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+++ b/articles/add_functions.html
@@ -0,0 +1,460 @@
+
+
+
+
+
+
+
+
+Adding new functions • chefStats
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Skip to contents
+
+
+
+
+
+
+
+
+
+
Adding new functions
+
+
+
+
add_functions.Rmd
+
+
+
+
+
To add new functions to chefStats, you follow three general
+steps:
+
+
Consider what type of function you need:
+stat_by_strata_by_trt,
+stat_by_strata_across_trt or
+stat_across_strata_across_trt (see article Function
+types.
+
Decide what information the function needs in order to compute the
+desired results. See section Interface
+with chef
+
+
Write the function definition (use use_chefStats() to
+help create the template)
+
Write the appropriate unit-tests for the function (using testthat framework)
+
+
+
+
Walk through example
+
+
Here we show how we would add the function
+n_subj_event(), which counts the number of subjects
+experiencing the event by stratification level and treatment level, if
+it didn’t already exist in chefStats.
+
+
Since the function produces a number by stratification level and by
+treatment level, this will be a stat_by_strata_by_trt
+
+
The function will need to know (see section Interface with chef for more details on
+how to pass this information from chef to chefStats):
+
+
Who was eligible to have the event
+
Who has the event
+
What the stratification “group” (e.g. SEX, AGE, etc) and level
+(“MALE”, “>65”, etc). is
+
What the treatment level is (e.g. “TreatmentA”)
+
+
+
The function definition might look like this:
+
+
+n_subj_event<-
+function(dat,
+event_index,
+cell_index,
+subjectid_var,
+...# the `...` are required for all chefStats functions to "collect" any unused arguments passed from chef
+){
+# Please see the "Interface with chef" section for details on what
+# `event_index` and `cell_index`
+
+# `intersect()` provides us with a vector of rows in `dat` that match both
+# `event_index` and `cell_index` - aka records that were BOTH eligible to
+# have the event (`cell_index`) AND had the event (`event_index`)
+index<-intersect(event_index, cell_index)
+
+# Return all matching rows in `dat` where `INDEX_`
+# matches `index`.
+event_rows<-dat[INDEX_%in%index]
+
+# `dat` contains event data, meaning subjects can appear more than once if
+# they have >1 event, so we need to remove these extra rows to get a proper
+# count
+event_rows_unique_by_subject<-unique(event_rows, by =subjectid_var)
+
+stat<-NROW(event_rows_unique_by_subject)
+
+# The return object has to be a data.table object with the following 3
+# columns. The `value` column always has to be a double (not an integer)
+return(
+data.table(
+ description ="Number of subjects with events",
+ label ="n_subj_events",
+ value =as.double(stat)
+)
+)
+
+}
+
+
+
+
+
Interface with chef
+
+
The statistical functions from chefStats will be called within the
+context of a chef pipeline. The category of the function determines what
+arguments are passed from chef to the function, however some arguments
+are passed to all categories.
+
The following table describes arguments that are passed to
+all chefStats function:
+
+
+Arguments always passed to chefStats functions
+
+
+
+Argument Names
+
+
+Description
+
+
+
+
+
+dat
+
+
+A data.table containing the analysis data set produced by
+the prepare_data function. To allow flexability for
+creative use of chefStats functions, this dataset is
+not filtered to the exact records needed for each
+analysis when passed to chefStats. Instead this filtering is done inside
+the chefStats functions. This is done using the INDEX_
+column from dat that serves as a row ID, and is used for
+filtering with, for example, cell_index or
+event_index
+
+
+
+
+event_index
+
+
+A vector of indicies indicating which rows (as specified in
+INDEX_ column of dat) are considered to be
+events for the endpoint specification under evaluation
+
+
+
+
+strata_var
+
+
+A character indicating which stratatification is being used
+(e.g. SEX, AGE, etc)
+
+
+
+
+treatment_var
+
+
+A character indicating the name of the column in
+dat containing the treatment information used for the
+endpoint
+
+
+
+
+subjectid_var
+
+
+A character specifying the name of the column in
+dat containing the subject ID. Defaults to “USUBJID”
+
+
+
+
+
+
Additionally, each function type receives the following arguments
+
+
+
+
+
+
+
+
+
+
+
+
+
+Additional arguments passed to by_strata_by_trt functions
+
+
+
+Argument Names
+
+
+Description
+
+
+
+
+
+cell_index
+
+
+A vector of indicies specifying which rows in
+dat are considered to be part of the analysis for the given
+strata level and treatment level under evaluation. For example, if the
+current instance of the function was analysis “Number of Events” for
+SEX==“M” and TRT01A == “Placebo”, then cell_index would be
+a vector of records in dat$INDEX_ that match those
+parameters. You can thus obtain the analysis set by filtering
+dat via: dat[cell_index %in% INDEX_]
+
+
+
+
+strata_val
+
+
+A character specifying the stratification level under
+evaluation. For example if strat_var =="SEX", then
+strat_val could be either "M" or
+"F"
+
+
+
+
+treatment_val
+
+
+A character specifying the treatment level (or treatment
+arm). *Not to be confused with the treatment_refval that
+specifies the reference treatment value.
+
+
+
+
+
+
+
+
+
+Additional arguments passed to by_strata_across_trt functions
+
+
+
+Argument Names
+
+
+Description
+
+
+
+
+
+cell_index
+
+
+A vector of indicies specifying which rows in
+dat are considered to be part of the analysis for the given
+strata level and treatment level under evaluation. For example, if the
+current instance of the function was analysis “Number of Events” for
+SEX==“M” and TRT01A == “Placebo”, then cell_index would be
+a vector of records in dat$INDEX_ that match those
+parameters. You can thus obtain the analysis set by filtering
+dat via: dat[cell_index %in% INDEX_]
+
+
+
+
+strata_val
+
+
+A character specifying the stratification level under
+evaluation. For example if strat_var =="SEX", then
+strat_val could be either "M" or
+"F"
+
+
+
+
+treatment_refval
+
+
+A character specifying the treatment reference level. *Not
+to be confused with the treatment_val that specifies the
+treatment value for by_strata_by_trt functions
+
+
+
+
+
+
+
+
+
+Additional arguments passed to across_strata_across_trt functions
+
+
+
+Argument Names
+
+
+Description
+
+
+
+
+
+strata_val
+
+
+A character specifying the stratification level under
+evaluation. For example if strat_var =="SEX", then
+strat_val could be either "M" or
+"F"
+
+
+
+
+treatment_refval
+
+
+A character specifying the treatment reference level. *Not
+to be confused with the treatment_val that specifies the
+treatment value for by_strata_by_trt functions
+
+
+
+
+
+
+
+
+
+
Using building-blocks
+
+
When possible, utilize building-block functions when making new
+statistical functions. For example, if the new functions requires a 2x2
+table, use the make_two_by_two_() function instead of
+writing a new one.
+
This also allows you to easily write functions that collapse several
+chefStats functions into one function call. For example, on call to
+count_set() is the same as one call each to
+n_sub(), n_event(),
+n_subj_event() and p_subj_event(). The only
+rational for combining functions like this is to save compute time, due
+to the way chef pipelines are constructed.
