Package 'formr'

Title: formr survey framework
Description: The formr R package provides a few convenience functions that may be useful to the users of formr (formr.org), an online survey framework which heavily relies on R via openCPU. Some of the functions are for conveniently generating individual feedback graphics, some are just shorthands to make certain common operations in formr more palatable to R novices.
Authors: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <[email protected]>
License: MIT + file LICENSE
Version: 0.10.2
Built: 2024-11-04 11:18:42 UTC
Source: https://github.com/rubenarslan/formr

Help Index


check whether a character string begins with a string

Description

Escapes any special RegExp characters in the search term. A way to check whether the search term (e.g. a variable name) is the beginning. Just a simple shorthand so that inexperienced R users won't have to use somewhat complex functions such as grepl() and stringr::str_detect(). You can also use \%starts_with\%.

Usage

haystack %begins_with% needle

Arguments

haystack

string in which you search

needle

string to search for

Examples

"1, 3, 4" %begins_with% "1" # TRUE
"1, 3, 4" %begins_with% 1 # unlike str_detect casts all needles as characters
"1, 3, 4" %begins_with% "." # FALSE

check whether a character string contains another as a word

Description

Looks for a string appearing on its own. This is needed e.g. when checking whether the replies to a mmc item, stored as a comma-separated list from 1 to 12 contain option 1 - you wouldn't want to get a hit for 11 and 12. Only works for search terms containing alphanumeric characters. Just a simple shorthand so that inexperienced R users don't have to use somewhat complex functions such as grepl() and stringr::str_detect().

Usage

haystack %contains_word% needle

Arguments

haystack

string in which you search

needle

string to search for

Examples

"1, 3, 4" %contains_word% "1" # TRUE
"1, 3, 4" %contains_word% 1 # TRUE unlike str_detect casts all needles as characters
"12, 14, 17" %contains_word% "1" # FALSE even though 12 contains 1

check whether a character string contains another

Description

Just a simple shorthand so that inexperienced R users don't have to use somewhat complex functions such as grepl() and stringr::str_detect() with non-default arguments (e.g. fixed params).

Usage

haystack %contains% needle

Arguments

haystack

string in which you search

needle

string to search for

Examples

"1, 2, 3, 4, you" %contains% "you"
"1, 2, 3, 4, you" %contains% 1 # unlike str_detect casts all needles as characters
"1, 2, 3, 4, you" %contains% 343

check whether a character string ends with a string

Description

Escapes any special RegExp characters in the search term. A way to check whether the search term (e.g. a variable name) is the ending. Just a simple shorthand so that inexperienced R users don't have to use somewhat complex functions such as grepl() and stringr::str_detect().

Usage

haystack %ends_with% needle

Arguments

haystack

string in which you search

needle

string to search for

Examples

"1, 3, 4" %ends_with% "4" # TRUE
"1, 3, 4" %ends_with% 4 # unlike str_detect casts all needles as characters
"1, 3, 4" %ends_with% "." # FALSE

Aggregate variables and remember which variables this were

Description

Copied from codebook. The resulting variables will have the attribute scale_item_names containing the basis for aggregation. Its label attribute will refer to the common stem of the aggregated variable names (if any), the number of variables, and the aggregation function.

Usage

aggregate_and_document_scale(items, fun = rowMeans, stem = NULL)

Arguments

items

data.frame of the items that should be aggregated

fun

aggregation function, defaults to rowMeans with na.rm = FALSE

stem

common stem for the variables, specify if it should not be auto-detected as the longest common stem of the variable names

Examples

testdf <- data.frame(bfi_neuro_1 = rnorm(20), bfi_neuro_2 = rnorm(20),
                    bfi_neuro_3R = rnorm(20), age = rpois(20, 30))
item_names <- c('bfi_neuro_1', 'bfi_neuro_2', 'bfi_neuro_3R')
testdf$bfi_neuro <- aggregate_and_document_scale(testdf[, item_names])
testdf$bfi_neuro

Transform formr_item_list into a data.frame for ease of use

Description

This function just turns a formr_item_list into a data.frame. The reason, these lists don't come as data.frames as default is because the 'choices' are a list themselves. When transforming, the choice column contains a collapsed choice list, which may be less useful for some purposes.

Usage

## S3 method for class 'formr_item_list'
as.data.frame(x, row.names, ...)

Arguments

x

a formr_item_list

row.names

not used

...

not used

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
as.data.frame(formr_items(survey_name = 'training_diary' ))

## End(Not run)
items = formr_items(path = 
system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))
items_df = as.data.frame(items)
items_df[1,]

knit_child as is

Description

This slightly modifies the knitr::knit_child() function to have different defaults.

  • the environment defaults to the calling environment.

  • the output receives the class knit_asis, so that the output will be rendered "as is" by knitr when calling inside a chunk (no need to set results='asis' as a chunk option).

  • defaults to quiet = TRUE

Usage

asis_knit_child(
  input = NULL,
  text = NULL,
  ...,
  quiet = TRUE,
  options = NULL,
  envir = parent.frame()
)

Arguments

input

if you specify a file path here, it will be read in before being passed to knitr (to avoid a working directory mess)

text

passed to knitr::knit_child()

...

passed to knitr::knit_child()

quiet

passed to knitr::knit_child()

options

defaults to NULL.

envir

passed to knitr::knit_child()

Details

Why default to the calling environment? Typically this function defaults to the global environment. This makes sense if you want to use knit_children in the same context as the rest of the document. However, you may also want to use knit_children inside functions to e.g. summarise a regression using a set of commands (e.g. plot some diagnostic graphs and a summary for a regression nicely formatted).

