/R/golem_utils_server.R +++ b/R/golem_utils_server.R @@ -64,7 +64,7 @@ drop_nulls <- function(x) { #' mtcars2 %|_|% mtcars "%|_|%" <- function(x, y, verbose = TRUE) { if (exists(deparse1(substitute(x)), envir = parent.frame())) { - if (verbose) warning(paste("Using user supplied", deparse(deparse1(substitute(x))), "instead of deriving."), call. = FALSE) + if (verbose) cat("Using user supplied", deparse(deparse1(substitute(x))), "instead of deriving.\n") x } else { y diff --git a/tests/testthat/test-golem_utils_server.R b/tests/testthat/test-golem_utils_server.R index b1bbe06e..929991bd 100644 --- a/tests/testthat/test-golem_utils_server.R +++ b/tests/testthat/test-golem_utils_server.R @@ -49,20 +49,26 @@ test_that("%|_|% works", { mtcarrs %|_|% iris, iris ) - expect_warning( - test_wrn <- mtcars %|_|% iris, - 'Using user supplied "mtcars" instead of deriving.' + test_wrn <- capture_output_lines( + test_out <- mtcars %|_|% iris ) expect_equal( test_wrn, + 'Using user supplied "mtcars" instead of deriving.' + ) + expect_equal( + test_out, mtcars ) - expect_warning( - test_wrn <- dplyr::mutate(mtcars, test = mpg %|_|% "RHS"), - 'Using user supplied "mpg" instead of deriving.' + test_wrn <- capture_output_lines( + test_out <- dplyr::mutate(mtcars, test = mpg %|_|% "RHS") ) expect_equal( test_wrn, + 'Using user supplied "mpg" instead of deriving.' + ) + expect_equal( + test_out, cbind(mtcars, list(test = mtcars$mpg)) ) expect_equal(