+
Building block function names are always suffixed with an underscore
+_ to indicate they cannot be called from inside a chef
+pipeline. For example, n_event_() is a building block that
+is used to make n_event(), but n_event_() can
+also be use to build other functions, such as count_set(),
+because it does not format it’s output for a chef pipeline. Conversely,
+n_event() does format the output, so it can be use in a
+chef pipeline, but not as a building block.
To add new functions to chefStats, you follow three general
-steps:
-
-
Consider what type of function you need:
-stat_by_strata_by_trt,
-stat_by_strata_across_trt or
-stat_across_strata_across_trt.
-
Decide what information the function needs in order to compute the
-desired results. See section Interface
-with chef
-
-
Write the function definition (use use_chefStats() to
-help create the template)
-
Write the appropriate unit-tests for the function (using testthat framework)
-
-
-
Walk through example
-
-
Here we show how we would add the function
-n_subj_event(), which counts the number of subjects
-experiencing the event by stratification level and treatment level, if
-it didn’t already exist in chefStats.
-
-
Since the function produces a number by stratification level and by
-treatment level, this will be a stat_by_strata_by_trt
-
-
The function will need to know (see section Interface with chef for more details on
-how to pass this information from chef to chefStats):
-
-
Who was eligible to have the event
-
Who has the event
-
What the stratification “group” (e.g. SEX, AGE, etc) and level
-(“MALE”, “>65”, etc). is
-
What the treatment level is (e.g. “TreatmentA”)
-
-
-
The function definition might look like this:
-
-
-n_subj_event<-
-function(dat,
-event_index,
-cell_index,
-subjectid_var,
-...# the `...` are required for all chefStats functions to "collect" any unused arguments passed from chef
-){
-# Please see the "Interface with chef" section for details on what
-# `event_index` and `cell_index`
-
-# `intersect()` provides us with a vector of rows in `dat` that match both
-# `event_index` and `cell_index` - aka records that were BOTH eligible to
-# have the event (`cell_index`) AND had the event (`event_index`)
-index<-intersect(event_index, cell_index)
-
-# Return all matching rows in `dat` where `INDEX_`
-# matches `index`.
-event_rows<-dat[INDEX_%in%index]
-
-# `dat` contains event data, meaning subjects can appear more than once if
-# they have >1 event, so we need to remove these extra rows to get a proper
-# count
-event_rows_unique_by_subject<-unique(event_rows, by =subjectid_var)
-
-stat<-NROW(event_rows_unique_by_subject)
-
-# The return object has to be a data.table object with the following 3
-# columns. The `value` column always has to be a double (not an integer)
-return(
-data.table(
- description ="Number of subjects with events",
- label ="n_subj_events",
- value =as.double(stat)
-)
-)
-
-}
-
-
-
-
Interface with chef
-
-
The statistical functions from chefStats will be called within the
-context of a chef pipeline. The category of the function determines what
-arguments are passed from chef to the function, however some arguments
-are passed to all categories.
-
The following table describes arguments that are passed to
-all chefStats function:
-
-
-Arguments always passed to chefStats functions
-
-
-
-Argument Names
-
-
-Description
-
-
-
-
-
-dat
-
-
-A data.table containing the analysis data set produced by
-the prepare_data function. To allow flexability for
-creative use of chefStats functions, this dataset is
-not filtered to the exact records needed for each
-analysis when passed to chefStats. Instead this filtering is done inside
-the chefStats functions. This is done using the INDEX_
-column from dat that serves as a row ID, and is used for
-filtering with, for example, cell_index or
-event_index
-
-
-
-
-event_index
-
-
-A vector of indicies indicating which rows (as specified in
-INDEX_ column of dat) are considered to be
-events for the endpoint specification under evaluation
-
-
-
-
-strata_var
-
-
-A character indicating which stratatification is being used
-(e.g. SEX, AGE, etc)
-
-
-
-
-treatment_var
-
-
-A character indicating the name of the column in
-dat containing the treatment information used for the
-endpoint
-
-
-
-
-subjectid_var
-
-
-A character specifying the name of the column in
-dat containing the subject ID. Defaults to “USUBJID”
-
-
-
-
-
Additionally, each function type receives the following arguments
-
-
-
-
-
-
-
-
-
-
-
-
-
-Additional arguments passed to by_strata_by_trt functions
-
-
-
-Argument Names
-
-
-Description
-
-
-
-
-
-cell_index
-
-
-A vector of indicies specifying which rows in
-dat are considered to be part of the analysis for the given
-strata level and treatment level under evaluation. For example, if the
-current instance of the function was analysis “Number of Events” for
-SEX==“M” and TRT01A == “Placebo”, then cell_index would be
-a vector of records in dat$INDEX_ that match those
-parameters. You can thus obtain the analysis set by filtering
-dat via: dat[cell_index %in% INDEX_]
-
-
-
-
-strata_val
-
-
-A character specifying the stratification level under
-evaluation. For example if strat_var =="SEX", then
-strat_val could be either "M" or
-"F"
-
-
-
-
-treatment_val
-
-
-A character specifying the treatment level (or treatment
-arm). *Not to be confused with the treatment_refval that
-specifies the reference treatment value.
-
-
-
-
-
-
-
-
-
-Additional arguments passed to by_strata_across_trt functions
-
-
-
-Argument Names
-
-
-Description
-
-
-
-
-
-cell_index
-
-
-A vector of indicies specifying which rows in
-dat are considered to be part of the analysis for the given
-strata level and treatment level under evaluation. For example, if the
-current instance of the function was analysis “Number of Events” for
-SEX==“M” and TRT01A == “Placebo”, then cell_index would be
-a vector of records in dat$INDEX_ that match those
-parameters. You can thus obtain the analysis set by filtering
-dat via: dat[cell_index %in% INDEX_]
-
-
-
-
-strata_val
-
-
-A character specifying the stratification level under
-evaluation. For example if strat_var =="SEX", then
-strat_val could be either "M" or
-"F"
-
-
-
-
-treatment_refval
-
-
-A character specifying the treatment reference level. *Not
-to be confused with the treatment_val that specifies the
-treatment value for by_strata_by_trt functions
-
-
-
-
-
-
-
-
-
-Additional arguments passed to across_strata_across_trt functions
-
-
-
-Argument Names
-
-
-Description
-
-
-
-
-
-strata_val
-
-
-A character specifying the stratification level under
-evaluation. For example if strat_var =="SEX", then
-strat_val could be either "M" or
-"F"
-
-
-
-
-treatment_refval
-
-
-A character specifying the treatment reference level. *Not
-to be confused with the treatment_val that specifies the
-treatment value for by_strata_by_trt functions
-
if TRUE Tarones correction is returned. Default = FALSE.