Some caveats:

  • the function has to return to the top-level. There's no way to cat() this from loops or an if-condition without without setting results='asis'. You can however concatenate these objects with paste.knit_asis()

Examples

## Not run: 
# an example of a wrapper function that calls asis_knit_child with an argument
# ensures distinct paths for cache and figures, so that these calls can be looped in parallel
regression_summary = function(model) {
   child_hash = digest::digest(model)
   options = list(
       fig.path = paste0(knitr::opts_chunk$get("fig.path"), child_hash, "-"), 
       cache.path = paste0(knitr::opts_chunk$get("cache.path"), child_hash, "-"))
   asis_knit_child("_regression_summary.Rmd", options = options)
}

## End(Not run)

switch choice values with labels

Description

formr display labels for multiple choice items, but stores their values. We assume you prefer to analyse the values (e.g. numeric values for Likert-type items, or English values for international surveys), but sometimes you may wish to switch this around.

Usage

choice_labels_for_values(survey, item_name)

Arguments

survey

survey with item_list attribute

item_name

item name

Examples

example(formr_post_process_results)
table(processed_results$BFIK_extra_4)
table(choice_labels_for_values(processed_results, "BFIK_extra_4"))

xtabs with sensible defaults

Description

xtabs requires two arguments (na.action and exclude) to show missing values along with other values. This function defaults to including missings and has only one argument

Usage

crosstabs(x, ..., exclude = NULL)

Arguments

x

passed to xtabs if it is a formula, transformed into a formula if it's a single object

...

passed to xtabs

exclude

defaults to NULL (i.e. includes NA)

Examples

x = NA
crosstabs(~ x)

Gives the last element, doesn't omit missings

Description

Just a simple shorthand to get the current element (in a formr df, where the last element is always the one from the current session).

Usage

current(x)

Arguments

x

vector of which you want the current element

Examples

current( c(1:10,NA) )
current( 1:10 )

generates valid email cids

Description

can be used as an argument to knitr::opts_knit. If you attach the images properly, you can then send knit emails including plots. See the formr OpenCPU module on Github for a sample implementation.

Usage

email_image(x, ext = ".png")

Arguments

x

image ID

ext

extension, defaults to .png

Examples

## Not run: 
library(knitr); library(formr)
opts_knit$set(upload.fun=formr::email_image)

## End(Not run)

How many surveys were expired?

Description

Just a simple to check how many times a survey (e.g. diary) has expired (i.e. user missed it). It defaults to checking the "expired" variable for this.

Usage

expired(survey, variable = "expired")

Arguments

survey

which survey are you asking about?

variable

which variable should be filled out, defaults to "ended"

Examples

survey = data.frame(expired = c(NA, "2016-05-29 10:11:00", NA))
expired(survey = survey)

Text feedback based on groups

Description

If you pass in a z-standardised value (x - Mean)/SD, and a vector of feedback text chunks, that has either three or five elements, the text chunks will be used in this order [very low], low, average, high, [very high] corresponding to these intervals [low, -2], [-2, -1], [-1, 1], [1, 2], [2, high]

Usage

feedback_chunk(normed_value, chunks)

Arguments

normed_value

a z-standardised value

chunks

a three or five element long character vector containing the text chunks for feedback

Examples

feedback_chunk(normed_value = 0.7, chunks = c("You are rather introverted.",
"You're approximately as extraverted as most people.","You are rather extraverted."))

How many surveys were finished?

Description

Just a simple to check how many times a survey (e.g. diary) was finished. It defaults to checking the "ended" variable for this.

Usage

finished(survey, variable = "ended")

Arguments

survey

which survey are you asking about?

variable

which variable should be filled out, defaults to "ended"

Examples

survey = data.frame(ended = c("2016-05-28 10:11:00", NA, "2016-05-30 11:18:28"))
finished(survey = survey)

Gives the first non-missing element

Description

Just a simple shorthand to get the first, non-missing argument per default. Can give more than one element and can include missing elements. The inverse of last().

Usage

first(x, n = 1, na.rm = TRUE)

Arguments

x

vector of which you want the first element

n

number of elements to take from the beginning

na.rm

whether to remove missings first, defaults to TRUE

Examples

first( c(NA,1:10) )
first( c(NA, 1:10), 2, TRUE )

Aggregate data based on item table

Description

If you've retrieved an item table using formr_items() you can use this function to aggregate your multiple choice items into mean scores. If you do not have a item table (e.g. your data was not collected using formr, you don't want another HTTP request in a time-sensitive process). Example: If your data contains Extraversion_1, Extraversion_2R and Extraversion_3, there will be two new variables in the result: Extraversion_2 (reversed to align with _1 and _2) and Extraversion, the mean score of the three.

