This function fills out the SwissEthics annual safety report template with a much as possible. Minor (formatting) changes will still be required after generation of the report.
Usage
asr(
data,
target = "tmp.docx",
trial_title = "TRIAL NAME",
protocol_number = "default",
basec_number = "default",
snctp_number = "default",
swissmedic_number = "default",
ec_name = "default",
tr_number = "default",
product_name = "default",
sponsor_contact = "default name, default number, default email",
inst_name_address = "default name, default address",
n_centers_t = "default",
n_centers_p = "default",
n_centers_c = "default",
n_centers_o = "default",
n_pat_t = 500,
n_pat_e = 300,
n_pat_c = 100,
n_pat_p = 15,
n_centers_t_ch = "default",
n_centers_p_ch = "default",
n_centers_c_ch = "default",
n_centers_o_ch = "default",
n_pat_t_ch = 500,
n_pat_e_ch = 300,
n_pat_c_ch = 100,
n_pat_p_ch = 15,
n_per_arm = c(grp1 = 150, grp2 = 150),
report_date = format(Sys.Date(), format = "%d/%m/%Y"),
period_from = as.Date("2020-11-02"),
period_to = as.Date("2020-11-17"),
template = system.file("extdata/clino_annual_safety_report_fm.docx", package =
"SwissASR"),
international = FALSE,
trial_type = "imp",
var_class = "class",
var_sae_n = "sae_n",
var_part_id = "record_id",
var_age = "age",
var_sex = "sex",
var_country = "country",
var_site = "site",
var_sae = "sae",
var_date_onset = "sae_date",
var_trt = "trt",
var_date_trt_start = "sae_trtstart",
var_date_trt_stop = "sae_trtstop",
var_outcome = "outcome",
var_comment = "comment",
var_relation = "related",
var_expected = "expected",
var_devdef = "devdef",
var_devattr = "devattr",
var_devint = "devint",
var_safetymeasure = "safetymeasure",
var_tx = NULL
)Arguments
- data
dataframe containing safety data
- target
filename to save the report to
- trial_title
name of the trial
- protocol_number
trial code/protocol number
- basec_number
BASEC number
- snctp_number
SNCTP number
- swissmedic_number
Swissmedic number
- ec_name
EC name (Lead EC and/concerned EC)
- tr_number
Number for Transplantation Clinical Trials (FOPH number)
- product_name
product name or intervention
- sponsor_contact
contact details of sponsor(-investigator)
- inst_name_address
name and address of institute
- n_centers_t
total number of participating centres
- n_centers_p
planned number of participating centres
- n_centers_c
number of closed centres
- n_centers_o
number of open centres
- n_pat_t
target number of participants
- n_pat_e
number of enrolled participants
- n_pat_c
number of completed participants
- n_pat_p
number of prematurely terminated participants
- n_centers_t_ch
total number of participating centres in CH
- n_centers_p_ch
planned number of participating centres in CH
- n_centers_c_ch
number of closed centres in CH
- n_centers_o_ch
number of open centres in CH
- n_pat_t_ch
target number of participants in CH
- n_pat_e_ch
number of enrolled participants in CH
- n_pat_c_ch
number of completed participants in CH
- n_pat_p_ch
number of prematurely terminated participants in CH
- n_per_arm
number of enrolled participants per arm, list with group 1 and 2, define here the names of your groups as in the data
- report_date
report date
- period_from
start of reporting period
- period_to
end of reporting period
- template
path to template file
- international
internation or national trial (logical)
- trial_type
one of
imp,medical device,other. Abbreviations OK.- var_class
variable containing SAE class. Options allowed are "SAE", "SADR", "SUSAR"
- var_sae_n
variable containing SAE ID
- var_part_id
variable containing participant ID
- var_age
variable containing participant age
- var_sex
variable containing participant sex
- var_country
variable containing participants country
- var_site
variable containing participants site
- var_sae
variable containing SAE type (description)
- var_date_onset
variable containing the date the SAE occured
- var_trt
variable containing the treatment used to alleviate the SAE
- var_date_trt_start
variable containing the date that the treatment started
- var_date_trt_stop
variable containing the date that the treatment ended
- var_outcome
variable containing the outcome of the SAE
- var_comment
variable containing any comment
- var_relation
variable containing the relationship to randomized intervention
- var_expected
variable saying whether the SAE was expected
- var_devdef
variable containing whether the SAE is a device deficiency
- var_devattr
variable containing whether the SAE is attributable to the device
- var_devint
variable containing whether the SAE is attributable to an intervention in the trial
- var_safetymeasure
variable containing whether the SAE required safety related measures
- var_tx
variable indicating the intervention group. If provided, this variable will be included in the line listing
Details
Use of the var_tx argument results in the indicated variable being included in the line listing.
Examples
data(asr_sae)
file <- tempfile("asr", fileext = ".docx")
asr(asr_sae, file)
#> Error in "run(\"osascript\", script_path)": ! System command 'osascript' failed
# # more usual use will require passing more information:
# asr(asr_sae, file,
# # trial info
# trial_title = "Example Trial Name",
# protocol_number = "20221002130",
# basec_number = "",
# snctp_number = "202200458",
# swissmedic_number = "....",
# ec_name = "Kantonale Ethikskommision Bern",
# tr_number = "",
# product_name = "Drug name",
# international = FALSE,
# trial_type = "imp",
# # Sponsor info
# sponsor_contact = "Sponsor name, Sponsor phone number, Sponsor email",
# inst_name_address = "Institute name, Institute address",
# # site info
# n_centers_t = 20, # total number
# n_centers_p = "default", # planned
# n_centers_c = "default", # closed
# n_centers_o = "default", # open
# # participant info
# n_pat_t = 1000, # target
# n_pat_e = 300, # enrolled
# n_pat_c = 0, # complete
# n_pat_p = 0, # prematurely terminated
# # report info
# report_date = format(Sys.Date(), format = "%d/%m/%Y"),
# period_from = as.Date("2020-11-02"),
# period_to = as.Date("2020-11-17"),
# # variable mapping
# var_class = "class",
# var_sae_n = "sae_n", #sae ID
# var_part_id = "record_id", #participant ID
# var_age = "age",
# var_sex ="sex",
# var_country = "country",
# var_site = "site",
# var_sae = "sae",
# var_date_onset = "sae_date",
# var_trt = "trt",
# var_date_trt_start = "sae_trtstart",
# var_date_trt_stop = "sae_trtstop",
# var_outcome = "outcome",
# var_comment = "comment",
# var_relation = "related",
# var_expected = "expected",
# var_safetymeasure = "safetymeasure"
# )