+
+
+
+
Value
+
+
+
A vector with three values statistic - Breslow and Day test
+statistic pval - p value evtl. based on the Tarone test statistic using a
+\(\chi^2(K-1)\) distribution
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/reference/count_set.html b/reference/count_set.html
new file mode 100644
index 0000000..62aefd8
--- /dev/null
+++ b/reference/count_set.html
@@ -0,0 +1,129 @@
+
+Produce counts of Number of subjects, number of events, number of
+subjects with events, and proportion of subjects with events — count_set • chefStats
+ Skip to contents
+
+
+
+
+
+
Produce counts of Number of subjects, number of events, number of
+subjects with events, and proportion of subjects with events
+
+
count_set.Rd
+
+
+
+
A short cut - instead of calling the individual function
+(n_sub, n_event, n_subj_event, p_subj_event), one call to this
+function will produce all the described functions. This can be useful to
+save compute time as inside the chef pipeline there will be fewer
+iterations.
vector of integers that index the rows in dat that match
+the definition of an 'event'. Matching is done via the INDEX_ column in
+dat.
+
+
+
cell_index
+
A vector of integers referencing the rows of dat (as
+specified by the INDEX_ column in dat) that match the population to be
+analyzed. See the "Endpoint Events" vignette in ramnog
+for more information.
+
+
+
subjectid_var
+
character. Name of the subject identifier variable in the data (default is "USUBJID").
Produce counts of Number of subjects, number of events, number of
+subjects with events, and proportion of subjects with events
By strata, across treatment levels
@@ -125,6 +132,63 @@
Across strata, across treatment le
Wrapper for P-value of interaction tests
+
Building-block functions
+
+
These are used as building blocks when making the chef-facing functions. They are exported so that they can also be use in chefCriteria but they cannot be called directly in a chef pipeline
vector of integers that index the rows in dat that match
+the definition of an 'event'. Matching is done via the INDEX_ column in
+dat.
+
+
+
cell_index
+
A vector of integers referencing the rows of dat (as
+specified by the INDEX_ column in dat) that match the population to be
+analyzed. See the "Endpoint Events" vignette in ramnog
+for more information.
+
+
+
treatment_var
+
character. The name of the treatment variable in dat.
+
+
+
treatment_refval
+
character. The reference value of the treatment variable in dat.
+
+
+
subjectid_var
+
character. Name of the subject identifier variable in dat (default is "USUBJID").
+
+
+
+
Value
+
+
+
A matrix
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/reference/make_two_by_two_by_k_.html b/reference/make_two_by_two_by_k_.html
new file mode 100644
index 0000000..18facc0
--- /dev/null
+++ b/reference/make_two_by_two_by_k_.html
@@ -0,0 +1,127 @@
+
+Make 2x2xk contingency tables from summarized adam data. This function is NOT
+generalized — make_two_by_two_by_k_ • chefStats
+ Skip to contents
+
+
+
+
+
+
Make 2x2xk contingency tables from summarized adam data. This function is NOT
+generalized
+
+
make_two_by_two_by_k_.Rd
+
+
+
+
Make 2x2xk contingency tables from summarized adam data. This function is NOT
+generalized
diff --git a/reference/n_sub_.html b/reference/n_sub_.html
new file mode 100644
index 0000000..8c78f20
--- /dev/null
+++ b/reference/n_sub_.html
@@ -0,0 +1,105 @@
+
+Building-block: Number of subjects — n_sub_ • chefStats
+ Skip to contents
+
+
+
+
+
+
Building-block: Number of subjects
+
+
n_sub_.Rd
+
+
+
+
Building-block: Number of subjects
+
+
+
+
Usage
+
n_sub_(dat, cell_index, subjectid_var)
+
+
+
+
Arguments
+
dat
+
data.table. The analysis data set.
+
+
+
cell_index
+
A vector of integers referencing the rows of dat (as
+specified by the INDEX_ column in dat) that match the population to be
+analyzed. See the "Endpoint Events" vignette in ramnog for more
+information.
+
+
+
subjectid_var
+
character. Name of the subject identifier variable in
+the data (default is "USUBJID").
diff --git a/reference/n_subj_event_.html b/reference/n_subj_event_.html
new file mode 100644
index 0000000..dacd653
--- /dev/null
+++ b/reference/n_subj_event_.html
@@ -0,0 +1,104 @@
+
+Building-block: Number of subjects with at least one event — n_subj_event_ • chefStats
+ Skip to contents
+
+
+
+
+
+
Building-block: Number of subjects with at least one event
+
+
n_subj_event_.Rd
+
+
+
+
Building-block: Number of subjects with at least one event
diff --git a/reference/p_subj_event_.html b/reference/p_subj_event_.html
new file mode 100644
index 0000000..134e464
--- /dev/null
+++ b/reference/p_subj_event_.html
@@ -0,0 +1,111 @@
+
+Building-block: Proportion of subjects having at least one event — p_subj_event_ • chefStats
+ Skip to contents
+
+
+
+
+
+
Building-block: Proportion of subjects having at least one event
+
+
p_subj_event_.Rd
+
+
+
+
Building-block: Proportion of subjects having at least one event
A vector of integers referencing the rows of dat (as
+specified by the INDEX_ column in dat) that match the population to be
+analyzed. See the "Endpoint Events" vignette in ramnog for more
+information.
+
+
+
intersect_index
+
A vector of intergers referencing the rows of dat
+that match both (1) the population to be analyzed and (2) the defenition of
+an event
+
+
+
subjectid_var
+
character. Name of the subject identifier variable in
+the data (default is "USUBJID").