Usage

formr_aggregate(
  survey_name,
  item_list = formr_items(survey_name, host = host),
  results = formr_raw_results(survey_name, host = host),
  host = formr_last_host(),
  compute_alphas = FALSE,
  fallback_max = 5,
  plot_likert = FALSE,
  quiet = FALSE,
  aggregation_function = rowMeans,
  ...
)

Arguments

survey_name

case-sensitive name of a survey your account owns

item_list

an item_list, will be auto-retrieved based on survey_name if omitted

results

survey results, will be auto-retrieved based on survey_name if omitted

host

defaults to formr_last_host(), which defaults to https://formr.org

compute_alphas

deprecated, functionality migrated to codebook package

fallback_max

defaults to 5 - if the item_list is set to null, we will use this to reverse

plot_likert

deprecated, functionality migrated to codebook package

quiet

defaults to FALSE - If set to true, likert plots and reliability computations are not echoed.

aggregation_function

defaults to rowMeans with na.rm = FALSE

...

passed to psych::alpha()

Examples

results = jsonlite::fromJSON(txt = 
	system.file('extdata/gods_example_results.json', package = 'formr', mustWork = TRUE))
items = formr_items(path = 
	system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))
results = formr_recognise(item_list = items, results = results)
agg = formr_aggregate(item_list = items, results = results, 
	compute_alphas = FALSE, plot_likert = FALSE)
agg[, c('religiousness', 'prefer')]

Connect to formr API

Description

Connects to formr using your client_id and client_secret (OAuth 2.0 grant type: client_credentials).

Usage

formr_api_access_token(
  client_id,
  client_secret,
  host = "https://api.formr.org/"
)

Arguments

client_id

your client_id

client_secret

your client_secret

host

defaults to https://formr.org

Examples

## Not run: 
formr_api_access_token(client_id = 'your_id', client_secret = 'your_secret' )

## End(Not run)

Get result from formr

Description

After obtaining a token from formr, use this request

Usage

formr_api_results(request = NULL, token = NULL)

Arguments

request

parameter (see example, API docs)

token

defaults to last used token

Examples

## Not run: 
request <- 
	list(
		"run[name]" = 'widgets',
		"run[sessions]" = 
		  'PJ_nACjFQDEBhx7pMUfZQz3mV-OtetnpEdqT88aiY8eXE4-HegFI7Sri4yifxPXO',
		"surveys[all_widgets]" = "abode, yourstory, mc_god"
)
formr_api_results(request)

## End(Not run)

Get current API session Return or set URL in list form for formr API (if available)

Description

Get current API session Return or set URL in list form for formr API (if available)

Usage

formr_api_session()

Connect to formr

Description

Connects to formr using your normal login and the httr library which supports persistent session cookies. Calling this function will persist the specified host (by default https://formr.org) in further formr_ function calls. You can change this by calling formr_last_host()

Usage

formr_connect(
  email = NULL,
  password = NULL,
  host = formr_last_host(),
  keyring = NULL
)

Arguments

email

your registered email address

password

your password

host

defaults to formr_last_host(), which defaults to https://formr.org

keyring

a shorthand for the account you're using

Examples

## Not run: 
formr_connect(keyring = "formr_diary_study_account" )

## End(Not run)

Disconnect from formr

Description

Disconnects from formr if connected.

Usage

formr_disconnect(host = formr_last_host())

Arguments

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_disconnect()

## End(Not run)

render inline text for formr

Description

Render text

Usage

formr_inline_render(text, self_contained = TRUE, ...)

Arguments

text

that will be written to a tmp file and used as the input argument

self_contained

passed to markdown_custom_options

...

all other arguments passed to rmarkdown::render()


Download detailed result timings and display counts from formr

Description

After connecting to formr using formr_connect() you can download detailed times and display counts for each item using this command.

Usage

formr_item_displays(survey_name, host = formr_last_host())

Arguments

survey_name

case-sensitive name of a survey your account owns

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
formr_item_displays(survey_name = 'training_diary' )

## End(Not run)

Download items from formr

Description

After connecting to formr using formr_connect() you can download items using this command. One of survey_name or path has to be specified, if both are specified, survey_name is preferred.

Usage

formr_items(survey_name = NULL, host = formr_last_host(), path = NULL)

Arguments

survey_name

case-sensitive name of a survey your account owns

host

defaults to formr_last_host(), which defaults to https://formr.org

path

path to local JSON copy of the item table

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
formr_items(survey_name = 'training_diary' )

## End(Not run)
formr_items(path = 
	system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))[1:2]

knit rmarkdown to markdown for formr

Description

Render text

Usage

formr_knit(text)

Arguments

text

rmarkdown that will be knit


Get the last specified host

Description

This function returns the default or the last specified host if called without an argument. It changes the host when called with an argument.

Usage

formr_last_host(host = NULL)

Arguments

host

defaults to https://formr.org

Value

the last specified host

Examples

formr_last_host("https://formr.org")
formr_last_host()

Processed, aggregated results

Description

This function chains formr_recognise() and formr_aggregate() in sequence. Useful if you want to post-process raw results before aggregating etc.

Usage

formr_post_process_results(
  item_list = NULL,
  results,
  compute_alphas = FALSE,
  fallback_max = 5,
  plot_likert = FALSE,
  quiet = FALSE,
  item_displays = NULL,
  tag_missings = !is.null(item_displays),
  remove_test_sessions = TRUE
)

Arguments

item_list

an item_list, defaults to NULL

results

survey results

compute_alphas

passed to formr_aggregate, defaults to TRUE

fallback_max

passed to formr_reverse, defaults to 5

plot_likert

passed to formr_aggregate, defaults to TRUE

quiet

passed to formr_aggregate, defaults to FALSE

item_displays

an item display table, necessary to tag missings

tag_missings

should missings that result from an item not being shown be distinguished from missings due to skipped questions?

remove_test_sessions

by default, formr removes results resulting from test session (animal names and null session codes)

Examples

results = jsonlite::fromJSON(txt = 
	system.file('extdata/BFI_post.json', package = 'formr', mustWork = TRUE))
items = formr_items(path = 
	system.file('extdata/BFI_post_items.json', package = 'formr', mustWork = TRUE))
item_displays = jsonlite::fromJSON(
	system.file('extdata/BFI_post_itemdisplay.json', package = 'formr', mustWork = TRUE))
processed_results = formr_post_process_results(items, results, item_displays = item_displays,
compute_alphas = FALSE, plot_likert = FALSE)

Download data from formr

Description

After connecting to formr using formr_connect() you can download data using this command.

