Package index • YESCDS

All functions

MA_cancer_rate_table(): simple tables of confidence intervals for cancer incidence
SEER_2018: a data.frame with SEER estimates of cancer incidence for 2018
brcamutSE: a SummarizedExperiment collecting BRCA mutations and colData from curatedTCGAData
build_deck(): make a deck of cards with 52 elements and unicode symbols for suits
build_simple_survival_curve(): utility for survival curve illustration
build_surv_for_mut(): use curatedTCGAData to produce survival time structure and mutation matrix for a TCGA tumor type
canada_crude: a data.frame with (rounded) crude rates of cancer as presented at https://www.statcan.gc.ca/en/dai/btd/asr
cancer_map_app(): use shiny for a simple cancer map, by type, for US
cancer_map_usa(): simple function for site-specific map
cancer_map_world(): simple map of cancer rates world wide
compare_tumors(): compare multiple tumor times with respect to survival
do_new_surv(): utility for survival curve, alternate shape
faces(): get faces of a collection of cards
filter_woncan(): generate site-specific rate table
full_house(): test for full house
get_hcc_spatial_path(): retrieve or cache SingleCellExperiment data for spatial transcriptomics of HCC
is_flush(): test for flush
make_comparison(): make an interactive histogram of rate ratios, or a scatterplot for rate comparisons, between two areas
make_hist(): make an interactive histogram for a given cancer site, based on a rate table
make_pair(): make interactive beeswarm or box plots for all cancer incidence rates in two areas
map_app(): use shiny to explore aspects of geographic mapping
mass_cancer_map(): map cancer rates for selected sites to MA counties
mass_map(): simple function to display HTML map of MA
metabric: a data.frame with clinical features of a breast cancer study (METABRIC) derived from cBioPortal
one_pair(): test for one pair
ordered_seg_cal(): big display of ordered CIs for California Lung and Bronchus incidence 2014-2018
plot_seer_trend(): plot the rate statistics over time for selected cancer sites and subgroups
plotwci(): simple display of confidence intervals for cancer incidence
prostate_met_adeno: a data.frame with clinical features of a metastatic prostate adenocarcinoma study
show_5y_estimate(): utility for survival curve illustration: 5y survprob estimate sketch
show_median_estimate(): utility for survival curve illustration: median estimate sketch
statcrunch_msa: geographic information from statcrunch.com on metropolitan statistical areas
suits(): get suits of a collection of cards
table_woncan(): simplify table view of WONDER CDC statistsics
two_pairs(): test for two pairs
url_1R(): give URL for responder example
url_6NR(): give URL for non-responder example
us_county_geo: locations of US counties
us_map(): simple function to display HTML map of US
variation_app(): simple app to show different ways of examining variation over body sites and MSAs
vjc_cancer_net: a table of data of Vince's contacts who developed cancer
woncan: cancer rate data by metropolitan statistical area, 1999-2018, from CDC WONDER system
woncan_meta: metadata on cancer rate data by metropolitan statistical area, 1999-2018, from CDC WONDER system
woncan_types(): generate vector of cancer sites in CDC Wonder table
world_cancer_2020_all: a table of cancer rate data by country, retrieved from https://gco.iarc.fr/today/online-analysis-map
world_geo_sf: a simple features (sf) instance with boundaries and centroids for 241 countries or other political geographic entities