diff --git a/search.json b/search.json
index bfed32a..15a3763 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://hta-pharma.github.io/chefStats/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 Novo Nordisk /S, Danish company registration . 24256790 Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/chefStats.html","id":"introcution-to-chefstats","dir":"Articles","previous_headings":"","what":"Introcution to chefStats","title":"chefStats","text":"making AMNOG analysis using chef, need pass one summarization/inference functions endpoint. chefStats package makes easier Providing collection fast, validated functions can dropped chef-pipelines “just work” Guiding creation new (validated) functions need one doesn’t yet exist (use_chefStats())","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/function_types.html","id":"statistical-method-types-in-chef-and-chefstats","dir":"Articles","previous_headings":"","what":"Statistical method types in chef and chefStats","title":"Function types","text":"chef framework categorizes statistical functions three main categories depending operate stratification levels treatment levels. Operations can either done per stratification level treatment level, can operate across levels. Figure 1 shows typical table safety analysis color codes result based function type creates : Figure 1 Table 1 provides description three function types, color coded outputs produce table 1 : Table 1 function type also determines function applied. example figure 1, stat_by_strata_by_trt function called combination stratification level treatment level, well TOTALS treatment level: SEX == “MALE” & TRT == “TreatmentA” SEX == “FEMALE” & TRT == “TreatmentA” SEX == “MALE” & TRT == “TreatmentB” SEX == “FEMALE” & TRT == “TreatmentB” AGE == “<65” & TRT == “TreatmentA” AGE == “>=65” & TRT == “TreatmentA” AGE == “<65” & TRT == “TreatmentB” AGE == “>=65” & TRT == “TreatmentB” TOTAL_ == “total” & TRT == “TreatmentA” TOTAL_ == “total” & TRT == “TreatmentB” Whereas stat_across_strata_across_trt called per stratification “group”, .e.: strata_var == “SEX” strata_var == “AGE”","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/function_types.html","id":"adding-new-functions","dir":"Articles","previous_headings":"","what":"Adding new functions","title":"Function types","text":"add new functions chefStats, follow three general steps: Consider type function need: stat_by_strata_by_trt, stat_by_strata_across_trt stat_across_strata_across_trt. Decide information function needs order compute desired results. See section Interface chef Write function definition (use use_chefStats() help create template) Write appropriate unit-tests function (using testthat framework)","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/function_types.html","id":"walk-through-example","dir":"Articles","previous_headings":"Adding new functions","what":"Walk through example","title":"Function types","text":"show add function n_subj_event(), counts number subjects experiencing event stratification level treatment level, didn’t already exist chefStats. Since function produces number stratification level treatment level, stat_by_strata_by_trt eligible event event stratification “group” (e.g. SEX, AGE, etc) level (“MALE”, “>65”, etc). treatment level (e.g. “TreatmentA”) function definition might look like :","code":"n_subj_event <- function(dat, event_index, cell_index, subjectid_var, ... # the `...` are required for all chefStats functions to \"collect\" any unused arguments passed from chef ) { # Please see the \"Interface with chef\" section for details on what # `event_index` and `cell_index` # `intersect()` provides us with a vector of rows in `dat` that match both # `event_index` and `cell_index` - aka records that were BOTH eligible to # have the event (`cell_index`) AND had the event (`event_index`) index <- intersect(event_index, cell_index) # Return all matching rows in `dat` where `INDEX_` # matches `index`. event_rows <- dat[INDEX_ %in% index] # `dat` contains event data, meaning subjects can appear more than once if # they have >1 event, so we need to remove these extra rows to get a proper # count event_rows_unique_by_subject <- unique(event_rows, by = subjectid_var) stat <- NROW(event_rows_unique_by_subject) # The return object has to be a data.table object with the following 3 # columns. The `value` column always has to be a double (not an integer) return( data.table( description = \"Number of subjects with events\", label = \"n_subj_events\", value = as.double(stat) ) ) }"},{"path":"https://hta-pharma.github.io/chefStats/articles/function_types.html","id":"interface-with-chef","dir":"Articles","previous_headings":"Adding new functions","what":"Interface with chef","title":"Function types","text":"statistical functions chefStats called within context chef pipeline. category function determines arguments passed chef function, however arguments passed categories. following table describes arguments passed chefStats function: Arguments always passed chefStats functions Additionally, function type receives following arguments stat_by_strata_by_trt stat_by_strata_across_trt stat_by_strata_across_trt Additional arguments passed by_strata_by_trt functions Additional arguments passed by_strata_across_trt functions Additional arguments passed across_strata_across_trt functions","code":""},{"path":"https://hta-pharma.github.io/chefStats/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"MEWP (Matthew Phelps). Author. NOSJ (Nicolai Skov Johnsen). Author. ABIU (Anders Bilgrau). Author. SCQY (scqy). Author. CINO (Christian Haargaard Olsen). Author, maintainer. Novo Nordisk /S. Copyright holder.","code":""},{"path":"https://hta-pharma.github.io/chefStats/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"MEWP (Matthew Phelps), NOSJ (Nicolai Skov Johnsen), ABIU (Anders Bilgrau), SCQY (scqy), CINO (Christian Haargaard Olsen) (2024). chefStats: Provide methods different statistics. R package version 0.1.1, https://app.codecov.io/github/hta-pharma/chefStats, https://hta-pharma.github.io/chefStats/.","code":"@Manual{, title = {chefStats: Provide methods for different statistics}, author = {{MEWP (Matthew Phelps)} and {NOSJ (Nicolai Skov Johnsen)} and {ABIU (Anders Bilgrau)} and {SCQY (scqy)} and {CINO (Christian Haargaard Olsen)}}, year = {2024}, note = {R package version 0.1.1, https://app.codecov.io/github/hta-pharma/chefStats}, url = {https://hta-pharma.github.io/chefStats/}, }"},{"path":"https://hta-pharma.github.io/chefStats/index.html","id":"a-library-of-statistical-methods-for-chef-style-amnog-analyses-","dir":"","previous_headings":"","what":"Provide methods for different statistics","title":"Provide methods for different statistics","text":"{chefStats} package aims provide library fast, validated methods use AMNOG analysis created chef package. functions found chefStats designed used chef, may unwieldy use functions independently.","code":""},{"path":"https://hta-pharma.github.io/chefStats/index.html","id":"developer-documentation","dir":"","previous_headings":"","what":"Developer Documentation","title":"Provide methods for different statistics","text":"Please refer {ramnog} general developer documentation. Ramnog Developer Documentation","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for Odds Ratio calculation — OR","title":"Wrapper for Odds Ratio calculation — OR","text":"Ensures input statistical function proper format, ensures output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for Odds Ratio calculation — OR","text":"","code":"OR( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for Odds Ratio calculation — OR","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for Odds Ratio calculation — OR","text":"data.table containing Odds Ratio statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for Risk Difference calculation — RD","title":"Wrapper for Risk Difference calculation — RD","text":"Ensures input statistical function proper format, ensures output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for Risk Difference calculation — RD","text":"","code":"RD( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, as_pct = TRUE, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for Risk Difference calculation — RD","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). as_pct Boolean. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for Risk Difference calculation — RD","text":"data.table containing Risk Difference statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":null,"dir":"Reference","previous_headings":"","what":"Relative Risk calculation — RR","title":"Relative Risk calculation — RR","text":"Ensures input statistical function proper format, ensure output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Relative Risk calculation — RR","text":"","code":"RR( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Relative Risk calculation — RR","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Relative Risk calculation — RR","text":"data.table containing Relative Risk statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_continuous.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate summary statistics for demographics on a continuous variable — demographics_continuous","title":"Calculate summary statistics for demographics on a continuous variable — demographics_continuous","text":"Calculate set summary statistics (mean, median, sd, min, max, n_non_missing, n_missing) continuous variable demographics endpoints.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_continuous.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate summary statistics for demographics on a continuous variable — demographics_continuous","text":"","code":"demographics_continuous(dat, event_index, cell_index, subjectid_var, var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_continuous.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate summary statistics for demographics on a continuous variable — demographics_continuous","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). var character. Name variable analysis data subject statistics. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_continuous.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate summary statistics for demographics on a continuous variable — demographics_continuous","text":"data.table containing summary statistics given continuous variable analysis data set.