Usage

formr_raw_results(survey_name, host = formr_last_host())

Arguments

survey_name

case-sensitive name of a survey your account owns

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_raw_results(survey_name = 'training_diary' )

## End(Not run)

Recognise data types based on item table

Description

Once you've retrieved an item table using formr_items() you can use this function to correctly type your variables based on the item table (e.g. formr free text types will be character, but select_add_one will be factor, dates are also typed as Date, datetimes as POSIXct).

Usage

formr_recognise(
  survey_name = NULL,
  item_list = formr_items(survey_name, host = host),
  results = formr_raw_results(survey_name, host = host),
  host = formr_last_host()
)

Arguments

survey_name

case-sensitive name of a survey your account owns

item_list

an item_list, will be auto-retrieved based on survey_name if omitted

results

survey results, will be auto-retrieved based on survey_name if omitted

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

results = jsonlite::fromJSON(txt = 
system.file('extdata/gods_example_results.json', package = 'formr', mustWork = TRUE))
class(results$created)
items = formr_items(path = 
system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))
results = formr_recognise(item_list = items, results = results)
class(results$created)

render text for formr

Description

Render text

Usage

formr_render(text, self_contained = FALSE, ...)

Arguments

text

that will be written to a tmp file and used as the input argument

self_contained

passed to markdown_custom_options

...

all other arguments passed to rmarkdown::render()


render inline text for formr

Description

Render text

Usage

formr_render_commonmark(text)

Arguments

text

that will be passed to knitr

Examples

formr_render_commonmark("There are only `r sample(2:3, 1)` types of people.")

Download processed, aggregated results from formr

Description

After connecting to formr using formr_connect() you can download data and process it. This approach calls the following functions in the right sequence: formr_raw_results() formr_items(), formr_item_displays() and formr_post_process_results(). So, results are downloaded, metadata on items (labels etc.) is added, normal and missing values are labelled. In the end, items like bfi_extra_3R are reversed in place (maintaining labels but changing underlying numbers), and scales are aggregated (bfi_extra_1, bfi_extra_2, bfi_extra_3R become bfi_extra)

Usage

formr_results(survey_name, host = formr_last_host(), ...)

Arguments

survey_name

case-sensitive name of a survey your account owns

host

defaults to formr_last_host(), which defaults to https://formr.org

...

passed to formr_post_process_results()

Examples

## Not run: 
formr_results(survey_name = 'training_diary' )

## End(Not run)

Reverse items based on item table or a fallback_max

Description

Example: If your data contains Extraversion_1, Extraversion_2R and Extraversion_3, there will be two new variables in the result: Extraversion_2 (reversed to align with _1 and _2) and Extraversion, the mean score of the three. If you supply an item table, the maximum possible answer to the item will be used to reverse it. If you don't, the maximum actually given answer or the fallback_max argument will be used to reverse it. It's faster to do this without an item table, but this can lead to problems, if you mis-specify the fallback max or the highest possible value does not occur in the data.

Usage

formr_reverse(results, item_list = NULL, fallback_max = 5)

Arguments

results

survey results

item_list

an item_list, defaults to NULL

fallback_max

defaults to 5 - if the item_list is set to null, we will use this to reverse

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
icar_items = formr_items(survey_name='ICAR',host = 'http://localhost:8888/formr/')
# get some simulated data and aggregate it
sim_results = formr_simulate_from_items(icar_items)
reversed_items = formr_reverse(item_list = icar_items, results = sim_results)

## End(Not run)
results = jsonlite::fromJSON(txt = 
	system.file('extdata/gods_example_results.json', package = 'formr', mustWork = TRUE))
items = formr_items(path = 
	system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))
formr_reverse(results, items)

Download random groups

Description

formr has a specific module for randomisation. After connecting using formr_connect() you can download the assigned random groups and merge them with your data.

Usage

formr_shuffled(run_name, host = formr_last_host())

Arguments

run_name

case-sensitive name of the run in which you randomised participants

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
formr_shuffled(run_name = 'different_drills' )

## End(Not run)

Simulate data based on item table

Description

Once you've retrieved an item table using formr_items() you can use this function to sample data from the possible choices. At the moment random data is only generated for choice-type items and numeric ones, as these are most likely to enter data analysis. Does not yet handle dates, times, text, locations, colors

Usage

formr_simulate_from_items(item_list, n = 300)

Arguments

item_list

the result of a call to formr_connect()

n

defaults to 300

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
sim = formr_simulate_from_items(item_list = formr_items('training_diary'), n = 100)
summary(lm(pushups ~ pullups, data = sim))

## End(Not run)
items = formr_items(path = 
system.file('extdata/gods_example_items.json', package = 'formr', mustWork = TRUE))
fakedata = formr_simulate_from_items(items, n = 20)
fakedata[1:2,]

Store keys in keyring

Description

Store keys in the system keyring/keychain instead of plaintext.