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate basic summary statistics for demographics — demographics_counts","title":"Calculate basic summary statistics for demographics — demographics_counts","text":"Calculate summary statistics (n_non_missing, n_missing) variable demographics endpoints.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate basic summary statistics for demographics — demographics_counts","text":"","code":"demographics_counts( dat, cell_index, subjectid_var, stratify_by, strata_var, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate basic summary statistics for demographics — demographics_counts","text":"dat data.table. analysis data set. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). stratify_by character vector. Set variables analysis data stratify . strata_var character. Variable analysis data stratify specific call. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/demographics_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate basic summary statistics for demographics — demographics_counts","text":"data.table containing summary statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/hedges_g.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to prepare data for Hedges G — hedges_g","title":"Wrapper to prepare data for Hedges G — hedges_g","text":"Wrapper prepare data Hedges G","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/hedges_g.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to prepare data for Hedges G — hedges_g","text":"","code":"hedges_g(dat, reference_val, safe_mode = FALSE, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/hedges_g.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to prepare data for Hedges G — hedges_g","text":"dat data.table. analysis data set. reference_val character. reference value treatment variable data. safe_mode Boolean determining function fail given input calculated (safe_mode = TRUE), silently return NA value (default ... optional arguments ","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/hedges_g.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to prepare data for Hedges G — hedges_g","text":"list containing Hedges G statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k.html","id":null,"dir":"Reference","previous_headings":"","what":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k","text":"Make 2x2xk contingency tables summarized adam data. function generalized","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k","text":"","code":"make_two_by_two_by_k( dat, event_index, strata_var, treatment_var, treatment_refval, subjectid_var )"},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. strata_var character. Variable dat stratify specific call. treatment_var character. name treatment variable dat. treatment_refval character. reference value treatment variable dat. subjectid_var character. Name subject identifier variable dat (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k","text":"two--two--k array k represents number subgroups (strata).","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate percentage of subjects with events — mean_value","title":"Calculate percentage of subjects with events — mean_value","text":"Calculate percentage subjects events treatment strata.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate percentage of subjects with events — mean_value","text":"","code":"mean_value(dat, event_index, cell_index, subjectid_var, var, ...) mean_value(dat, event_index, cell_index, subjectid_var, var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate percentage of subjects with events — mean_value","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). var character. Name variable analysis data subject statistics. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate percentage of subjects with events — mean_value","text":"data.table containing percentage subjects events treatment. data.table containing mean value.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mk_two_by_two.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a two-by-two table — mk_two_by_two","title":"Make a two-by-two table — mk_two_by_two","text":"Makes two--two contingency table takes visual form: , B, C, D distinct number subjects satisfying criteria 2x2 cell. observations Treatment value recorded returned.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mk_two_by_two.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a two-by-two table — mk_two_by_two","text":"","code":"mk_two_by_two( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var )"},{"path":"https://hta-pharma.github.io/chefStats/reference/mk_two_by_two.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a two-by-two table — mk_two_by_two","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable dat. treatment_refval character. reference value treatment variable dat. subjectid_var character. Name subject identifier variable dat (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mk_two_by_two.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a two-by-two table — mk_two_by_two","text":"matrix","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of events by treatment and stratum — n_event","title":"Calculate number of events by treatment and stratum — n_event","text":"Calculate number events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of events by treatment and stratum — n_event","text":"","code":"n_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of events by treatment and stratum — n_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of events by treatment and stratum — n_event","text":"data.table containing number events given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of events per 100 years of exposure — n_event_100y","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"Calculate number events per 100 years exposure","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"","code":"n_event_100y( dat, event_index, cell_index, subjectid_var, treatment_var, treatment_value, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). treatment_var character. Name treatment variable data. treatment_value character. Value treatment variable data. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"data.table containing number events per 100 years exposure.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of subjects by treatment and stratum — n_subj","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"Calculate number subjects treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"","code":"n_subj(dat, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"dat data.table. analysis data set. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"data.table containing number subjects given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of subjects with events by treatment and stratum — n_subj_event","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"Calculate number subjects events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"","code":"n_subj_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"data.table containing number subjects events given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate observation time by treatment — obs_time_by_trt","title":"Calculate observation time by treatment — obs_time_by_trt","text":"Calculate observation time treatment","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate observation time by treatment — obs_time_by_trt","text":"","code":"obs_time_by_trt(dat, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate observation time by treatment — obs_time_by_trt","text":"dat data.table. analysis data set. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate observation time by treatment — obs_time_by_trt","text":"data.table containing observation time treatment.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"Calculate percentage subjects events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"","code":"p_subj_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"data.table containing percentage subjects events given combination treatment stratum","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate percentage of subjects with events — p_subj_event_by_trt","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"Calculate percentage subjects events treatment strata.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"","code":"p_subj_event_by_trt( dat, event_index, cell_index, subjectid_var, treatment_var, treatment_value, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). treatment_var character. Name treatment variable data. treatment_value character. Value treatment variable data. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"data.table containing percentage subjects events treatment.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for P-value calculations — p_val","title":"Wrapper for P-value calculations — p_val","text":"Ensures input statistical function proper format, enruse output formated need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for P-value calculations — p_val","text":"","code":"p_val( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, safe_mode = FALSE, threshold_lower = 5, threshold_upper = 200, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for P-value calculations — p_val","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). safe_mode Boolean determing function fail given input calculated (safe_mode = TRUE), silently return NA value (default). threshold_lower numeric. Lower threshold limit selecting Fischer vs. Barnard. threshold_upper numeric. Upper threshold limit selecting Fischer vs. Barnard. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for P-value calculations — p_val","text":"data.table containing p-value statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for P-value of interaction tests — p_val_interaction","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"Wrapper P-value interaction tests","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"","code":"p_val_interaction( dat, event_index, treatment_var, treatment_refval, subjectid_var, strata_var, odds_ratio = NA, correct = FALSE, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). strata_var character. Variable analysis data stratify specific call. odds_ratio numeric. Odds Ration (default = NA). correct logical. TRUE Tarones correction returned (default = FALSE). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"data.table containing statistics p-value interaction tests.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard deviation — sd_value","title":"Standard deviation — sd_value","text":"Standard deviation","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standard deviation — sd_value","text":"","code":"sd_value(dat, event_index, cell_index, subjectid_var, var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard deviation — sd_value","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). var Character. Name variable analysis data subject statistics. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard deviation — sd_value","text":"data.table containing standard deviation.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":null,"dir":"Reference","previous_headings":"","what":"Make new chefStats functions — use_chefStats","title":"Make new chefStats functions — use_chefStats","text":"Make new chefStats functions","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make new chefStats functions — use_chefStats","text":"","code":"use_chefStats( fn_name, fn_type = c(\"stat_by_strata_by_trt\", \"stat_by_strata_across_trt\", \"stat_across_strata_across_trt\"), file_name = NULL )"},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make new chefStats functions — use_chefStats","text":"fn_name Name function. file_name NULL fn_name used make file name fn_type Type statistical function, one stat_by_strata_by_trt, stat_by_strata_across_trt, stat_across_strata_across_trt file_name Name file store function (different fn_name)","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make new chefStats functions — use_chefStats","text":"Nothing, run side-effect (writes file disk)","code":""},{"path":"https://hta-pharma.github.io/chefStats/news/index.html","id":"chefstats-011","dir":"Changelog","previous_headings":"","what":"chefStats 0.1.1","title":"chefStats 0.1.1","text":"Centralized Git-Actions {ramnog}","code":""},{"path":"https://hta-pharma.github.io/chefStats/news/index.html","id":"chefstats-010","dir":"Changelog","previous_headings":"","what":"chefStats 0.1.0","title":"chefStats 0.1.0","text":"Initial release chefstats Contains initial selection statistical functions use {ramnog} ecosystem.","code":""}]
+[{"path":"https://hta-pharma.github.io/chefStats/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 Novo Nordisk /S, Danish company registration . 24256790 Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/add_functions.html","id":"walk-through-example","dir":"Articles","previous_headings":"","what":"Walk through example","title":"Adding new functions","text":"show add function n_subj_event(), counts number subjects experiencing event stratification level treatment level, didn’t already exist chefStats. Since function produces number stratification level treatment level, stat_by_strata_by_trt eligible event event stratification “group” (e.g. SEX, AGE, etc) level (“MALE”, “>65”, etc). treatment level (e.g. “TreatmentA”) function definition might look like :","code":"n_subj_event <- function(dat, event_index, cell_index, subjectid_var, ... # the `...` are required for all chefStats functions to \"collect\" any unused arguments passed from chef ) { # Please see the \"Interface with chef\" section for details on what # `event_index` and `cell_index` # `intersect()` provides us with a vector of rows in `dat` that match both # `event_index` and `cell_index` - aka records that were BOTH eligible to # have the event (`cell_index`) AND had the event (`event_index`) index <- intersect(event_index, cell_index) # Return all matching rows in `dat` where `INDEX_` # matches `index`. event_rows <- dat[INDEX_ %in% index] # `dat` contains event data, meaning subjects can appear more than once if # they have >1 event, so we need to remove these extra rows to get a proper # count event_rows_unique_by_subject <- unique(event_rows, by = subjectid_var) stat <- NROW(event_rows_unique_by_subject) # The return object has to be a data.table object with the following 3 # columns. The `value` column always has to be a double (not an integer) return( data.table( description = \"Number of subjects with events\", label = \"n_subj_events\", value = as.double(stat) ) ) }"},{"path":"https://hta-pharma.github.io/chefStats/articles/add_functions.html","id":"interface-with-chef","dir":"Articles","previous_headings":"","what":"Interface with chef","title":"Adding new functions","text":"statistical functions chefStats called within context chef pipeline. category function determines arguments passed chef function, however arguments passed categories. following table describes arguments passed chefStats function: Arguments always passed chefStats functions Additionally, function type receives following arguments stat_by_strata_by_trt stat_by_strata_across_trt stat_by_strata_across_trt Additional arguments passed by_strata_by_trt functions Additional arguments passed by_strata_across_trt functions Additional arguments passed across_strata_across_trt functions","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/add_functions.html","id":"using-building-blocks","dir":"Articles","previous_headings":"","what":"Using building-blocks","title":"Adding new functions","text":"possible, utilize building-block functions making new statistical functions. example, new functions requires 2x2 table, use make_two_by_two_() function instead writing new one. also allows easily write functions collapse several chefStats functions one function call. example, call count_set() one call n_sub(), n_event(), n_subj_event() p_subj_event(). rational combining functions like save compute time, due way chef pipelines constructed. Building block function names always suffixed underscore _ indicate called inside chef pipeline. example, n_event_() building block used make n_event(), n_event_() can also use build functions, count_set(), format ’s output chef pipeline. Conversely, n_event() format output, can use chef pipeline, building block.","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/chefStats.html","id":"introcution-to-chefstats","dir":"Articles","previous_headings":"","what":"Introcution to chefStats","title":"chefStats","text":"making AMNOG analysis using chef, need pass one summarization/inference functions endpoint. chefStats package makes easier Providing collection fast, validated functions can dropped chef-pipelines “just work” Guiding creation new (validated) functions need one doesn’t yet exist (use_chefStats())","code":""},{"path":"https://hta-pharma.github.io/chefStats/articles/function_types.html","id":"statistical-method-types-in-chef-and-chefstats","dir":"Articles","previous_headings":"","what":"Statistical method types in chef and chefStats","title":"Function types","text":"chef framework categorizes statistical functions three main categories depending operate stratification levels treatment levels. Operations can either done per stratification level treatment level, can operate across levels. Figure 1 shows typical table safety analysis color codes result based function type creates : Figure 1 Table 1 provides description three function types, color coded outputs produce table 1 : Table 1 function type also determines function applied. example figure 1, stat_by_strata_by_trt function called combination stratification level treatment level, well TOTALS treatment level: SEX == “MALE” & TRT == “TreatmentA” SEX == “FEMALE” & TRT == “TreatmentA” SEX == “MALE” & TRT == “TreatmentB” SEX == “FEMALE” & TRT == “TreatmentB” AGE == “<65” & TRT == “TreatmentA” AGE == “>=65” & TRT == “TreatmentA” AGE == “<65” & TRT == “TreatmentB” AGE == “>=65” & TRT == “TreatmentB” TOTAL_ == “total” & TRT == “TreatmentA” TOTAL_ == “total” & TRT == “TreatmentB” Whereas stat_across_strata_across_trt called per stratification “group”, .e.: strata_var == “SEX” strata_var == “AGE”","code":""},{"path":"https://hta-pharma.github.io/chefStats/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"MEWP (Matthew Phelps). Author. NOSJ (Nicolai Skov Johnsen). Author. ABIU (Anders Bilgrau). Author. SCQY (scqy). Author. CINO (Christian Haargaard Olsen). Author, maintainer. Novo Nordisk /S. Copyright holder.","code":""},{"path":"https://hta-pharma.github.io/chefStats/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"MEWP (Matthew Phelps), NOSJ (Nicolai Skov Johnsen), ABIU (Anders Bilgrau), SCQY (scqy), CINO (Christian Haargaard Olsen) (2024). chefStats: Provide methods different statistics. R package version 0.1.1, https://app.codecov.io/github/hta-pharma/chefStats, https://hta-pharma.github.io/chefStats/.","code":"@Manual{, title = {chefStats: Provide methods for different statistics}, author = {{MEWP (Matthew Phelps)} and {NOSJ (Nicolai Skov Johnsen)} and {ABIU (Anders Bilgrau)} and {SCQY (scqy)} and {CINO (Christian Haargaard Olsen)}}, year = {2024}, note = {R package version 0.1.1, https://app.codecov.io/github/hta-pharma/chefStats}, url = {https://hta-pharma.github.io/chefStats/}, }"},{"path":"https://hta-pharma.github.io/chefStats/index.html","id":"a-library-of-statistical-methods-for-chef-style-amnog-analyses-","dir":"","previous_headings":"","what":"Provide methods for different statistics","title":"Provide methods for different statistics","text":"{chefStats} package aims provide library fast, validated methods use AMNOG analysis created chef package. functions found chefStats designed used chef, may unwieldy use functions independently.","code":""},{"path":"https://hta-pharma.github.io/chefStats/index.html","id":"developer-documentation","dir":"","previous_headings":"","what":"Developer Documentation","title":"Provide methods for different statistics","text":"Please refer {ramnog} general developer documentation. Ramnog Developer Documentation","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for Odds Ratio calculation — OR","title":"Wrapper for Odds Ratio calculation — OR","text":"Ensures input statistical function proper format, ensures output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for Odds Ratio calculation — OR","text":"","code":"OR( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for Odds Ratio calculation — OR","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/OR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for Odds Ratio calculation — OR","text":"data.table containing Odds Ratio statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for Risk Difference calculation — RD","title":"Wrapper for Risk Difference calculation — RD","text":"Ensures input statistical function proper format, ensures output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for Risk Difference calculation — RD","text":"","code":"RD( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, as_pct = TRUE, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for Risk Difference calculation — RD","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). as_pct Boolean. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for Risk Difference calculation — RD","text":"data.table containing Risk Difference statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":null,"dir":"Reference","previous_headings":"","what":"Relative Risk calculation — RR","title":"Relative Risk calculation — RR","text":"Ensures input statistical function proper format, ensure output formatted need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Relative Risk calculation — RR","text":"","code":"RR( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Relative Risk calculation — RR","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/RR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Relative Risk calculation — RR","text":"data.table containing Relative Risk statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/barnard_test_.html","id":null,"dir":"Reference","previous_headings":"","what":"Barnards Unconditional Exact Test with trial data — barnard_test_","title":"Barnards Unconditional Exact Test with trial data — barnard_test_","text":"Barnards Unconditional Exact Test trial data","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/barnard_test_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Barnards Unconditional Exact Test with trial data — barnard_test_","text":"","code":"barnard_test_(two_by_two, verbose = FALSE, safe_mode = TRUE)"},{"path":"https://hta-pharma.github.io/chefStats/reference/barnard_test_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Barnards Unconditional Exact Test with trial data — barnard_test_","text":"two_by_two two--two table first column contains counts events. verbose Set TRUE want normal output running barnard.test print console. Default FALSE safe_mode invalid input provided, function stop error (default), return NA (safe_mode = FALSE)","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/barnard_test_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Barnards Unconditional Exact Test with trial data — barnard_test_","text":"2-sided p-value Barnards Unconditional Exact test","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/breslowdaytest_.html","id":null,"dir":"Reference","previous_headings":"","what":"Breslow-Day test — breslowdaytest_","title":"Breslow-Day test — breslowdaytest_","text":"Breslow-Day test","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/breslowdaytest_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Breslow-Day test — breslowdaytest_","text":"","code":"breslowdaytest_(x, odds_ratio = NA, correct = FALSE)"},{"path":"https://hta-pharma.github.io/chefStats/reference/breslowdaytest_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Breslow-Day test — breslowdaytest_","text":"x 2x2xK contingency table odds_ratio Odds Ration (default = NA) correct TRUE Tarones correction returned. Default = FALSE.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/breslowdaytest_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Breslow-Day test — breslowdaytest_","text":"vector three values statistic - Breslow Day test statistic pval - p value evtl. based Tarone test statistic using \\(\\chi^2(K-1)\\) distribution","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/count_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Produce counts of Number of subjects, number of events, number of\nsubjects with events, and proportion of subjects with events — count_set","title":"Produce counts of Number of subjects, number of events, number of\nsubjects with events, and proportion of subjects with events — count_set","text":"short cut - instead calling individual function (n_sub, n_event, n_subj_event, p_subj_event), one call function produce described functions. can useful save compute time inside chef pipeline fewer iterations.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/count_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Produce counts of Number of subjects, number of events, number of\nsubjects with events, and proportion of subjects with events — count_set","text":"","code":"count_set(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/count_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Produce counts of Number of subjects, number of events, number of\nsubjects with events, and proportion of subjects with events — count_set","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... 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Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable dat. treatment_refval character. reference value treatment variable dat. subjectid_var character. Name subject identifier variable dat (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a two-by-two table — make_two_by_two_","text":"matrix","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k_.html","id":null,"dir":"Reference","previous_headings":"","what":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k_","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k_","text":"Make 2x2xk contingency tables summarized adam data. function generalized","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k_","text":"","code":"make_two_by_two_by_k_( dat, event_index, strata_var, treatment_var, treatment_refval, subjectid_var )"},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k_","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. strata_var character. Variable dat stratify specific call. treatment_var character. name treatment variable dat. treatment_refval character. reference value treatment variable dat. subjectid_var character. Name subject identifier variable dat (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make 2x2xk contingency tables from summarized adam data. This function is NOT\ngeneralized — make_two_by_two_by_k_","text":"two--two--k array k represents number subgroups (strata).","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean value — mean_value","title":"Calculate mean value — mean_value","text":"Calculate mean value variable","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean value — mean_value","text":"","code":"mean_value(dat, event_index, cell_index, subjectid_var, var, ...) mean_value(dat, event_index, cell_index, subjectid_var, var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean value — mean_value","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). var character. Name variable analysis data subject statistics. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/mean_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean value — mean_value","text":"data.table containing percentage subjects events treatment. data.table containing mean value.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of events by treatment and stratum — n_event","title":"Calculate number of events by treatment and stratum — n_event","text":"Calculate number events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of events by treatment and stratum — n_event","text":"","code":"n_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of events by treatment and stratum — n_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of events by treatment and stratum — n_event","text":"data.table containing number events given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_.html","id":null,"dir":"Reference","previous_headings":"","what":"Building-block: Number of events (multiple events counted multiple times) — n_event_","title":"Building-block: Number of events (multiple events counted multiple times) — n_event_","text":"Building-block: Number events (multiple events counted multiple times)","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Building-block: Number of events (multiple events counted multiple times) — n_event_","text":"","code":"n_event_(dat, intersect_index)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Building-block: Number of events (multiple events counted multiple times) — n_event_","text":"dat data.table. analysis data set. intersect_index vector intergers referencing rows dat match (1) population analyzed (2) defenition event","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Building-block: Number of events (multiple events counted multiple times) — n_event_","text":"integer value","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of events per 100 years of exposure — n_event_100y","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"Calculate number events per 100 years exposure","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"","code":"n_event_100y( dat, event_index, cell_index, subjectid_var, treatment_var, treatment_value, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). treatment_var character. Name treatment variable data. treatment_value character. Value treatment variable data. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_event_100y.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of events per 100 years of exposure — n_event_100y","text":"data.table containing number events per 100 years exposure.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_sub_.html","id":null,"dir":"Reference","previous_headings":"","what":"Building-block: Number of subjects — n_sub_","title":"Building-block: Number of subjects — n_sub_","text":"Building-block: Number subjects","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_sub_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Building-block: Number of subjects — n_sub_","text":"","code":"n_sub_(dat, cell_index, subjectid_var)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_sub_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Building-block: Number of subjects — n_sub_","text":"dat data.table. analysis data set. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. 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Name subject identifier variable data (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_sub_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Building-block: Number of subjects — n_sub_","text":"integer","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of subjects by treatment and stratum — n_subj","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"Calculate number subjects treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"","code":"n_subj(dat, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"dat data.table. analysis data set. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of subjects by treatment and stratum — n_subj","text":"data.table containing number subjects given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate number of subjects with events by treatment and stratum — n_subj_event","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"Calculate number subjects events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"","code":"n_subj_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate number of subjects with events by treatment and stratum — n_subj_event","text":"data.table containing number subjects events given combination treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event_.html","id":null,"dir":"Reference","previous_headings":"","what":"Building-block: Number of subjects with at least one event — n_subj_event_","title":"Building-block: Number of subjects with at least one event — n_subj_event_","text":"Building-block: Number subjects least one event","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event_.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Building-block: Number of subjects with at least one event — n_subj_event_","text":"","code":"n_subj_event_(dat, intersect_index, subjectid_var)"},{"path":"https://hta-pharma.github.io/chefStats/reference/n_subj_event_.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Building-block: Number of subjects with at least one event — n_subj_event_","text":"dat data.table. analysis data set. intersect_index vector intergers referencing rows dat match (1) population analyzed (2) defenition event subjectid_var character. 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See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate observation time by treatment — obs_time_by_trt","text":"data.table containing observation time treatment.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"Calculate percentage subjects events treatment stratum.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"","code":"p_subj_event(dat, event_index, cell_index, subjectid_var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate percentage of subjects with events by treatment and stratum — p_subj_event","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). ... 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See \"Endpoint Events\" vignette ramnog information. intersect_index vector intergers referencing rows dat match (1) population analyzed (2) defenition event subjectid_var character. Name subject identifier variable data (default \"USUBJID\").","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Building-block: Proportion of subjects having at least one event — p_subj_event_","text":"integer value","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate percentage of subjects with events — p_subj_event_by_trt","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"Calculate percentage subjects events treatment strata.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"","code":"p_subj_event_by_trt( dat, event_index, cell_index, subjectid_var, treatment_var, treatment_value, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). treatment_var character. Name treatment variable data. treatment_value character. Value treatment variable data. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate percentage of subjects with events — p_subj_event_by_trt","text":"data.table containing percentage subjects events treatment.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for P-value calculations — p_val","title":"Wrapper for P-value calculations — p_val","text":"Ensures input statistical function proper format, enruse output formated need AMNOG workflow.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for P-value calculations — p_val","text":"","code":"p_val( dat, event_index, cell_index, treatment_var, treatment_refval, subjectid_var, safe_mode = FALSE, threshold_lower = 5, threshold_upper = 200, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for P-value calculations — p_val","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). safe_mode Boolean determing function fail given input calculated (safe_mode = TRUE), silently return NA value (default). threshold_lower numeric. Lower threshold limit selecting Fischer vs. Barnard. threshold_upper numeric. Upper threshold limit selecting Fischer vs. Barnard. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for P-value calculations — p_val","text":"data.table containing p-value statistics.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper for P-value of interaction tests — p_val_interaction","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"Wrapper P-value interaction tests","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"","code":"p_val_interaction( dat, event_index, treatment_var, treatment_refval, subjectid_var, strata_var, odds_ratio = NA, correct = FALSE, ... )"},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. treatment_var character. name treatment variable data. treatment_refval character. reference value treatment variable data. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). strata_var character. Variable analysis data stratify specific call. odds_ratio numeric. Odds Ration (default = NA). correct logical. TRUE Tarones correction returned (default = FALSE). ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/p_val_interaction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper for P-value of interaction tests — p_val_interaction","text":"data.table containing statistics p-value interaction tests.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard deviation — sd_value","title":"Standard deviation — sd_value","text":"Standard deviation","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standard deviation — sd_value","text":"","code":"sd_value(dat, event_index, cell_index, subjectid_var, var, ...)"},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard deviation — sd_value","text":"dat data.table. analysis data set. event_index vector integers index rows dat match definition 'event'. Matching done via INDEX_ column dat. cell_index vector integers referencing rows dat (specified INDEX_ column dat) match population analyzed. See \"Endpoint Events\" vignette ramnog information. subjectid_var character. Name subject identifier variable data (default \"USUBJID\"). var Character. Name variable analysis data subject statistics. ... Optional parameters.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/sd_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard deviation — sd_value","text":"data.table containing standard deviation.","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":null,"dir":"Reference","previous_headings":"","what":"Make new chefStats functions — use_chefStats","title":"Make new chefStats functions — use_chefStats","text":"Make new chefStats functions","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make new chefStats functions — use_chefStats","text":"","code":"use_chefStats( fn_name, fn_type = c(\"stat_by_strata_by_trt\", \"stat_by_strata_across_trt\", \"stat_across_strata_across_trt\"), file_name = NULL )"},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make new chefStats functions — use_chefStats","text":"fn_name Name function. file_name NULL fn_name used make file name fn_type Type statistical function, one stat_by_strata_by_trt, stat_by_strata_across_trt, stat_across_strata_across_trt file_name Name file store function (different fn_name)","code":""},{"path":"https://hta-pharma.github.io/chefStats/reference/use_chefStats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make new chefStats functions — use_chefStats","text":"Nothing, run side-effect (writes file disk)","code":""},{"path":"https://hta-pharma.github.io/chefStats/news/index.html","id":"chefstats-011","dir":"Changelog","previous_headings":"","what":"chefStats 0.1.1","title":"chefStats 0.1.1","text":"Centralized Git-Actions {ramnog}","code":""},{"path":"https://hta-pharma.github.io/chefStats/news/index.html","id":"chefstats-010","dir":"Changelog","previous_headings":"","what":"chefStats 0.1.0","title":"chefStats 0.1.0","text":"Initial release chefstats Contains initial selection statistical functions use {ramnog} ecosystem.","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index b470ef0..754192f 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -9,6 +9,9 @@
https://hta-pharma.github.io/chefStats/LICENSE.html
+
+ https://hta-pharma.github.io/chefStats/articles/add_functions.html
+ https://hta-pharma.github.io/chefStats/articles/chefStats.html
@@ -36,6 +39,15 @@
https://hta-pharma.github.io/chefStats/reference/RR.html
+
+ https://hta-pharma.github.io/chefStats/reference/barnard_test_.html
+
+
+ https://hta-pharma.github.io/chefStats/reference/breslowdaytest_.html
+
+
+ https://hta-pharma.github.io/chefStats/reference/count_set.html
+ https://hta-pharma.github.io/chefStats/reference/demographics_continuous.html
@@ -49,32 +61,44 @@
https://hta-pharma.github.io/chefStats/reference/index.html
- https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k.html
+ https://hta-pharma.github.io/chefStats/reference/make_two_by_two_.html
- https://hta-pharma.github.io/chefStats/reference/mean_value.html
+ https://hta-pharma.github.io/chefStats/reference/make_two_by_two_by_k_.html
- https://hta-pharma.github.io/chefStats/reference/mk_two_by_two.html
+ https://hta-pharma.github.io/chefStats/reference/mean_value.htmlhttps://hta-pharma.github.io/chefStats/reference/n_event.html
+
+ https://hta-pharma.github.io/chefStats/reference/n_event_.html
+ https://hta-pharma.github.io/chefStats/reference/n_event_100y.html
+
+ https://hta-pharma.github.io/chefStats/reference/n_sub_.html
+ https://hta-pharma.github.io/chefStats/reference/n_subj.htmlhttps://hta-pharma.github.io/chefStats/reference/n_subj_event.html
+
+ https://hta-pharma.github.io/chefStats/reference/n_subj_event_.html
+ https://hta-pharma.github.io/chefStats/reference/obs_time_by_trt.htmlhttps://hta-pharma.github.io/chefStats/reference/p_subj_event.html
+
+ https://hta-pharma.github.io/chefStats/reference/p_subj_event_.html
+ https://hta-pharma.github.io/chefStats/reference/p_subj_event_by_trt.html