Usage

formr_store_keys(account_name)

Arguments

account_name

a shorthand for the account you're using

Examples

## Not run: 
formr_store_keys("formr_diary_study_account")

## End(Not run)

Upload new item table

Description

To automatically create surveys using formr, you can upload survey item tables from R. Only file uploads are available. The file name determines the survey name. Updating existing surveys is not implemented and not recommended (because of the sanity checks we require to prevent data deletion).

Usage

formr_upload_items(survey_file_path, host = formr_last_host())

Arguments

survey_file_path

the path to an item table in csv/json/xlsx etc.

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
items <- system.file('extdata/gods_example_items.json', package = 'formr', 
mustWork = TRUE)
formr_upload_items(items)

## End(Not run)

Download random groups

Description

formr collects information about users' progression through the run After connecting using formr_connect() you can download a table showing their progression through the run.

Usage

formr_user_detail(run_name, host = formr_last_host())

Arguments

run_name

case-sensitive name of the run in which you randomised participants

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
formr_user_detail(run_name = 'different_drills' )

## End(Not run)

Download random groups

Description

formr collects information about users' progression through the run After connecting using formr_connect() you can download a table showing where they are in the run.

Usage

formr_user_overview(run_name, host = formr_last_host())

Arguments

run_name

case-sensitive name of the run in which you randomised participants

host

defaults to formr_last_host(), which defaults to https://formr.org

Examples

## Not run: 
formr_connect(email = '[email protected]', password = 'zebrafinch' )
formr_user_overview(run_name = 'different_drills' )

## End(Not run)

pass in the url to the RDS representation of a openCPU session object, get the object

Description

useful to programmatically access openCPU session object stored in character variables etc.

Usage

get_opencpu_rds(session_url, local = TRUE)

Arguments

session_url

the session url, e.g. https://public.opencpu.org/ocpu/tmp/x02a93ec/R/.val/rds

local

defaults to FALSE, if true, will assume that the session is not on another server, and do some not-very-smart substitution to load it via the file system instead of HTTP/HTTPS

Examples

## Not run: 
get_opencpu_rds('https://public.opencpu.org/ocpu/tmp/x02a93ec/R/.val/rds')

## End(Not run)

Replace NA values with something else

Description

Often, you want to substitute missing values with some implicit known value (e.g. if the question on number of sexual partners was skipped for sexually inactive people, you know the missing should turn into zero)

Usage

if_na(x, missing)

Arguments

x

the variable

missing

What to replace missing values with

Examples

number_of_sex_partners <- c(1, 3, 5, 10, NA, 29)
if_na(number_of_sex_partners, 0)

This function makes sure you know what to expect when evaluating uncertain results in an if-clause. In most cases, you should not use this function, because it can lump a lot of very different cases together, but it may have some use for fool-proofing certain if-clauses on formr.org, where a field in a survey may either not exist, be missing or have a value to check.

Description

This function makes sure you know what to expect when evaluating uncertain results in an if-clause. In most cases, you should not use this function, because it can lump a lot of very different cases together, but it may have some use for fool-proofing certain if-clauses on formr.org, where a field in a survey may either not exist, be missing or have a value to check.

Usage

if_na_null(test, na = FALSE, null = FALSE)

Arguments

test

condition. can only have length 0 or length 1

na

returned if the condition has a missing value

null

passed to ifelse

Examples

testdf = data.frame(test1 = 1, test2 = NA)
if ( if_na_null(testdf$test1 == 1) ) { print("go on") }
if ( if_na_null(testdf$test2 == 1) ) { print("not shown") }
if ( if_na_null(testdf$test3 == 1) ) { print("not shown") }
tryCatch({ if ( if_na_null(testdf2$test1 == 1) ) { print("causes error") } }, 
   error = function(e) { warning(e) })

Like ifelse(), but allows you to assign a third value to missings.

Description

Deprecated. Please use dplyr::if_else() in the future. Defaults to assigning the "no" value to missing values as well. Often missings encapsulate some sort of meaning for the variable you're trying to define.

Usage

ifelsena(test, yes, no, missing = no)

Arguments

test

passed to ifelse

yes

passed to ifelse

no

passed to ifelse

missing

defaults to the value for no

Examples

## Not run: 
data(beavers)
beaver1$activ[1:10] = NA
beaver1$hyperactive = ifelse(beaver1$activ > 1, 1, 0)
table(beaver1$hyperactive)
beaver1$hyperactive = ifelsena(beaver1$activ > 1, 1, 0)
table(beaver1$hyperactive)

## End(Not run)

checks whether the current time is in a certain time window

Description

supply min,max as POSIXct

Usage

in_time_window(min, max)

Arguments

min

POSIXct < max

max

POSIXct > min

Examples

in_time_window(Sys.time() - 1, Sys.time() + 1)

get item from survey attribute

Description

Shortcut for attributes(survey$item_name)$item. Fails with a warning.

Usage

item(survey, item_name)

Arguments

survey

survey with item_list attribute

item_name

item name

Examples

example(formr_post_process_results)
item(processed_results, "BFIK_extra_4")

get item list from survey attributes

Description

get item list from survey attributes

Usage

items(survey)

Arguments

survey

survey with item_list attribute

Examples

example(formr_post_process_results)
items(processed_results)[[1]]

knit prefixed

Description

Knit using knitr, but prefix file name to figure and cache folder (to knit in parallel on e.g. a cluster)

Usage

knit_prefixed(input, ...)

Arguments

input

input document

...

all arguments passed to knitr::knit()


Gives the last non-missing element

Description

Just a simple shorthand to get the last, non-missing argument per default. Can give more than one element and can include missing elements. The inverse of first().

Usage

last(x, n = 1, na.rm = TRUE)

Arguments

x

vector of which you want the last element

n

number of elements to take from the end

na.rm

whether to remove missings first, defaults to TRUE

Examples

last( c(1:10,NA) )
last( c(1:10,NA), 2, TRUE )

loads an RDS object, assigns it to an object of the base-filename

Description

saveRDS() saves an object to a file, so unlike save() and load() you can assign the loaded object to a new variable using readRDS(). However, sometimes it may be more convenient to assign the object in the RDS file to an object of the same name as the file. This is what loadRDS() does. It extracts the filename using basename() and tools::file_path_sans_ext()

Usage

loadRDS(file, refhook = NULL, overwrite = FALSE)

Arguments

file

path to file

refhook

passed to readRDS

overwrite

whether to overwrite an existing object of the same name. defaults to false.

Examples

## Not run: 
loadRDS(file = '~/Models/Spouses.rds') # assigns object contained in file to variable 'Spouses'

## End(Not run)

get functions in the environment by their class. Useful to find e.g. all regression models you've stored in interactive programming.

Description

get functions in the environment by their class. Useful to find e.g. all regression models you've stored in interactive programming.

Usage

ls_by_class(classes, envir = parent.frame(), top_class_only = FALSE, ...)

Arguments

classes

objects should have one of these classes

envir

defaults to looking in the calling environment of this function, passed to ls

top_class_only

defaults to FALSE. If false, also returns objects inheriting from one of the specified classes.

...

passed to ls

Examples

data(ChickWeight)
chickweight.m1 <- glm(weight ~ Time + Diet, family = gaussian, data = ChickWeight)
ls_by_class('lm')
c('chickweight.m1') %in% ls_by_class('lm')
c('chickweight.m1') %in% ls_by_class('lm', top_class_only = TRUE)

custom markdown options for rmarkdown's pandoc

Description

custom markdown options for rmarkdown's pandoc

Usage

markdown_custom_options(
  add_to_format = c("+autolink_bare_uris", "+ascii_identifiers",
    "+tex_math_single_backslash", "-implicit_figures"),
  fragment.only = FALSE,
  section_divs = TRUE,
  break_on_error = FALSE,
  ...
)

Arguments

add_to_format

add these arguments to the default specification

fragment.only

whether to get only a html fragment

section_divs

whether to disable –section-divs (headings generate section including everything up to the next same-or-higher-level heading)

break_on_error

should an error in the R code execution interrupt the rendering or should rendering continue, defaults to FALSE

...

all other arguments passed to rmarkdown::html_document()

Custom rmarkdown input format options based on the standard rmarkdown::html_document(), but with options that you can specify. Find the format options here in the pandoc documentation: http://johnmacfarlane.net/pandoc/demo/example9/pandocs-markdown.html Pandoc's enhanced version of markdown includes syntax for footnotes, tables, flexible ordered lists, definition lists, fenced code blocks, superscript, subscript, strikeout, title blocks, automatic tables of contents, embedded LaTeX math, citations, and markdown inside HTML block elements or spoken in options: +escaped_line_breaks, +header_attributes, +yaml_metadata_block, +auto_identifiers, +implicit_header_references, +blank_before_blockquote, +fenced_code_blocks, +fenced_code_attributes, +line_blocks, +definition_lists, +startnum, +fancy_lists, +pipe_tables, +pandoc_title_block, +intraword_underscores, +strikeout, +superscript, +subscript, +tex_math_dollars, +raw_html, +markdown_in_html_blocks, +implicit_figures, +footnotes, +inline_notes, +citations. The current default rmarkdown additions to Pandoc's enhanced markdown are: +autolink_bare_uris, +ascii_identifiers, +tex_math_single_backslash, -implicit_figures.


github_markdown for rmarkdown

Description

Custom template with github-flavoured markdown based on the standard rmarkdown::html_document(). Adds +pipe_tables, +raw_html, +tex_math_single_backslash, +fenced_code_blocks, +auto_identifiers, +ascii_identifiers, +backtick_code_blocks, +autolink_bare_uris, +intraword_underscores, +strikeout, +hard_line_breaks over markdown_strict. A number of pandoc features are disabled (see markdown_custom_options()), but +yaml_metadata_block is re-enabled, so that it is possible to specify this output function using YAML.

Usage

markdown_github(fragment.only = FALSE, break_on_error = FALSE, ...)

Arguments

fragment.only

whether to get only a html fragment

break_on_error

should an error in the R code execution interrupt the rendering or should rendering continue, defaults to FALSE

...

all other arguments passed to rmarkdown::html_document()


hard line breaks

Description

Custom rmarkdown template based on the standard rmarkdown::html_document(), but with hard line breaks. Will add the pandoc '+hard_line_breaks' argument if the origin format is markdown.

Usage

markdown_hard_line_breaks(...)

Arguments

...

all other arguments passed to rmarkdown::html_document()


percentage of missings for each variable in a data.frame

Description

This functions simply reports the number of missings as the percentage of the maximum number of rows. It also works on single variables.

Usage

miss_frac(df, vars = 1:NCOL(df))

Arguments

df

data.frame or variable

vars

subset of variables, defaults to all

Examples

fruits = c('apple', 'banana', NA, 'pear', 'pinapple', NA)
pets = c('cat', 'dog', 'anteater', NA, NA, NA)
favorites = data.frame(fruits, pets)
miss_frac(favorites)
miss_frac(favorites$fruits)
miss_frac(favorites, 2)

Returns the number of missings in a variable or dataset. If missings are an explicit level in a factor variable, this function defaults to reporting them anyway.

Description

Returns the number of missings in a variable or dataset. If missings are an explicit level in a factor variable, this function defaults to reporting them anyway.

Usage

n_missing(x, exclude = NA)

Arguments

x

variable

exclude

only needed for factors. defaults to NA (count level=missing as missing), setting to 0 allows you to count level=missing as nonmissing

Examples

data(beavers)
beaver1$activ[1:10] = NA
n_missing(beaver1$activ)
beaver1$activ = factor(beaver1$activ, exclude = NULL)
sum(is.na(beaver1$activ))
n_missing(beaver1$activ)
n_missing(beaver1$activ, exclude = NULL)

Returns the number of nonmissings in a variable or dataset. If missings are an explicit level in a factor variable, this function defaults to excluding them anyway.

Description

Returns the number of nonmissings in a variable or dataset. If missings are an explicit level in a factor variable, this function defaults to excluding them anyway.

Usage

n_nonmissing(x, exclude = NA)

Arguments

x

variable

exclude

only needed for factors. defaults to NA (count level=missing as missing), setting to 0 allows you to count level=missing as nonmissing

Examples

data(beavers)
beaver1$activ[1:10] = NA
n_nonmissing(beaver1$activ)
beaver1$activ = factor(beaver1$activ, exclude = NULL)
sum(!is.na(beaver1$activ))
n_nonmissing(beaver1$activ)
n_nonmissing(beaver1$activ, exclude = NULL)

checks whether a new day has broken (date has increased by at least one day)

Description

a simple utility functions to avoid that looped Skip Backwards/Skip Forwards in formr are true repeatedly.

Usage

next_day(date = NULL)

Arguments

date

defaults to .formr$last_action_date, a hidden variable that is automatically set by formr.org. Will be coerced to POSIXct.

Examples

next_day(Sys.time())

paste.knit_asis

Description

Helper function for knit_asis objects, useful when e.g. asis_knit_child() was used in a loop.

Usage

paste.knit_asis(..., sep = "\n\n\n", collapse = "\n\n\n")

Arguments

...

passed to paste()

sep

defaults to two empty lines, passed to paste()

collapse

defaults to two empty lines, passed to paste()

Details

Works like paste() with both the sep and the collapse argument set to two empty lines

Examples

paste.knit_asis("# Headline 1", "## Headline 2")

Print new lines in knit_asis outputs

Description

Print new lines in knit_asis outputs

Usage

## S3 method for class 'knit_asis'
print(x, ...)

Arguments

x

the knit_asis object

...

ignored


proportions table

Description

quick and easy function to show proportions of values of a variable, defaults to including missings

Usage

props(..., exclude = NULL)

Arguments

...

passed to crosstabs

exclude

defaults to NULL (i.e. includes NA)

Examples

x = NA
props(~ x)

Plot normed values as a barchart

Description

Pass in a data.frame with z-standardised values (x - Mean)/SD, and variable names, get a bar chart. Getting your data.frame into this shape probably will mean using tidyr and dplyr If the data.frame has an se column or ymax/ymin columns, these will be displayed on top of the bars and the bars will become transparent.

Usage

qplot_on_bar(
  normed_data,
  ylab = "Your value",
  xlab = "Trait",
  title = "",
  y_ticks = c("--", "-", "0", "+", "++")
)

Arguments

normed_data

a dataset with a value column containing z-standardised value and a variable column containing labels for those values

ylab

Y-axis label, defaults to "Percentage of other people with this value"

xlab

X-axis label, empty by default, useful for labeling the plotted trait

title

Plot title

y_ticks

the ticks labels for -2,1,0,1 and 2 SDs around the mean, default to minuses, pluses and the average sign

Examples

normed_data = data.frame(variable = c("Extraversion","Openness",
"Agreeableness","Neuroticism","Conscientiousness"), 
value = c(-3,1,-1,0.5,2)) # standardise value
qplot_on_bar(normed_data, title = "Your personality")
normed_data = data.frame(variable = c("Extraversion","Openness",
"Agreeableness","Neuroticism","Conscientiousness"), 
value = c(-3,1,-1,0.5,2), se = c(0.2,0.3,0.2,0.25,0.4)) # standardise value
qplot_on_bar(normed_data, title = "Your personality")

Plot a normed value on the standard normal

Description

Pass in a z-standardised value (x - Mean)/SD, get a standard normal distribution.

Usage

qplot_on_normal(
  normed_value,
  ylab = "Percentage of other people with this value",
  xlab = "",
  colour = "blue",
  x_ticks = c("--", "-", "0", "+", "++")
)

Arguments

normed_value

a z-standardised value

ylab

Y-axis label, defaults to "Percentage of other people with this value"

xlab

X-axis label, empty by default, useful for labeling the plotted trait

colour

defaults to blue

x_ticks

the ticks labels for -2,1,0,1 and 2 SDs around the mean, default to minuses, pluses and the average sign

Examples

normed_value = scale(x = 20, center = 14, scale = 5) # standardise value
qplot_on_normal(normed_value, xlab = "Extraversion")

Time-polar plot

Description

Pass in a data.frame with z-standardised values (x - Mean)/SD, and variable names, get a bar chart. Getting your data.frame into this shape probably will mean using tidyr + dplyr. If the data.frame has an se column or ymax/ymin columns, these will be displayed on top of the bars and the bars will become transparent.

Usage

qplot_on_polar(normed_data, ylab = "Your value", title = "")

Arguments

normed_data

a dataset with a value column containing z-standardised value and a variable column containing labels for those values

ylab

Y-axis label, defaults to "Percentage of other people with this value"

title

Plot title

Examples

weekdays = c("Monday","Tuesday","Wednesday","Thursday","Friday","Saturday","Sunday")
normed_data = data.frame(variable = factor(weekdays, weekdays), 
	value = c(0,1,0.2,0.5,1.5,2,1)) # standardise value
qplot_on_polar(normed_data, title = "Your alcohol consumption across the week")
normed_data = data.frame(variable = factor(1:24,1:24), 
	value = 3+rnorm(24), se = rep(0.2,24)) # standardise value
qplot_on_polar(normed_data, title = "Your mood around the clock")

Random date in range

Description

taken from Dirk Eddelbuettel's answer here http://stackoverflow.com/a/14721124/263054

Usage

random_date_in_range(N, lower = "2012/01/01", upper = "2012/12/31")

Arguments

N

desired number of random dates

lower

lower limit

upper

upper limit


render text

Description

Render text

Usage

render_text(text, ...)

Arguments

text

that will be written to a tmp file and used as the input argument

...

all other arguments passed to rmarkdown::render()


Rescue lost attributes

Description

Taken from codebook You can use this function if some of your items have lost their attributes during wrangling Variables have to have the same name (Duh) and no attributes should be overwritten. But use with care. Similar to labelled::copy_labels().

Usage

rescue_attributes(df_no_attributes, df_with_attributes)

Arguments

df_no_attributes

the data frame with missing attributes

df_with_attributes

the data frame from which you want to restore attributes


Reverse labelled values

Description

Taken from codebook package reverse the underlying values for a numeric haven::labelled() vector while keeping the labels correct

Usage

reverse_labelled_values(x)

Arguments

x

a labelled vector

Value

return the labelled vector with the underlying values having been reversed

Examples

x <- haven::labelled(rep(1:3, each = 3), c(Bad = 1, Good = 5))
x
reverse_labelled_values(x)

Send text message via Clickatell

Description

Connects to Clickatell using your token and sends a text message.

Usage

text_message_clickatell(To, Body, Token, return_result = F)

Arguments

To

the number you're texting to (usually without zeroes at the beginning)

Body

the text message body/text

Token

your Clickatell token

return_result

whether to return simply TRUE/FALSE on success/failure or the whole result

Examples

## Not run: 
text_message_clickatell(
	To = '492222', 
	Body = 'Hello friend', 
	Token = 'Tokentokentoken')
	
## End(Not run)

Send text message via Massenversand.de

Description

Connects to Massenversand.de using your token and sends a text message.

Usage

text_message_massenversand(
  To,
  From,
  Body,
  id,
  pw,
  time = "0",
  msgtype = "t",
  tarif = "OA",
  test = "0",
  return_result = F
)

Arguments

To

the number you're texting to (usually without zeroes at the beginning)

From

the number you're texting from

Body

the text message body/text

id

your Massenversand ID

pw

your Massenversand password

time

see provider API (defaults to immediate sending)

msgtype

see provider API

tarif

see provider API

test

see provider API

return_result

whether to return simply TRUE/FALSE on success/failure or the whole result

Examples

## Not run: 
text_message_massenversand(
	To = '492222', 
	From = '15005000', 
	Body = 'Hello friend',
	id = 'ID', 
	pw = 'Tokentokentoken')
	
## End(Not run)

Send text message via Twilio

Description

Connects to Twilio using your token and sends a text message.

Usage

text_message_twilio(To, From, Body, Account, Token, return_result = F)

Arguments

To

the number you're texting to (usually without zeroes at the beginning)

From

the number you're texting from

Body

the text message body/text

Account

your Twilio account ID

Token

your Twili token

return_result

whether to return simply TRUE/FALSE on success/failure or the whole result

Examples

text_message_twilio(
	To = '492222', 
	From = '15005000', 
	Body = 'Hello friend',
	Account = 'ID', Token = 'Tokentokentoken')

checks how much time has passed relative to the user's last action

Description

checks how much time has passed. You can choose the unit. Implemented via lubridate::dseconds(), not periods, i.e. a minute has 60 seconds, an hour 60 minutes, a day 24 hours. Months and years are not well-defined durations, but we offer them anyway for convenience. Returns true or false.

Usage

time_passed(
  years = 0,
  months = 0,
  weeks = 0,
  days = 0,
  hours = 0,
  minutes = 0,
  seconds = 0,
  time = NULL
)

Arguments

years

365 days

months

30 days

weeks

7 days

days

24 hours

hours

60 minutes

minutes

60 seconds

seconds

argument to lubridate::dseconds()

time

defaults to .formr$last_action_time, a hidden variable that is automatically set by formr.org

Examples

time_passed(hours = 7, time = Sys.time())

word_document from rmarkdown, but has an added option not to break on error

Description

Exactly like rmarkdown::word_document(), but with one added argument

Usage

word_document(..., break_on_error = FALSE)

Arguments

...

all other arguments passed to rmarkdown::word_document()

break_on_error

should an error in the R code execution interrupt the rendering or should rendering continue, defaults to FALSE